0.020627 0.000000 0.006890 0.000000 0.029369 0.000000 0.000000 0.000000 0.020143 0.00000 0.00000 0.00000 Joint Center for Structural Genomics (JCSG) Partnership for Nuclear Receptor Signaling Code Biology (NHRS) http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 4 90.000 108.470 90.000 48.480 34.050 52.340 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 C3 H7 N O2 S 121.158 y CYSTEINE L-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 C5 H9 N O2 115.130 y PROLINE L-peptide linking C3 H7 N O3 105.093 y SERINE L-peptide linking O4 S -2 96.063 SULFATE ION non-polymer 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 To be published 0353 Crystal structure of a nuclear receptor binding factor 2 MIT domain (NRBF2) from Homo sapiens at 1.50 A resolution 10.2210/pdb4zey/pdb pdb_00004zey 100 1 Vertical focusing mirror; double crystal Si(111) monochromator CCD 2014-12-05 MARMOSAIC 325 mm CCD double crystal Si(111) MAD M x-ray 1 0.95369 1.0 0.97968 1.0 0.97943 1.0 BL14-1 SSRL 0.95369,0.97968,0.97943 SYNCHROTRON SSRL BEAMLINE BL14-1 9855.853 Nuclear receptor-binding factor 2 UNP residues 4-86 1 man polymer 96.063 SULFATE ION 2 syn non-polymer 18.015 water 102 nat water NRBF-2,Comodulator of PPAR and RXR no yes G(MSE)EGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEA(MSE)KLTQSEQAHLSLELQRDSH(MSE)KQLLL IQERWKRAQREERLKA GMEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRAQREE RLKA A JCSG-429611 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 Human sample 1 84 NRBF2, COPR 9606 Homo sapiens 562 Escherichia Coli PB1 Plasmid Biological sequence SpeedET 1 2.08 40.83 VAPOR DIFFUSION, SITTING DROP 25.0% Glycerol, 1.50M ammonium sulfate 293 Joint Center for Structural Genomics JCSG PSI:Biology Partnership for Nuclear Receptor Signaling Code Biology NHRs PSI:Biology audit_author entity_src_gen pdbx_struct_oper_list software citation_author database_2 struct_ref_seq_dif repository Initial release Derived calculations Refinement description Source and taxonomy Structure summary Database references Database references 1 0 2015-05-06 1 1 2017-11-22 1 2 2018-01-24 1 3 2023-02-01 _audit_author.name _entity_src_gen.pdbx_alt_source_flag _pdbx_struct_oper_list.symmetry_operation _citation_author.name _database_2.pdbx_DOI _database_2.pdbx_database_accession _struct_ref_seq_dif.details Y RCSB Y RCSB 2015-04-20 REL REL SO4 SULFATE ION HOH water THE CONSTRUCT (4-86) WAS EXPRESSED WITH A PURIFICATION TAG MGSDKIHHHHHHENLYFQG. THE TAG WAS REMOVED WITH TEV PROTEASE LEAVING ONLY A GLYCINE (0) FOLLOWED BY THE TARGET SEQUENCE. SO4 401 2 SO4 SO4 401 A SO4 402 2 SO4 SO4 402 A HOH 427 3 HOH HOH 501 A HOH 425 3 HOH HOH 502 A HOH 422 3 HOH HOH 503 A HOH 435 3 HOH HOH 504 A HOH 433 3 HOH HOH 505 A HOH 447 3 HOH HOH 506 A HOH 455 3 HOH HOH 507 A HOH 436 3 HOH HOH 508 A HOH 491 3 HOH HOH 509 A HOH 417 3 HOH HOH 510 A HOH 463 3 HOH HOH 511 A HOH 430 3 HOH HOH 512 A HOH 419 3 HOH HOH 513 A HOH 453 3 HOH HOH 514 A HOH 450 3 HOH HOH 515 A HOH 411 3 HOH HOH 516 A HOH 449 3 HOH HOH 517 A HOH 442 3 HOH HOH 518 A HOH 428 3 HOH HOH 519 A HOH 467 3 HOH HOH 520 A HOH 420 3 HOH HOH 521 A HOH 408 3 HOH HOH 522 A HOH 434 3 HOH HOH 523 A HOH 437 3 HOH HOH 524 A HOH 406 3 HOH HOH 525 A HOH 403 3 HOH HOH 526 A HOH 409 3 HOH HOH 527 A HOH 421 3 HOH HOH 528 A HOH 487 3 HOH HOH 529 A HOH 415 3 HOH HOH 530 A HOH 488 3 HOH HOH 531 A HOH 446 3 HOH HOH 532 A HOH 429 3 HOH HOH 533 A HOH 439 3 HOH HOH 534 A HOH 457 3 HOH HOH 535 A HOH 413 3 HOH HOH 536 A HOH 445 3 HOH HOH 537 A HOH 464 3 HOH HOH 538 A HOH 412 3 HOH HOH 539 A HOH 458 3 HOH HOH 540 A HOH 424 3 HOH HOH 541 A HOH 503 3 HOH HOH 542 A HOH 438 3 HOH HOH 543 A HOH 461 3 HOH HOH 544 A HOH 451 3 HOH HOH 545 A HOH 471 3 HOH HOH 546 A HOH 462 3 HOH HOH 547 A HOH 468 3 HOH HOH 548 A HOH 490 3 HOH HOH 549 A HOH 497 3 HOH HOH 550 A HOH 459 3 HOH HOH 551 A HOH 493 3 HOH HOH 552 A HOH 452 3 HOH HOH 553 A HOH 444 3 HOH HOH 554 A HOH 407 3 HOH HOH 555 A HOH 431 3 HOH HOH 556 A HOH 454 3 HOH HOH 557 A HOH 476 3 HOH HOH 558 A HOH 469 3 HOH HOH 559 A HOH 478 3 HOH HOH 560 A HOH 410 3 HOH HOH 561 A HOH 480 3 HOH HOH 562 A HOH 466 3 HOH HOH 563 A HOH 485 3 HOH HOH 564 A HOH 423 3 HOH HOH 565 A HOH 414 3 HOH HOH 566 A HOH 443 3 HOH HOH 567 A HOH 492 3 HOH HOH 568 A HOH 426 3 HOH HOH 569 A HOH 404 3 HOH HOH 570 A HOH 473 3 HOH HOH 571 A HOH 498 3 HOH HOH 572 A HOH 460 3 HOH HOH 573 A HOH 405 3 HOH HOH 574 A HOH 475 3 HOH HOH 575 A HOH 448 3 HOH HOH 576 A HOH 440 3 HOH HOH 577 A HOH 456 3 HOH HOH 578 A HOH 432 3 HOH HOH 579 A HOH 484 3 HOH HOH 580 A HOH 479 3 HOH HOH 581 A HOH 441 3 HOH HOH 582 A HOH 416 3 HOH HOH 583 A HOH 486 3 HOH HOH 584 A HOH 465 3 HOH HOH 585 A HOH 504 3 HOH HOH 586 A HOH 496 3 HOH HOH 587 A HOH 489 3 HOH HOH 588 A HOH 495 3 HOH HOH 589 A HOH 418 3 HOH HOH 590 A HOH 482 3 HOH HOH 591 A HOH 477 3 HOH HOH 592 A HOH 474 3 HOH HOH 593 A HOH 470 3 HOH HOH 594 A HOH 502 3 HOH HOH 595 A HOH 501 3 HOH HOH 596 A HOH 483 3 HOH HOH 597 A HOH 500 3 HOH HOH 598 A HOH 494 3 HOH HOH 599 A HOH 481 3 HOH HOH 600 A HOH 472 3 HOH HOH 601 A HOH 499 3 HOH HOH 602 A GLY 0 n 1 GLY 0 A MSE 4 n 2 MSE 4 A GLU 5 n 3 GLU 5 A GLY 6 n 4 GLY 6 A PRO 7 n 5 PRO 7 A LEU 8 n 6 LEU 8 A ASN 9 n 7 ASN 9 A LEU 10 n 8 LEU 10 A ALA 11 n 9 ALA 11 A HIS 12 n 10 HIS 12 A GLN 13 n 11 GLN 13 A GLN 14 n 12 GLN 14 A SER 15 n 13 SER 15 A ARG 16 n 14 ARG 16 A ARG 17 n 15 ARG 17 A ALA 18 n 16 ALA 18 A ASP 19 n 17 ASP 19 A ARG 20 n 18 ARG 20 A LEU 21 n 19 LEU 21 A LEU 22 n 20 LEU 22 A ALA 23 n 21 ALA 23 A ALA 24 n 22 ALA 24 A GLY 25 n 23 GLY 25 A LYS 26 n 24 LYS 26 A TYR 27 n 25 TYR 27 A GLU 28 n 26 GLU 28 A GLU 29 n 27 GLU 29 A ALA 30 n 28 ALA 30 A ILE 31 n 29 ILE 31 A SER 32 n 30 SER 32 A CYS 33 n 31 CYS 33 A HIS 34 n 32 HIS 34 A LYS 35 n 33 LYS 35 A LYS 36 n 34 LYS 36 A ALA 37 n 35 ALA 37 A ALA 38 n 36 ALA 38 A ALA 39 n 37 ALA 39 A TYR 40 n 38 TYR 40 A LEU 41 n 39 LEU 41 A SER 42 n 40 SER 42 A GLU 43 n 41 GLU 43 A ALA 44 n 42 ALA 44 A MSE 45 n 43 MSE 45 A LYS 46 n 44 LYS 46 A LEU 47 n 45 LEU 47 A THR 48 n 46 THR 48 A GLN 49 n 47 GLN 49 A SER 50 n 48 SER 50 A GLU 51 n 49 GLU 51 A GLN 52 n 50 GLN 52 A ALA 53 n 51 ALA 53 A HIS 54 n 52 HIS 54 A LEU 55 n 53 LEU 55 A SER 56 n 54 SER 56 A LEU 57 n 55 LEU 57 A GLU 58 n 56 GLU 58 A LEU 59 n 57 LEU 59 A GLN 60 n 58 GLN 60 A ARG 61 n 59 ARG 61 A ASP 62 n 60 ASP 62 A SER 63 n 61 SER 63 A HIS 64 n 62 HIS 64 A MSE 65 n 63 MSE 65 A LYS 66 n 64 LYS 66 A GLN 67 n 65 GLN 67 A LEU 68 n 66 LEU 68 A LEU 69 n 67 LEU 69 A LEU 70 n 68 LEU 70 A ILE 71 n 69 ILE 71 A GLN 72 n 70 GLN 72 A GLU 73 n 71 GLU 73 A ARG 74 n 72 ARG 74 A TRP 75 n 73 TRP 75 A LYS 76 n 74 LYS 76 A ARG 77 n 75 ARG 77 A ALA 78 n 76 ALA 78 A GLN 79 n 77 GLN 79 A ARG 80 n 78 ARG 80 A GLU 81 n 79 GLU 81 A GLU 82 n 80 GLU 82 A ARG 83 n 81 ARG 83 A LEU 84 n 82 LEU 84 A LYS 85 n 83 LYS 85 A ALA 86 n 84 ALA 86 A 0.7284 0.2111 0.4411 0.4439 0.3387 1.0412 0.0285 0.0443 0.0377 -0.0622 0.0025 -0.0372 -0.0164 0.0212 -0.0310 -0.0469 0.0081 0.0891 0.0666 0.0008 -0.0762 refined 5.8667 5.6877 -6.0783 X-RAY DIFFRACTION A 0 A 86 X-RAY DIFFRACTION 1 {A|0 - 86} author_defined_assembly 1 monomeric software_defined_assembly PISA 2 dimeric 2680 -46 10210 A MSE 4 modified residue A MSE 2 MET A MSE 45 modified residue A MSE 43 MET A MSE 65 modified residue A MSE 63 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 -1.0000000000 0.0000000000 0.0000000000 0.0000000000 1.0000000000 0.0000000000 0.0000000000 0.0000000000 -1.0000000000 2_555 -x,y,-z crystal symmetry operation 0.0000000000 0.0000000000 0.0000000000 1 A SO4 401 B SO4 1 A HOH 548 D HOH 1 A MSE 4 -37.68 144.07 89.890 25.7253 11.970 1.4756 0.0000 0.5040 -2.3193 0.0000 0.8436 0.9483 0.9332 1. ATOM RECORDS CONTAIN SUM OF TLS AND RESIDUAL B FACTORS. 2. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS. 3. 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. 4. THE MAD PHASES WERE USED AS RESTRAINTS DURING REFINEMENT 0.2482 0.2089 0.2107 1.5000 27.366 618 12871 4.8000 97.9200 1.000 0.500 RANDOM 1 THROUGHOUT 0.000 MAD 0.201 1.5000 27.366 102 791 10 0 679 357 SINUSOIDAL 2.000 21 HARMONIC 2.000 100 HARMONIC 5.000 702 HARMONIC 20.000 85 SEMIHARMONIC 5.000 907 SEMIHARMONIC 4.000 0.010 702 HARMONIC 2.000 0.900 938 HARMONIC 2.000 2.490 2.490 0.1999 0.1881 0.1886 1.6400 144 2919 3063 6 4.7000 97.9200 17.415 0.984 1.50 27.366 4ZEY 12873 -3.000 0.092 0.128 1 7.560 39652 1.685 92.400 0.782 0.392 1.500 1.550 1.8 3742 2425 2234 0.538 1 92.100 0.860 0.320 1.550 1.620 2.0 4494 2851 2661 0.439 93.300 0.907 0.252 1.620 1.690 2.6 3697 2353 2188 0.346 93.000 0.920 0.215 1.690 1.780 3.2 4090 2605 2432 0.297 93.400 0.962 0.153 1.780 1.890 4.3 3888 2510 2319 0.211 92.400 0.966 0.122 1.890 2.040 5.8 3937 2586 2363 0.171 91.400 0.979 0.086 2.040 2.240 8.6 3605 2467 2193 0.121 88.900 0.958 0.102 2.240 2.560 11.4 3869 2542 2305 0.143 90.700 0.942 0.111 2.560 3.230 15.3 4294 2580 2491 0.155 96.600 0.986 0.057 3.230 20.4 4036 2555 2341 0.080 91.600 data extraction PDB_EXTRACT 3.10 phasing SOLVE data scaling XSCALE November 3, 2014 BUILT=20141118 refinement BUSTER-TNT 2.10.2 refinement BUSTER 2.10.2 data reduction XDS Crystal structure of a nuclear receptor binding factor 2 MIT domain (NRBF2) from Homo sapiens at 1.50 A resolution 1 N N 2 N N 2 N N 3 N N A GLY 6 A GLY 4 HELX_P A ALA 24 A ALA 22 1 AA1 19 A LYS 26 A LYS 24 HELX_P A LYS 46 A LYS 44 1 AA2 21 A SER 50 A SER 48 HELX_P A ALA 86 A ALA 84 1 AA3 37 covale 1.359 both A GLY 0 A C GLY 1 1_555 A MSE 4 A N MSE 2 1_555 covale 1.348 both A MSE 4 A C MSE 2 1_555 A GLU 5 A N GLU 3 1_555 covale 1.338 both A ALA 44 A C ALA 42 1_555 A MSE 45 A N MSE 43 1_555 covale 1.341 both A MSE 45 A C MSE 43 1_555 A LYS 46 A N LYS 44 1_555 covale 1.360 both A HIS 64 A C HIS 62 1_555 A MSE 65 A N MSE 63 1_555 covale 1.354 both A MSE 65 A C MSE 63 1_555 A LYS 66 A N LYS 64 1_555 TRANSCRIPTION REGULATOR Structural Genomics, Joint Center for Structural Genomics, JCSG, Partnership for Nuclear Receptor Signaling Code Biology, NHRs, PSI-BIOLOGY, TRANSCRIPTION REGULATOR NRBF2_HUMAN UNP 1 4 Q96F24 MEGPLNLAHQQSRRADRLLAAGKYEEAISCHKKAAAYLSEAMKLTQSEQAHLSLELQRDSHMKQLLLIQERWKRAQREER LKA 4 86 4ZEY 4 86 Q96F24 A 1 2 84 1 expression tag GLY 0 4ZEY A Q96F24 UNP 1 binding site for residue SO4 A 401 A SO4 401 Software 6 binding site for residue SO4 A 402 A SO4 402 Software 6 A HIS 12 A HIS 10 6 2_555 A HIS 12 A HIS 10 6 1_555 A SER 15 A SER 13 6 1_555 A SER 15 A SER 13 6 2_555 A HOH 548 D HOH 6 2_555 A HOH 548 D HOH 6 1_555 A TRP 75 A TRP 73 6 1_555 A GLN 79 A GLN 77 6 2_554 A GLN 79 A GLN 77 6 1_555 A HOH 504 D HOH 6 1_555 A HOH 552 D HOH 6 1_555 A HOH 552 D HOH 6 2_554 5 C 1 2 1