0.010504 0.000000 0.002478 0.000000 0.016843 0.000000 0.000000 0.000000 0.016752 0.000000 0.000000 0.000000 Joint Center for Structural Genomics (JCSG) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.000 103.270 90.000 95.205 59.373 61.333 C3 H7 N O2 89.093 y ALANINE L-peptide linking C6 H15 N4 O2 1 175.209 y ARGININE L-peptide linking C4 H8 N2 O3 132.118 y ASPARAGINE L-peptide linking C4 H7 N O4 133.103 y ASPARTIC ACID L-peptide linking C5 H9 N O4 147.129 D-GLUTAMIC ACID D-peptide linking C5 H10 N2 O3 146.144 y GLUTAMINE L-peptide linking C5 H9 N O4 147.129 y GLUTAMIC ACID L-peptide linking C2 H5 N O2 75.067 y GLYCINE peptide linking C6 H10 N3 O2 1 156.162 y HISTIDINE L-peptide linking H2 O 18.015 WATER non-polymer C6 H13 N O2 131.173 y ISOLEUCINE L-peptide linking C6 H13 N O2 131.173 y LEUCINE L-peptide linking C6 H15 N2 O2 1 147.195 y LYSINE L-peptide linking C5 H11 N O2 Se 196.106 n SELENOMETHIONINE L-peptide linking C3 H7 N O5 S 169.156 n CYSTEINESULFONIC ACID L-peptide linking C8 H18 O5 194.226 TETRAETHYLENE GLYCOL non-polymer C9 H11 N O2 165.189 y PHENYLALANINE L-peptide linking O4 P -3 94.971 PHOSPHATE ION non-polymer C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking C4 H9 N O3 119.119 y THREONINE L-peptide linking C11 H12 N2 O2 204.225 y TRYPTOPHAN L-peptide linking C9 H11 N O3 181.189 y TYROSINE L-peptide linking C5 H11 N O2 117.146 y VALINE L-peptide linking DK Acta Crystallogr.,Sect.F 1744-3091 66 1354 1364 10.1107/S1744309110021214 20944232 Structure of the gamma-D-glutamyl-L-diamino acid endopeptidase YkfC from Bacillus cereus in complex with L-Ala-[gamma]-D-Glu: insights into substrate recognition by NlpC/P60 cysteine peptidases 2010 10.2210/pdb3h41/pdb pdb_00003h41 100 1 Flat mirror (vertical focusing) CCD 2009-03-27 MARMOSAIC 325 mm CCD Single crystal Si(111) bent monochromator (horizontal focusing) MAD M x-ray 1 0.97860 1.0 0.91837 1.0 0.97985 1.0 BL11-1 SSRL 0.97860,0.91837,0.97985 SYNCHROTRON SSRL BEAMLINE BL11-1 35168.770 NLP/P60 family protein 1 man polymer 89.093 ALANINE 1 syn non-polymer 147.129 D-GLUTAMIC ACID 1 syn non-polymer 94.971 PHOSPHATE ION 1 syn non-polymer 194.226 TETRAETHYLENE GLYCOL 6 syn non-polymer 18.015 water 265 nat water no yes GEEKKDSKAFIDVSAATLWTAPDSLRPIDVPSATNPVDLWKWTKS(MSE)TLDEKLWLTNANKLETQALLGQEVTVVDKK GDWVKVLVHGQPTPRNEEGYPGW(MSE)PEKQLTYNQEFADKTNEPFVLVTKPTAILYINPSEKHKSLEVSYNTRLPLLS EDTISYRVLLPNGQKAWLRKNDGTFYRSQNDIPTPAADDLINTGK(MSE)FLGLPYIWAGTSGFGFD(OCS)SGFTHTIY KSHGITIPRDSGPQSRNGVAVDKEHLQKGDLIFFAHDQGKGSVHHVA(MSE)YIGDGN(MSE)IHSPRAERSVEIIPLNT PGYIEEYAGARRYLP GEEKKDSKAFIDVSAATLWTAPDSLRPIDVPSATNPVDLWKWTKSMTLDEKLWLTNANKLETQALLGQEVTVVDKKGDWV KVLVHGQPTPRNEEGYPGWMPEKQLTYNQEFADKTNEPFVLVTKPTAILYINPSEKHKSLEVSYNTRLPLLSEDTISYRV LLPNGQKAWLRKNDGTFYRSQNDIPTPAADDLINTGKMFLGLPYIWAGTSGFGFDCSGFTHTIYKSHGITIPRDSGPQSR NGVAVDKEHLQKGDLIFFAHDQGKGSVHHVAMYIGDGNMIHSPRAERSVEIIPLNTPGYIEEYAGARRYLP A 396160 polypeptide(L) n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n sample 10987 BCE_2878, NP_979181.1 222523 Bacillus cereus ATCC 10987 562 Escherichia coli HK100 Plasmid SpeedET 1 2.39 48.59 VAPOR DIFFUSION, SITTING DROP 4.2 0.2000M NaCl, 50.0000% PEG-200, 0.1M Phosphate Citrate pH 4.2, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K 277 Joint Center for Structural Genomics JCSG PSI, Protein Structure Initiative software software struct_conn database_2 struct_ref_seq_dif struct_site repository Initial release Version format compliance Refinement description Data collection Derived calculations Refinement description Database references Derived calculations 1 0 2009-05-05 1 1 2011-07-13 1 2 2017-11-01 1 3 2019-07-24 1 4 2023-02-01 _software.classification _software.name _software.classification _software.contact_author _software.contact_author_email _software.language _software.location _software.name _software.type _software.version _struct_conn.pdbx_leaving_atom_flag _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details _struct_site.pdbx_auth_asym_id _struct_site.pdbx_auth_comp_id _struct_site.pdbx_auth_seq_id Y RCSB Y RCSB 2009-04-17 REL REL ALA ALANINE DGL D-GLUTAMIC ACID PO4 PHOSPHATE ION PG4 TETRAETHYLENE GLYCOL HOH water THE CONSTRUCT WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. THE CLONED CONSTRUCT CONTAINS RESIDUES 24-333 OF THE FULL LENGTH PROTEIN. ALA 501 2 ALA ALA 501 A DGL 502 3 DGL DGL 502 A PO4 1 4 PO4 PO4 1 A PG4 2 5 PG4 PG4 2 A PG4 3 5 PG4 PG4 3 A PG4 4 5 PG4 PG4 4 A PG4 5 5 PG4 PG4 5 A PG4 6 5 PG4 PG4 6 A PG4 7 5 PG4 PG4 7 A HOH 8 6 HOH HOH 8 A HOH 9 6 HOH HOH 9 A HOH 10 6 HOH HOH 10 A HOH 11 6 HOH HOH 11 A HOH 12 6 HOH HOH 12 A HOH 13 6 HOH HOH 13 A HOH 14 6 HOH HOH 14 A HOH 15 6 HOH HOH 15 A HOH 16 6 HOH HOH 16 A HOH 17 6 HOH HOH 17 A HOH 18 6 HOH HOH 18 A HOH 19 6 HOH HOH 19 A HOH 20 6 HOH HOH 20 A HOH 21 6 HOH HOH 21 A HOH 22 6 HOH HOH 22 A HOH 23 6 HOH HOH 503 A HOH 24 6 HOH HOH 504 A HOH 25 6 HOH HOH 505 A HOH 26 6 HOH HOH 506 A HOH 27 6 HOH HOH 507 A HOH 28 6 HOH HOH 508 A HOH 29 6 HOH HOH 509 A HOH 30 6 HOH HOH 510 A HOH 31 6 HOH HOH 511 A HOH 32 6 HOH HOH 512 A HOH 33 6 HOH HOH 513 A HOH 34 6 HOH HOH 514 A HOH 35 6 HOH HOH 515 A HOH 36 6 HOH HOH 516 A HOH 37 6 HOH HOH 517 A HOH 38 6 HOH HOH 518 A HOH 39 6 HOH HOH 519 A HOH 40 6 HOH HOH 520 A HOH 41 6 HOH HOH 521 A HOH 42 6 HOH HOH 522 A HOH 43 6 HOH HOH 523 A HOH 44 6 HOH HOH 524 A HOH 45 6 HOH HOH 525 A HOH 46 6 HOH HOH 526 A HOH 47 6 HOH HOH 527 A HOH 48 6 HOH HOH 528 A HOH 49 6 HOH HOH 529 A HOH 50 6 HOH HOH 530 A HOH 51 6 HOH HOH 531 A HOH 52 6 HOH HOH 532 A HOH 53 6 HOH HOH 533 A HOH 54 6 HOH HOH 534 A HOH 55 6 HOH HOH 535 A HOH 56 6 HOH HOH 536 A HOH 57 6 HOH HOH 537 A HOH 58 6 HOH HOH 538 A HOH 59 6 HOH HOH 539 A HOH 60 6 HOH HOH 540 A HOH 61 6 HOH HOH 541 A HOH 62 6 HOH HOH 542 A HOH 63 6 HOH HOH 543 A HOH 64 6 HOH HOH 544 A HOH 65 6 HOH HOH 545 A HOH 66 6 HOH HOH 546 A HOH 67 6 HOH HOH 547 A HOH 68 6 HOH HOH 548 A HOH 69 6 HOH HOH 549 A HOH 70 6 HOH HOH 550 A HOH 71 6 HOH HOH 551 A HOH 72 6 HOH HOH 552 A HOH 73 6 HOH HOH 553 A HOH 74 6 HOH HOH 554 A HOH 75 6 HOH HOH 555 A HOH 76 6 HOH HOH 556 A HOH 77 6 HOH HOH 557 A HOH 78 6 HOH HOH 558 A HOH 79 6 HOH HOH 559 A HOH 80 6 HOH HOH 560 A HOH 81 6 HOH HOH 561 A HOH 82 6 HOH HOH 562 A HOH 83 6 HOH HOH 563 A HOH 84 6 HOH HOH 564 A HOH 85 6 HOH HOH 565 A HOH 86 6 HOH HOH 566 A HOH 87 6 HOH HOH 567 A HOH 88 6 HOH HOH 568 A HOH 89 6 HOH HOH 569 A HOH 90 6 HOH HOH 570 A HOH 91 6 HOH HOH 571 A HOH 92 6 HOH HOH 572 A HOH 93 6 HOH HOH 573 A HOH 94 6 HOH HOH 574 A HOH 95 6 HOH HOH 575 A HOH 96 6 HOH HOH 576 A HOH 97 6 HOH HOH 577 A HOH 98 6 HOH HOH 578 A HOH 99 6 HOH HOH 579 A HOH 100 6 HOH HOH 580 A HOH 101 6 HOH HOH 581 A HOH 102 6 HOH HOH 582 A HOH 103 6 HOH HOH 583 A HOH 104 6 HOH HOH 584 A HOH 105 6 HOH HOH 585 A HOH 106 6 HOH HOH 586 A HOH 107 6 HOH HOH 587 A HOH 108 6 HOH HOH 588 A HOH 109 6 HOH HOH 589 A HOH 110 6 HOH HOH 590 A HOH 111 6 HOH HOH 591 A HOH 112 6 HOH HOH 592 A HOH 113 6 HOH HOH 593 A HOH 114 6 HOH HOH 594 A HOH 115 6 HOH HOH 595 A HOH 116 6 HOH HOH 596 A HOH 117 6 HOH HOH 597 A HOH 118 6 HOH HOH 598 A HOH 119 6 HOH HOH 599 A HOH 120 6 HOH HOH 600 A HOH 121 6 HOH HOH 601 A HOH 122 6 HOH HOH 602 A HOH 123 6 HOH HOH 603 A HOH 124 6 HOH HOH 604 A HOH 125 6 HOH HOH 605 A HOH 126 6 HOH HOH 606 A HOH 127 6 HOH HOH 607 A HOH 128 6 HOH HOH 608 A HOH 129 6 HOH HOH 609 A HOH 130 6 HOH HOH 610 A HOH 131 6 HOH HOH 611 A HOH 132 6 HOH HOH 612 A HOH 133 6 HOH HOH 613 A HOH 134 6 HOH HOH 614 A HOH 135 6 HOH HOH 615 A HOH 136 6 HOH HOH 616 A HOH 137 6 HOH HOH 617 A HOH 138 6 HOH HOH 618 A HOH 139 6 HOH HOH 619 A HOH 140 6 HOH HOH 620 A HOH 141 6 HOH HOH 621 A HOH 142 6 HOH HOH 622 A HOH 143 6 HOH HOH 623 A HOH 144 6 HOH HOH 624 A HOH 145 6 HOH HOH 625 A HOH 146 6 HOH HOH 626 A HOH 147 6 HOH HOH 627 A HOH 148 6 HOH HOH 628 A HOH 149 6 HOH HOH 629 A HOH 150 6 HOH HOH 630 A HOH 151 6 HOH HOH 631 A HOH 152 6 HOH HOH 632 A HOH 153 6 HOH HOH 633 A HOH 154 6 HOH HOH 634 A HOH 155 6 HOH HOH 635 A HOH 156 6 HOH HOH 636 A HOH 157 6 HOH HOH 637 A HOH 158 6 HOH HOH 638 A HOH 159 6 HOH HOH 639 A HOH 160 6 HOH HOH 640 A HOH 161 6 HOH HOH 641 A HOH 162 6 HOH HOH 642 A HOH 163 6 HOH HOH 643 A HOH 164 6 HOH HOH 644 A HOH 165 6 HOH HOH 645 A HOH 166 6 HOH HOH 646 A HOH 167 6 HOH HOH 647 A HOH 168 6 HOH HOH 648 A HOH 169 6 HOH HOH 649 A HOH 170 6 HOH HOH 650 A HOH 171 6 HOH HOH 651 A HOH 172 6 HOH HOH 652 A HOH 173 6 HOH HOH 653 A HOH 174 6 HOH HOH 654 A HOH 175 6 HOH HOH 655 A HOH 176 6 HOH HOH 656 A HOH 177 6 HOH HOH 657 A HOH 178 6 HOH HOH 658 A HOH 179 6 HOH HOH 659 A HOH 180 6 HOH HOH 660 A HOH 181 6 HOH HOH 661 A HOH 182 6 HOH HOH 662 A HOH 183 6 HOH HOH 663 A HOH 184 6 HOH HOH 664 A HOH 185 6 HOH HOH 665 A HOH 186 6 HOH HOH 666 A HOH 187 6 HOH HOH 667 A HOH 188 6 HOH HOH 668 A HOH 189 6 HOH HOH 669 A HOH 190 6 HOH HOH 670 A HOH 191 6 HOH HOH 671 A HOH 192 6 HOH HOH 672 A HOH 193 6 HOH HOH 673 A HOH 194 6 HOH HOH 674 A HOH 195 6 HOH HOH 675 A HOH 196 6 HOH HOH 676 A HOH 197 6 HOH HOH 677 A HOH 198 6 HOH HOH 678 A HOH 199 6 HOH HOH 679 A HOH 200 6 HOH HOH 680 A HOH 201 6 HOH HOH 681 A HOH 202 6 HOH HOH 682 A HOH 203 6 HOH HOH 683 A HOH 204 6 HOH HOH 684 A HOH 205 6 HOH HOH 685 A HOH 206 6 HOH HOH 686 A HOH 207 6 HOH HOH 687 A HOH 208 6 HOH HOH 688 A HOH 209 6 HOH HOH 689 A HOH 210 6 HOH HOH 690 A HOH 211 6 HOH HOH 691 A HOH 212 6 HOH HOH 692 A HOH 213 6 HOH HOH 693 A HOH 214 6 HOH HOH 694 A HOH 215 6 HOH HOH 695 A HOH 216 6 HOH HOH 696 A HOH 217 6 HOH HOH 697 A HOH 218 6 HOH HOH 698 A HOH 219 6 HOH HOH 699 A HOH 220 6 HOH HOH 700 A HOH 221 6 HOH HOH 701 A HOH 222 6 HOH HOH 702 A HOH 223 6 HOH HOH 703 A HOH 224 6 HOH HOH 704 A HOH 225 6 HOH HOH 705 A HOH 226 6 HOH HOH 706 A HOH 227 6 HOH HOH 707 A HOH 228 6 HOH HOH 708 A HOH 229 6 HOH HOH 709 A HOH 230 6 HOH HOH 710 A HOH 231 6 HOH HOH 711 A HOH 232 6 HOH HOH 712 A HOH 233 6 HOH HOH 713 A HOH 234 6 HOH HOH 714 A HOH 235 6 HOH HOH 715 A HOH 236 6 HOH HOH 716 A HOH 237 6 HOH HOH 717 A HOH 238 6 HOH HOH 718 A HOH 239 6 HOH HOH 719 A HOH 240 6 HOH HOH 720 A HOH 241 6 HOH HOH 721 A HOH 242 6 HOH HOH 722 A HOH 243 6 HOH HOH 723 A HOH 244 6 HOH HOH 724 A HOH 245 6 HOH HOH 725 A HOH 246 6 HOH HOH 726 A HOH 247 6 HOH HOH 727 A HOH 248 6 HOH HOH 728 A HOH 249 6 HOH HOH 729 A HOH 250 6 HOH HOH 730 A HOH 251 6 HOH HOH 731 A HOH 252 6 HOH HOH 732 A HOH 253 6 HOH HOH 733 A HOH 254 6 HOH HOH 734 A HOH 255 6 HOH HOH 735 A HOH 256 6 HOH HOH 736 A HOH 257 6 HOH HOH 737 A HOH 258 6 HOH HOH 738 A HOH 259 6 HOH HOH 739 A HOH 260 6 HOH HOH 740 A HOH 261 6 HOH HOH 741 A HOH 262 6 HOH HOH 742 A HOH 263 6 HOH HOH 743 A HOH 264 6 HOH HOH 744 A HOH 265 6 HOH HOH 745 A HOH 266 6 HOH HOH 746 A HOH 267 6 HOH HOH 747 A HOH 268 6 HOH HOH 748 A HOH 269 6 HOH HOH 749 A HOH 270 6 HOH HOH 750 A HOH 271 6 HOH HOH 751 A HOH 272 6 HOH HOH 752 A n 1 0 A n 2 24 A n 3 25 A n 4 26 A n 5 27 A n 6 28 A SER 29 n 7 SER 29 A LYS 30 n 8 LYS 30 A ALA 31 n 9 ALA 31 A PHE 32 n 10 PHE 32 A ILE 33 n 11 ILE 33 A ASP 34 n 12 ASP 34 A VAL 35 n 13 VAL 35 A SER 36 n 14 SER 36 A ALA 37 n 15 ALA 37 A ALA 38 n 16 ALA 38 A THR 39 n 17 THR 39 A LEU 40 n 18 LEU 40 A TRP 41 n 19 TRP 41 A THR 42 n 20 THR 42 A ALA 43 n 21 ALA 43 A PRO 44 n 22 PRO 44 A ASP 45 n 23 ASP 45 A SER 46 n 24 SER 46 A LEU 47 n 25 LEU 47 A ARG 48 n 26 ARG 48 A PRO 49 n 27 PRO 49 A ILE 50 n 28 ILE 50 A ASP 51 n 29 ASP 51 A VAL 52 n 30 VAL 52 A PRO 53 n 31 PRO 53 A SER 54 n 32 SER 54 A ALA 55 n 33 ALA 55 A THR 56 n 34 THR 56 A ASN 57 n 35 ASN 57 A PRO 58 n 36 PRO 58 A VAL 59 n 37 VAL 59 A ASP 60 n 38 ASP 60 A LEU 61 n 39 LEU 61 A TRP 62 n 40 TRP 62 A LYS 63 n 41 LYS 63 A TRP 64 n 42 TRP 64 A THR 65 n 43 THR 65 A LYS 66 n 44 LYS 66 A SER 67 n 45 SER 67 A MSE 68 n 46 MSE 68 A THR 69 n 47 THR 69 A LEU 70 n 48 LEU 70 A ASP 71 n 49 ASP 71 A GLU 72 n 50 GLU 72 A LYS 73 n 51 LYS 73 A LEU 74 n 52 LEU 74 A TRP 75 n 53 TRP 75 A LEU 76 n 54 LEU 76 A THR 77 n 55 THR 77 A ASN 78 n 56 ASN 78 A ALA 79 n 57 ALA 79 A ASN 80 n 58 ASN 80 A LYS 81 n 59 LYS 81 A LEU 82 n 60 LEU 82 A GLU 83 n 61 GLU 83 A THR 84 n 62 THR 84 A GLN 85 n 63 GLN 85 A ALA 86 n 64 ALA 86 A LEU 87 n 65 LEU 87 A LEU 88 n 66 LEU 88 A GLY 89 n 67 GLY 89 A GLN 90 n 68 GLN 90 A GLU 91 n 69 GLU 91 A VAL 92 n 70 VAL 92 A THR 93 n 71 THR 93 A VAL 94 n 72 VAL 94 A VAL 95 n 73 VAL 95 A ASP 96 n 74 ASP 96 A LYS 97 n 75 LYS 97 A LYS 98 n 76 LYS 98 A GLY 99 n 77 GLY 99 A ASP 100 n 78 ASP 100 A TRP 101 n 79 TRP 101 A VAL 102 n 80 VAL 102 A LYS 103 n 81 LYS 103 A VAL 104 n 82 VAL 104 A LEU 105 n 83 LEU 105 A VAL 106 n 84 VAL 106 A HIS 107 n 85 HIS 107 A GLY 108 n 86 GLY 108 A GLN 109 n 87 GLN 109 A PRO 110 n 88 PRO 110 A THR 111 n 89 THR 111 A PRO 112 n 90 PRO 112 A ARG 113 n 91 ARG 113 A ASN 114 n 92 ASN 114 A GLU 115 n 93 GLU 115 A GLU 116 n 94 GLU 116 A GLY 117 n 95 GLY 117 A TYR 118 n 96 TYR 118 A PRO 119 n 97 PRO 119 A GLY 120 n 98 GLY 120 A TRP 121 n 99 TRP 121 A MSE 122 n 100 MSE 122 A PRO 123 n 101 PRO 123 A GLU 124 n 102 GLU 124 A LYS 125 n 103 LYS 125 A GLN 126 n 104 GLN 126 A LEU 127 n 105 LEU 127 A THR 128 n 106 THR 128 A TYR 129 n 107 TYR 129 A ASN 130 n 108 ASN 130 A GLN 131 n 109 GLN 131 A GLU 132 n 110 GLU 132 A PHE 133 n 111 PHE 133 A ALA 134 n 112 ALA 134 A ASP 135 n 113 ASP 135 A LYS 136 n 114 LYS 136 A THR 137 n 115 THR 137 A ASN 138 n 116 ASN 138 A GLU 139 n 117 GLU 139 A PRO 140 n 118 PRO 140 A PHE 141 n 119 PHE 141 A VAL 142 n 120 VAL 142 A LEU 143 n 121 LEU 143 A VAL 144 n 122 VAL 144 A THR 145 n 123 THR 145 A LYS 146 n 124 LYS 146 A PRO 147 n 125 PRO 147 A THR 148 n 126 THR 148 A ALA 149 n 127 ALA 149 A ILE 150 n 128 ILE 150 A LEU 151 n 129 LEU 151 A TYR 152 n 130 TYR 152 A ILE 153 n 131 ILE 153 A ASN 154 n 132 ASN 154 A PRO 155 n 133 PRO 155 A SER 156 n 134 SER 156 A GLU 157 n 135 GLU 157 A LYS 158 n 136 LYS 158 A HIS 159 n 137 HIS 159 A LYS 160 n 138 LYS 160 A SER 161 n 139 SER 161 A LEU 162 n 140 LEU 162 A GLU 163 n 141 GLU 163 A VAL 164 n 142 VAL 164 A SER 165 n 143 SER 165 A TYR 166 n 144 TYR 166 A ASN 167 n 145 ASN 167 A THR 168 n 146 THR 168 A ARG 169 n 147 ARG 169 A LEU 170 n 148 LEU 170 A PRO 171 n 149 PRO 171 A LEU 172 n 150 LEU 172 A LEU 173 n 151 LEU 173 A SER 174 n 152 SER 174 A GLU 175 n 153 GLU 175 A ASP 176 n 154 ASP 176 A THR 177 n 155 THR 177 A ILE 178 n 156 ILE 178 A SER 179 n 157 SER 179 A TYR 180 n 158 TYR 180 A ARG 181 n 159 ARG 181 A VAL 182 n 160 VAL 182 A LEU 183 n 161 LEU 183 A LEU 184 n 162 LEU 184 A PRO 185 n 163 PRO 185 A ASN 186 n 164 ASN 186 A GLY 187 n 165 GLY 187 A GLN 188 n 166 GLN 188 A LYS 189 n 167 LYS 189 A ALA 190 n 168 ALA 190 A TRP 191 n 169 TRP 191 A LEU 192 n 170 LEU 192 A ARG 193 n 171 ARG 193 A LYS 194 n 172 LYS 194 A ASN 195 n 173 ASN 195 A ASP 196 n 174 ASP 196 A GLY 197 n 175 GLY 197 A THR 198 n 176 THR 198 A PHE 199 n 177 PHE 199 A TYR 200 n 178 TYR 200 A ARG 201 n 179 ARG 201 A SER 202 n 180 SER 202 A GLN 203 n 181 GLN 203 A ASN 204 n 182 ASN 204 A ASP 205 n 183 ASP 205 A ILE 206 n 184 ILE 206 A PRO 207 n 185 PRO 207 A THR 208 n 186 THR 208 A PRO 209 n 187 PRO 209 A ALA 210 n 188 ALA 210 A ALA 211 n 189 ALA 211 A ASP 212 n 190 ASP 212 A ASP 213 n 191 ASP 213 A LEU 214 n 192 LEU 214 A ILE 215 n 193 ILE 215 A ASN 216 n 194 ASN 216 A THR 217 n 195 THR 217 A GLY 218 n 196 GLY 218 A LYS 219 n 197 LYS 219 A MSE 220 n 198 MSE 220 A PHE 221 n 199 PHE 221 A LEU 222 n 200 LEU 222 A GLY 223 n 201 GLY 223 A LEU 224 n 202 LEU 224 A PRO 225 n 203 PRO 225 A TYR 226 n 204 TYR 226 A ILE 227 n 205 ILE 227 A TRP 228 n 206 TRP 228 A ALA 229 n 207 ALA 229 A GLY 230 n 208 GLY 230 A THR 231 n 209 THR 231 A SER 232 n 210 SER 232 A GLY 233 n 211 GLY 233 A PHE 234 n 212 PHE 234 A GLY 235 n 213 GLY 235 A PHE 236 n 214 PHE 236 A ASP 237 n 215 ASP 237 A OCS 238 n 216 OCS 238 A SER 239 n 217 SER 239 A GLY 240 n 218 GLY 240 A PHE 241 n 219 PHE 241 A THR 242 n 220 THR 242 A HIS 243 n 221 HIS 243 A THR 244 n 222 THR 244 A ILE 245 n 223 ILE 245 A TYR 246 n 224 TYR 246 A LYS 247 n 225 LYS 247 A SER 248 n 226 SER 248 A HIS 249 n 227 HIS 249 A GLY 250 n 228 GLY 250 A ILE 251 n 229 ILE 251 A THR 252 n 230 THR 252 A ILE 253 n 231 ILE 253 A PRO 254 n 232 PRO 254 A ARG 255 n 233 ARG 255 A ASP 256 n 234 ASP 256 A SER 257 n 235 SER 257 A GLY 258 n 236 GLY 258 A PRO 259 n 237 PRO 259 A GLN 260 n 238 GLN 260 A SER 261 n 239 SER 261 A ARG 262 n 240 ARG 262 A ASN 263 n 241 ASN 263 A GLY 264 n 242 GLY 264 A VAL 265 n 243 VAL 265 A ALA 266 n 244 ALA 266 A VAL 267 n 245 VAL 267 A ASP 268 n 246 ASP 268 A LYS 269 n 247 LYS 269 A GLU 270 n 248 GLU 270 A HIS 271 n 249 HIS 271 A LEU 272 n 250 LEU 272 A GLN 273 n 251 GLN 273 A LYS 274 n 252 LYS 274 A GLY 275 n 253 GLY 275 A ASP 276 n 254 ASP 276 A LEU 277 n 255 LEU 277 A ILE 278 n 256 ILE 278 A PHE 279 n 257 PHE 279 A PHE 280 n 258 PHE 280 A ALA 281 n 259 ALA 281 A HIS 282 n 260 HIS 282 A ASP 283 n 261 ASP 283 A GLN 284 n 262 GLN 284 A GLY 285 n 263 GLY 285 A LYS 286 n 264 LYS 286 A GLY 287 n 265 GLY 287 A SER 288 n 266 SER 288 A VAL 289 n 267 VAL 289 A HIS 290 n 268 HIS 290 A HIS 291 n 269 HIS 291 A VAL 292 n 270 VAL 292 A ALA 293 n 271 ALA 293 A MSE 294 n 272 MSE 294 A TYR 295 n 273 TYR 295 A ILE 296 n 274 ILE 296 A GLY 297 n 275 GLY 297 A ASP 298 n 276 ASP 298 A GLY 299 n 277 GLY 299 A ASN 300 n 278 ASN 300 A MSE 301 n 279 MSE 301 A ILE 302 n 280 ILE 302 A HIS 303 n 281 HIS 303 A SER 304 n 282 SER 304 A PRO 305 n 283 PRO 305 A ARG 306 n 284 ARG 306 A ALA 307 n 285 ALA 307 A GLU 308 n 286 GLU 308 A ARG 309 n 287 ARG 309 A SER 310 n 288 SER 310 A VAL 311 n 289 VAL 311 A GLU 312 n 290 GLU 312 A ILE 313 n 291 ILE 313 A ILE 314 n 292 ILE 314 A PRO 315 n 293 PRO 315 A LEU 316 n 294 LEU 316 A ASN 317 n 295 ASN 317 A THR 318 n 296 THR 318 A PRO 319 n 297 PRO 319 A GLY 320 n 298 GLY 320 A TYR 321 n 299 TYR 321 A ILE 322 n 300 ILE 322 A GLU 323 n 301 GLU 323 A GLU 324 n 302 GLU 324 A TYR 325 n 303 TYR 325 A ALA 326 n 304 ALA 326 A GLY 327 n 305 GLY 327 A ALA 328 n 306 ALA 328 A ARG 329 n 307 ARG 329 A ARG 330 n 308 ARG 330 A TYR 331 n 309 TYR 331 A LEU 332 n 310 LEU 332 A PRO 333 n 311 PRO 333 A author_and_software_defined_assembly PISA 1 monomeric A MSE 68 SELENOMETHIONINE A MSE 46 MET A MSE 122 SELENOMETHIONINE A MSE 100 MET A MSE 220 SELENOMETHIONINE A MSE 198 MET A OCS 238 CYSTEINESULFONIC ACID A OCS 216 CYS A MSE 294 SELENOMETHIONINE A MSE 272 MET A MSE 301 SELENOMETHIONINE A MSE 279 MET 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 1_555 x,y,z identity operation 0.0000000000 0.0000000000 0.0000000000 A O MSE 122 A O MSE 100 A N VAL 102 A N VAL 80 A O TRP 101 A O TRP 79 A N LYS 98 A N LYS 76 A O VAL 92 A O VAL 70 A N ALA 31 A N ALA 9 A N PHE 32 A N PHE 10 A O THR 128 A O THR 106 A N LEU 40 A N LEU 18 A O GLU 83 A O GLU 61 A O VAL 164 A O VAL 142 A N ALA 149 A N ALA 127 A N TYR 152 A N TYR 130 A O TRP 191 A O TRP 169 A O ALA 190 A O ALA 168 A N VAL 182 A N VAL 160 A O ARG 181 A O ARG 159 A N LEU 173 A N LEU 151 A O LEU 170 A O LEU 148 A N VAL 142 A N VAL 120 A N LEU 143 A N LEU 121 A O THR 198 A O THR 176 A N SER 232 A N SER 210 A O GLY 235 A O GLY 213 A N VAL 267 A N VAL 245 A O ALA 328 A O ALA 306 A O ALA 326 A O ALA 304 A N PHE 279 A N PHE 257 A N ILE 278 A N ILE 256 A O ALA 293 A O ALA 271 A N MSE 294 A N MSE 272 A O ILE 302 A O ILE 280 A N MSE 301 A N MSE 279 A O ILE 314 A O ILE 292 1 A CD ARG 201 A CD ARG 179 1 Y 1 A NE ARG 201 A NE ARG 179 1 Y 1 A CZ ARG 201 A CZ ARG 179 1 Y 1 A NH1 ARG 201 A NH1 ARG 179 1 Y 1 A NH2 ARG 201 A NH2 ARG 179 1 Y 1 A CG GLU 270 A CG GLU 248 1 Y 1 A CD GLU 270 A CD GLU 248 1 Y 1 A OE1 GLU 270 A OE1 GLU 248 1 Y 1 A OE2 GLU 270 A OE2 GLU 248 1 Y 1 A C7 PG4 3 F C7 PG4 1 1 N 1 A C8 PG4 3 F C8 PG4 1 1 N 1 A O5 PG4 3 F O5 PG4 1 1 N 1 A C5 PG4 4 G C5 PG4 1 1 N 1 A C6 PG4 4 G C6 PG4 1 1 N 1 A O4 PG4 4 G O4 PG4 1 1 N 1 A C7 PG4 4 G C7 PG4 1 1 N 1 A C8 PG4 4 G C8 PG4 1 1 N 1 A O5 PG4 4 G O5 PG4 1 1 N 1 A C7 PG4 5 H C7 PG4 1 1 N 1 A C8 PG4 5 H C8 PG4 1 1 N 1 A O5 PG4 5 H O5 PG4 1 1 N 1 A C5 PG4 7 J C5 PG4 1 1 N 1 A C6 PG4 7 J C6 PG4 1 1 N 1 A O4 PG4 7 J O4 PG4 1 1 N 1 A C7 PG4 7 J C7 PG4 1 1 N 1 A C8 PG4 7 J C8 PG4 1 1 N 1 A O5 PG4 7 J O5 PG4 1 1 N 1 A GLY 0 A GLY 1 1 Y 1 A GLU 24 A GLU 2 1 Y 1 A GLU 25 A GLU 3 1 Y 1 A LYS 26 A LYS 4 1 Y 1 A LYS 27 A LYS 5 1 Y 1 A ASP 28 A ASP 6 1 Y 1 A A OD2 ND1 OCS HIS 238 291 2.10 A 1 A A O O HOH HOH 562 746 2.18 1 A A OE2 O1 GLU PO4 157 1 2.18 1_555 2_655 1 A LEU 88 -36.32 127.58 1 A TYR 166 -34.08 134.47 1 A ASN 167 83.98 2.19 1 A ASP 176 -119.92 -163.97 1 A THR 231 -140.99 37.86 65.68 19.859 7.59 -0.380 0.000 -0.500 -0.490 0.000 0.640 0.958 0.943 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. RAMACHANDRAN OUTLIER PRO305 IS SUPPORTED BY DENSITY. 4. CYS238 IS OXIDIZED AS CYSTEINE SULFONIC ACID (OCS). 5. THE ALA-D-GAMMA-GLU MODELED IN THE ACTIVE SITE IS BASED ON DENSITY AND FUNCTION OF THE PROTEIN. PHOSPHATE AND PEG FRAGEMENTS ARE PRESENTS IN CRYSTALLIZATION CONDITIONS. 0.197 0.163 0.165 1.790 41.523 1564 31083 5.000 97.980 1.00 0.30 2.305 0.071 RANDOM 1 THROUGHOUT 0.00 MAD 0.117 0.111 0.800 0.800 1.200 MAXIMUM LIKELIHOOD WITH PHASES MASK 1.790 41.523 265 2754 80 0 2409 0.015 0.022 2615 0.001 0.020 1800 1.499 1.973 3558 0.914 3.000 4421 6.563 5.000 327 31.371 24.336 113 12.889 15.000 420 21.671 15.000 12 0.089 0.200 383 0.008 0.021 2856 0.001 0.020 500 1.823 3.000 1567 0.571 3.000 624 2.866 5.000 2557 4.588 8.000 1048 6.708 11.000 990 0.279 0.250 1.833 119 2083 2202 20 94.380 16.976 1.79 41.523 3H41 31085 -3.00 0.111 1 9.590 97.100 0.771 1.78 1.84 1.8 9426 2578 86.20 0.574 1.84 1.92 2.5 12802 3378 97.10 0.399 1.92 2.00 3.6 10804 2853 97.80 0.299 2.00 2.11 4.7 12341 3255 97.90 0.214 2.11 2.24 6.3 11745 3098 98.20 0.171 2.24 2.41 7.7 11574 3069 98.40 0.145 2.41 2.66 9.0 12488 3300 98.60 0.101 2.66 3.04 12.2 11682 3107 98.90 0.055 3.04 3.83 19.6 11982 3191 98.70 0.042 3.83 41.523 26.5 11969 3253 98.40 refinement Garib N. Murshudov garib@ysbl.york.ac.uk Fortran_77 http://www.ccp4.ac.uk/dist/html/refmac5.html REFMAC program 5.5.0053 refinement P.D. Adams PDAdams@lbl.gov C++ http://www.phenix-online.org/ PHENIX package phasing George M. Sheldrick gsheldr@shelx.uni-ac.gwdg.de Fortran_77 http://shelx.uni-ac.gwdg.de/SHELX/ SHELX package model building D.C. & J.S. Richardson lab molprobity@kinemage.biochem.duke.edu http://kinemage.biochem.duke.edu/molprobity/ MolProbity package 3beta29 data scaling Wolfgang Kabsch http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html XSCALE package data extraction PDB help@deposit.rcsb.org June 11, 2008 C++ http://sw-tools.pdb.org/apps/PDB_EXTRACT/ PDB_EXTRACT package 3.006 data reduction XDS phasing SHELXD phasing autoSHARP CRYSTAL STRUCTURE OF A NLPC/P60 FAMILY PROTEIN (BCE_2878) FROM BACILLUS CEREUS ATCC 10987 AT 1.79 A RESOLUTION 1 N N 2 N N 3 N N 4 N N 5 N N 5 N N 5 N N 5 N N 5 N N 5 N N 6 N N A ARG 48 A ARG 26 HELX_P A ILE 50 A ILE 28 5 1 3 A ASP 51 A ASP 29 HELX_P A THR 56 A THR 34 1 2 6 A ASP 60 A ASP 38 HELX_P A MSE 68 A MSE 46 1 3 9 A THR 69 A THR 47 HELX_P A ALA 79 A ALA 57 1 4 11 A ASN 130 A ASN 108 HELX_P A LYS 136 A LYS 114 1 5 7 A SER 202 A SER 180 HELX_P A ILE 206 A ILE 184 5 6 5 A ALA 210 A ALA 188 HELX_P A MSE 220 A MSE 198 1 7 11 A ASP 237 A ASP 215 HELX_P A SER 248 A SER 226 1 8 12 A ASP 256 A ASP 234 HELX_P A SER 261 A SER 239 1 9 6 A ASP 268 A ASP 246 HELX_P A LEU 272 A LEU 250 5 10 5 A HIS 282 A HIS 260 HELX_P A LYS 286 A LYS 264 1 11 5 A GLY 320 A GLY 298 HELX_P A GLU 324 A GLU 302 1 12 5 covale 1.335 both A SER 67 A C SER 45 1_555 A MSE 68 A N MSE 46 1_555 covale 1.321 both A MSE 68 A C MSE 46 1_555 A THR 69 A N THR 47 1_555 covale 1.327 both A TRP 121 A C TRP 99 1_555 A MSE 122 A N MSE 100 1_555 covale 1.348 both A MSE 122 A C MSE 100 1_555 A PRO 123 A N PRO 101 1_555 covale 1.343 both A LYS 219 A C LYS 197 1_555 A MSE 220 A N MSE 198 1_555 covale 1.333 both A MSE 220 A C MSE 198 1_555 A PHE 221 A N PHE 199 1_555 covale 1.322 both A ASP 237 A C ASP 215 1_555 A OCS 238 A N OCS 216 1_555 covale 1.336 both A OCS 238 A C OCS 216 1_555 A SER 239 A N SER 217 1_555 covale 1.322 both A ALA 293 A C ALA 271 1_555 A MSE 294 A N MSE 272 1_555 covale 1.331 both A MSE 294 A C MSE 272 1_555 A TYR 295 A N TYR 273 1_555 covale 1.327 both A ASN 300 A C ASN 278 1_555 A MSE 301 A N MSE 279 1_555 covale 1.325 both A MSE 301 A C MSE 279 1_555 A ILE 302 A N ILE 280 1_555 covale 1.334 both A ALA 501 B C ALA 1_555 A DGL 502 C N DGL 1_555 HYDROLASE NLPC/P60 FAMILY PROTEIN, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI-2, HYDROLASE A ASN 57 A ASN 35 1 A PRO 58 A PRO 36 0.91 A ASN 154 A ASN 132 1 A PRO 155 A PRO 133 2.57 Q736M3_BACC1 UNP 1 24 Q736M3 EEKKDSKAFIDVSAATLWTAPDSLRPIDVPSATNPVDLWKWTKSMTLDEKLWLTNANKLETQALLGQEVTVVDKKGDWVK VLVHGQPTPRNEEGYPGWMPEKQLTYNQEFADKTNEPFVLVTKPTAILYINPSEKHKSLEVSYNTRLPLLSEDTISYRVL LPNGQKAWLRKNDGTFYRSQNDIPTPAADDLINTGKMFLGLPYIWAGTSGFGFDCSGFTHTIYKSHGITIPRDSGPQSRN GVAVDKEHLQKGDLIFFAHDQGKGSVHHVAMYIGDGNMIHSPRAERSVEIIPLNTPGYIEEYAGARRYLP 24 333 3H41 24 333 Q736M3 A 1 2 311 1 expression tag GLY 0 3H41 A Q736M3 UNP 1 5 2 7 2 6 anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel anti-parallel A TYR 118 A TYR 96 A PRO 123 A PRO 101 A TRP 101 A TRP 79 A VAL 106 A VAL 84 A GLU 91 A GLU 69 A LYS 98 A LYS 76 A LYS 30 A LYS 8 A ILE 33 A ILE 11 A LEU 127 A LEU 105 A THR 128 A THR 106 A ALA 37 A ALA 15 A TRP 41 A TRP 19 A LEU 82 A LEU 60 A LEU 87 A LEU 65 A SER 161 A SER 139 A SER 165 A SER 143 A THR 148 A THR 126 A ILE 153 A ILE 131 A LYS 189 A LYS 167 A ARG 193 A ARG 171 A SER 179 A SER 157 A LEU 183 A LEU 161 A ARG 169 A ARG 147 A GLU 175 A GLU 153 A PHE 141 A PHE 119 A VAL 144 A VAL 122 A GLY 197 A GLY 175 A TYR 200 A TYR 178 A THR 231 A THR 209 A SER 232 A SER 210 A GLY 235 A GLY 213 A PHE 236 A PHE 214 A VAL 265 A VAL 243 A VAL 267 A VAL 245 A TYR 325 A TYR 303 A ARG 330 A ARG 308 A LEU 277 A LEU 255 A ALA 281 A ALA 259 A VAL 289 A VAL 267 A GLY 297 A GLY 275 A ASN 300 A ASN 278 A HIS 303 A HIS 281 A GLU 312 A GLU 290 A PRO 315 A PRO 293 BINDING SITE FOR RESIDUE ALA A 501 A ALA 501 Software 7 BINDING SITE FOR RESIDUE DGL A 502 A DGL 502 Software 10 BINDING SITE FOR RESIDUE PO4 A 1 A PO4 1 Software 8 BINDING SITE FOR RESIDUE PG4 A 2 A PG4 2 Software 4 BINDING SITE FOR RESIDUE PG4 A 3 A PG4 3 Software 6 BINDING SITE FOR RESIDUE PG4 A 4 A PG4 4 Software 6 BINDING SITE FOR RESIDUE PG4 A 5 A PG4 5 Software 6 BINDING SITE FOR RESIDUE PG4 A 6 A PG4 6 Software 7 BINDING SITE FOR RESIDUE PG4 A 7 A PG4 7 Software 9 A GLU 83 A GLU 61 7 1_555 A TYR 118 A TYR 96 7 1_555 A TRP 228 A TRP 206 7 1_555 A ASP 237 A ASP 215 7 1_555 A ASP 256 A ASP 234 7 1_555 A DGL 502 C DGL 7 1_555 A HOH 583 K HOH 7 1_555 A TRP 228 A TRP 206 10 1_555 A ASP 237 A ASP 215 10 1_555 A OCS 238 A OCS 216 10 1_555 A SER 239 A SER 217 10 1_555 A ASP 256 A ASP 234 10 1_555 A SER 257 A SER 235 10 1_555 A HIS 290 A HIS 268 10 1_555 A ALA 501 B ALA 10 1_555 A HOH 555 K HOH 10 1_555 A HOH 722 K HOH 10 1_555 A SER 156 A SER 134 8 1_555 A GLU 157 A GLU 135 8 2_655 A GLU 157 A GLU 135 8 1_555 A LYS 158 A LYS 136 8 1_555 A LYS 160 A LYS 138 8 1_555 A GLN 188 A GLN 166 8 1_555 A HOH 609 K HOH 8 1_555 A HOH 620 K HOH 8 1_555 A ILE 215 A ILE 193 4 1_555 A ASN 216 A ASN 194 4 1_555 A LYS 219 A LYS 197 4 1_555 A ILE 296 A ILE 274 4 1_555 A LEU 47 A LEU 25 6 1_555 A THR 56 A THR 34 6 1_555 A ASP 100 A ASP 78 6 1_555 A LYS 125 A LYS 103 6 1_555 A HOH 541 K HOH 6 1_555 A HOH 702 K HOH 6 1_555 A ASP 34 A ASP 12 6 1_555 A ILE 153 A ILE 131 6 1_555 A PRO 185 A PRO 163 6 1_555 A ASN 186 A ASN 164 6 1_555 A HOH 511 K HOH 6 1_555 A HOH 603 K HOH 6 1_555 A THR 208 A THR 186 6 4_546 A ALA 210 A ALA 188 6 4_546 A GLY 258 A GLY 236 6 1_555 A ARG 262 A ARG 240 6 1_555 A SER 288 A SER 266 6 1_555 A HOH 622 K HOH 6 4_546 A ASN 154 A ASN 132 7 1_555 A SER 174 A SER 152 7 1_555 A ASP 176 A ASP 154 7 1_555 A ILE 178 A ILE 156 7 1_555 A SER 179 A SER 157 7 1_555 A TRP 191 A TRP 169 7 1_555 A HOH 569 K HOH 7 1_555 A MSE 68 A MSE 46 9 1_555 A THR 69 A THR 47 9 1_555 A LEU 70 A LEU 48 9 1_555 A LYS 73 A LYS 51 9 1_555 A ALA 307 A ALA 285 9 1_555 A GLU 308 A GLU 286 9 1_555 A ARG 309 A ARG 287 9 1_555 A SER 310 A SER 288 9 1_555 A HOH 559 K HOH 9 1_555 5 C 1 2 1