HEADER LIGASE 14-JUN-14 4UPA TITLE CRYSTAL STRUCTURE OF ENTAMOEBA HISTOLYTICA LYSYL-TRNA SYNTHETASE IN TITLE 2 COMPLEX WITH AMPPNP COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSINE--TRNA LIGASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYSYL-TRNA SYNTHETASE; COMPND 5 EC: 6.1.1.6; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTAMOEBA HISTOLYTICA; SOURCE 3 ORGANISM_TAXID: 5759; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VARIANT: C41(DE3) ROSETTA; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET-30 EK/LIC KEYWDS LIGASE, AMINOACYLATION EXPDTA X-RAY DIFFRACTION AUTHOR L.BONNEFOND,O.NUREKI REVDAT 6 10-JAN-24 4UPA 1 REMARK REVDAT 5 11-FEB-15 4UPA 1 REMARK REVDAT 4 10-DEC-14 4UPA 1 JRNL REVDAT 3 26-NOV-14 4UPA 1 JRNL REVDAT 2 05-NOV-14 4UPA 1 JRNL REVDAT 1 29-OCT-14 4UPA 0 JRNL AUTH L.BONNEFOND,M.CASTRO DE MOURA,L.RIBAS DE POUPLANA,O.NUREKI JRNL TITL CRYSTAL STRUCTURES OF ENTAMOEBA HISTOLYTICA LYSYL-TRNA JRNL TITL 2 SYNTHETASE REVEAL CONFORMATIONAL CHANGES UPON LYSINE BINDING JRNL TITL 3 AND A SPECIFIC HELIX BUNDLE DOMAIN. JRNL REF FEBS LETT. V. 588 4478 2014 JRNL REFN ISSN 0014-5793 JRNL PMID 25448989 JRNL DOI 10.1016/J.FEBSLET.2014.10.019 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.68 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 29222 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1420 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 38.6861 - 6.2422 0.99 2841 143 0.2042 0.2363 REMARK 3 2 6.2422 - 4.9579 1.00 2779 153 0.1903 0.2124 REMARK 3 3 4.9579 - 4.3321 1.00 2813 138 0.1483 0.1679 REMARK 3 4 4.3321 - 3.9365 1.00 2785 117 0.1647 0.2168 REMARK 3 5 3.9365 - 3.6545 1.00 2789 150 0.1896 0.2371 REMARK 3 6 3.6545 - 3.4392 1.00 2781 128 0.2193 0.2551 REMARK 3 7 3.4392 - 3.2671 1.00 2737 149 0.2521 0.2923 REMARK 3 8 3.2671 - 3.1249 1.00 2793 151 0.2728 0.3022 REMARK 3 9 3.1249 - 3.0047 1.00 2773 138 0.3110 0.3511 REMARK 3 10 3.0047 - 2.9010 0.99 2711 153 0.3816 0.3812 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.460 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 84.21 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 80.70 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 4217 REMARK 3 ANGLE : 0.987 5701 REMARK 3 CHIRALITY : 0.038 638 REMARK 3 PLANARITY : 0.007 729 REMARK 3 DIHEDRAL : 15.022 1599 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 147.0406 126.8564 15.5773 REMARK 3 T TENSOR REMARK 3 T11: 0.3786 T22: 0.6554 REMARK 3 T33: 0.4919 T12: -0.0844 REMARK 3 T13: 0.0665 T23: -0.0126 REMARK 3 L TENSOR REMARK 3 L11: 0.2087 L22: 3.4215 REMARK 3 L33: 0.6836 L12: -0.3081 REMARK 3 L13: 0.0128 L23: 0.0350 REMARK 3 S TENSOR REMARK 3 S11: -0.0806 S12: -0.0761 S13: -0.1001 REMARK 3 S21: 0.5629 S22: 0.0840 S23: 0.6816 REMARK 3 S31: 0.0382 S32: -0.1621 S33: 0.0379 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4UPA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 14-JUN-14. REMARK 100 THE DEPOSITION ID IS D_1290060940. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-DEC-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NE3A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC Q270 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29250 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 39.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.100 REMARK 200 R MERGE (I) : 0.11000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 15.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.100 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 3BJU REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 50 MM HEPES PH 8.0, 50 MM NACL, 7.5% REMARK 280 PEG 4000, 1.2 MM SPERMINE, PH 7.5 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.75467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 31.37733 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 62.75467 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 31.37733 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10240 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 44880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.3 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 313.64000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 271.62021 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -7 REMARK 465 HIS A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 ASP A 304 REMARK 465 ARG A 305 REMARK 465 LEU A 306 REMARK 465 MET A 307 REMARK 465 ASP A 308 REMARK 465 ILE A 309 REMARK 465 ASN A 310 REMARK 465 ASN A 311 REMARK 465 GLU A 312 REMARK 465 GLU A 313 REMARK 465 ASP A 314 REMARK 465 ILE A 315 REMARK 465 LYS A 316 REMARK 465 MET A 317 REMARK 465 LEU A 318 REMARK 465 GLU A 319 REMARK 465 LYS A 320 REMARK 465 PHE A 321 REMARK 465 PHE A 322 REMARK 465 LYS A 323 REMARK 465 GLU A 324 REMARK 465 PRO A 325 REMARK 465 ILE A 326 REMARK 465 PRO A 327 REMARK 465 ARG A 328 REMARK 465 PRO A 329 REMARK 465 PHE A 330 REMARK 465 ASN A 331 REMARK 465 SER A 332 REMARK 465 ALA A 333 REMARK 465 GLU A 334 REMARK 465 CYS A 335 REMARK 465 SER A 336 REMARK 465 LYS A 337 REMARK 465 VAL A 338 REMARK 465 ILE A 339 REMARK 465 GLU A 340 REMARK 465 LYS A 341 REMARK 465 HIS A 342 REMARK 465 CYS A 343 REMARK 465 THR A 344 REMARK 465 GLU A 345 REMARK 465 LEU A 346 REMARK 465 ASN A 347 REMARK 465 TYR A 348 REMARK 465 TYR A 349 REMARK 465 TYR A 350 REMARK 465 ASP A 351 REMARK 465 GLY A 352 REMARK 465 ASN A 353 REMARK 465 ASN A 354 REMARK 465 GLU A 355 REMARK 465 LYS A 356 REMARK 465 ALA A 357 REMARK 465 MET A 358 REMARK 465 LYS A 359 REMARK 465 LYS A 360 REMARK 465 LEU A 361 REMARK 465 PHE A 362 REMARK 465 ALA A 363 REMARK 465 ASP A 364 REMARK 465 PHE A 365 REMARK 465 VAL A 366 REMARK 465 THR A 367 REMARK 465 GLU A 368 REMARK 465 ALA A 507 REMARK 465 GLY A 508 REMARK 465 ASP A 509 REMARK 465 ASP A 510 REMARK 465 GLU A 511 REMARK 465 ALA A 512 REMARK 465 GLN A 513 REMARK 465 ALA A 584 REMARK 465 THR A 585 REMARK 465 GLU A 586 REMARK 465 GLU A 587 REMARK 465 LYS A 588 REMARK 465 GLY A 589 REMARK 465 GLY A 590 REMARK 465 LYS A 591 REMARK 465 LYS A 592 REMARK 465 VAL A 593 REMARK 465 VAL A 594 REMARK 465 LYS A 595 REMARK 465 PRO A 596 REMARK 465 LYS A 597 REMARK 465 ALA A 598 REMARK 465 ASN A 599 REMARK 465 LYS A 600 REMARK 465 GLN A 601 REMARK 465 GLN A 602 REMARK 465 PRO A 603 REMARK 465 VAL A 604 REMARK 465 LYS A 605 REMARK 465 GLU A 606 REMARK 465 VAL A 607 REMARK 465 LEU A 608 REMARK 465 ASP A 609 REMARK 465 GLY A 610 REMARK 465 PHE A 611 REMARK 465 GLN A 612 REMARK 465 LEU A 613 REMARK 465 GLU A 614 REMARK 465 ILE A 615 REMARK 465 ARG A 616 REMARK 465 VAL A 617 REMARK 465 GLY A 618 REMARK 465 LYS A 619 REMARK 465 ILE A 620 REMARK 465 VAL A 621 REMARK 465 GLU A 622 REMARK 465 ALA A 623 REMARK 465 GLY A 624 REMARK 465 PRO A 625 REMARK 465 HIS A 626 REMARK 465 PRO A 627 REMARK 465 ASN A 628 REMARK 465 SER A 629 REMARK 465 GLU A 630 REMARK 465 HIS A 631 REMARK 465 LEU A 632 REMARK 465 LEU A 633 REMARK 465 ALA A 634 REMARK 465 LEU A 635 REMARK 465 LYS A 636 REMARK 465 VAL A 637 REMARK 465 ASP A 638 REMARK 465 VAL A 639 REMARK 465 GLY A 640 REMARK 465 GLU A 641 REMARK 465 GLU A 642 REMARK 465 LYS A 643 REMARK 465 PRO A 644 REMARK 465 ARG A 645 REMARK 465 SER A 646 REMARK 465 VAL A 647 REMARK 465 VAL A 648 REMARK 465 ALA A 649 REMARK 465 GLY A 650 REMARK 465 LEU A 651 REMARK 465 ALA A 652 REMARK 465 GLU A 653 REMARK 465 HIS A 654 REMARK 465 TYR A 655 REMARK 465 LYS A 656 REMARK 465 PRO A 657 REMARK 465 GLU A 658 REMARK 465 GLU A 659 REMARK 465 LEU A 660 REMARK 465 LEU A 661 REMARK 465 ASN A 662 REMARK 465 GLN A 663 REMARK 465 LYS A 664 REMARK 465 ALA A 665 REMARK 465 THR A 666 REMARK 465 PHE A 667 REMARK 465 VAL A 668 REMARK 465 CYS A 669 REMARK 465 ASN A 670 REMARK 465 LEU A 671 REMARK 465 LYS A 672 REMARK 465 PRO A 673 REMARK 465 SER A 674 REMARK 465 LYS A 675 REMARK 465 LEU A 676 REMARK 465 ARG A 677 REMARK 465 GLY A 678 REMARK 465 VAL A 679 REMARK 465 ALA A 680 REMARK 465 SER A 681 REMARK 465 GLU A 682 REMARK 465 ALA A 683 REMARK 465 MET A 684 REMARK 465 ILE A 685 REMARK 465 LEU A 686 REMARK 465 ALA A 687 REMARK 465 ALA A 688 REMARK 465 THR A 689 REMARK 465 SER A 690 REMARK 465 LEU A 691 REMARK 465 ASP A 692 REMARK 465 GLY A 693 REMARK 465 THR A 694 REMARK 465 LYS A 695 REMARK 465 VAL A 696 REMARK 465 LYS A 697 REMARK 465 PHE A 698 REMARK 465 CYS A 699 REMARK 465 HIS A 700 REMARK 465 PRO A 701 REMARK 465 SER A 702 REMARK 465 ALA A 703 REMARK 465 ASP A 704 REMARK 465 ALA A 705 REMARK 465 ALA A 706 REMARK 465 ILE A 707 REMARK 465 GLY A 708 REMARK 465 ALA A 709 REMARK 465 GLN A 710 REMARK 465 VAL A 711 REMARK 465 ILE A 712 REMARK 465 PRO A 713 REMARK 465 LYS A 714 REMARK 465 GLU A 715 REMARK 465 GLY A 716 REMARK 465 LYS A 717 REMARK 465 VAL A 718 REMARK 465 THR A 719 REMARK 465 ILE A 720 REMARK 465 SER A 721 REMARK 465 ALA A 722 REMARK 465 LYS A 723 REMARK 465 LYS A 724 REMARK 465 ILE A 725 REMARK 465 SER A 726 REMARK 465 ILE A 727 REMARK 465 ASP A 728 REMARK 465 VAL A 729 REMARK 465 VAL A 730 REMARK 465 GLY A 731 REMARK 465 LYS A 732 REMARK 465 MET A 733 REMARK 465 ASN A 734 REMARK 465 LEU A 735 REMARK 465 ALA A 736 REMARK 465 LEU A 737 REMARK 465 LYS A 738 REMARK 465 GLY A 739 REMARK 465 GLY A 740 REMARK 465 LEU A 741 REMARK 465 VAL A 742 REMARK 465 ARG A 743 REMARK 465 THR A 744 REMARK 465 ASN A 745 REMARK 465 ASP A 746 REMARK 465 VAL A 747 REMARK 465 PRO A 748 REMARK 465 LEU A 749 REMARK 465 ILE A 750 REMARK 465 VAL A 751 REMARK 465 LYS A 752 REMARK 465 ASP A 753 REMARK 465 THR A 754 REMARK 465 GLU A 755 REMARK 465 LEU A 756 REMARK 465 THR A 757 REMARK 465 VAL A 758 REMARK 465 THR A 759 REMARK 465 VAL A 760 REMARK 465 ASP A 761 REMARK 465 GLU A 762 REMARK 465 VAL A 763 REMARK 465 ILE A 764 REMARK 465 ASP A 765 REMARK 465 GLY A 766 REMARK 465 THR A 767 REMARK 465 VAL A 768 REMARK 465 ARG A 769 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 92 CG CD OE1 OE2 REMARK 470 GLU A 95 CG CD OE1 OE2 REMARK 470 GLU A 301 CG CD OE1 OE2 REMARK 470 ASN A 417 CG OD1 ND2 REMARK 470 GLU A 422 CG CD OE1 OE2 REMARK 470 LEU A 565 CG CD1 CD2 REMARK 470 LYS A 568 CG CD CE NZ REMARK 470 MET A 577 CG SD CE REMARK 470 GLN A 580 CG CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 NZ LYS A 299 O LEU A 544 2.10 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 HIS A -2 127.43 -26.73 REMARK 500 GLU A 92 -71.88 -59.68 REMARK 500 LYS A 157 72.97 -104.71 REMARK 500 GLU A 253 -154.58 -128.44 REMARK 500 TYR A 384 -74.76 -52.09 REMARK 500 PRO A 399 87.36 27.97 REMARK 500 PHE A 416 -82.22 -101.40 REMARK 500 ALA A 418 10.20 58.01 REMARK 500 CYS A 420 -176.90 -170.31 REMARK 500 SER A 464 -58.70 -120.91 REMARK 500 ALA A 526 105.81 85.05 REMARK 500 ASP A 563 -165.67 -79.75 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 LYS A 369 LYS A 370 -149.39 REMARK 500 ARG A 398 PRO A 399 -139.61 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 DETERMINATION METHOD: DSSP REMARK 700 THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS REMARK 700 BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY REMARK 700 A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS REMARK 700 ARE IDENTICAL. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ANP A 1584 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4UP7 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ENTAMOEBA HISTOLYTICA LYSYL-TRNA SYNTHETASE IN REMARK 900 COMPLEX WITH LYSYL-ADENYLATE REMARK 900 RELATED ID: 4UP8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ENTAMOEBA HISTOLYTICA LYSYL-TRNA SYNTHETASE REMARK 900 APO FORM REMARK 900 RELATED ID: 4UP9 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF ENTAMOEBA HISTOLYTICA LYSYL-TRNA SYNTHETASE IN REMARK 900 COMPLEX WITH ATP DBREF 4UPA A 2 769 UNP C4M7X2 C4M7X2_ENTHI 2 769 SEQADV 4UPA MET A -7 UNP C4M7X2 EXPRESSION TAG SEQADV 4UPA HIS A -6 UNP C4M7X2 EXPRESSION TAG SEQADV 4UPA HIS A -5 UNP C4M7X2 EXPRESSION TAG SEQADV 4UPA HIS A -4 UNP C4M7X2 EXPRESSION TAG SEQADV 4UPA HIS A -3 UNP C4M7X2 EXPRESSION TAG SEQADV 4UPA HIS A -2 UNP C4M7X2 EXPRESSION TAG SEQADV 4UPA HIS A -1 UNP C4M7X2 EXPRESSION TAG SEQADV 4UPA MET A 0 UNP C4M7X2 EXPRESSION TAG SEQADV 4UPA LEU A 1 UNP C4M7X2 EXPRESSION TAG SEQADV 4UPA LYS A 582 UNP C4M7X2 LEU 582 CONFLICT SEQADV 4UPA ILE A 764 UNP C4M7X2 VAL 764 ENGINEERED MUTATION SEQRES 1 A 777 MET HIS HIS HIS HIS HIS HIS MET LEU SER LYS GLN LEU SEQRES 2 A 777 PHE LEU ASN ARG CYS LYS ASP VAL GLU GLU TYR GLN LYS SEQRES 3 A 777 ALA GLY HIS ASN PRO TRP PRO HIS LYS PHE ASN VAL SER SEQRES 4 A 777 ILE THR VAL PRO GLU PHE ILE ALA LYS TYR SER GLY LEU SEQRES 5 A 777 GLU LYS SER GLN VAL SER ASP ASP ILE VAL SER VAL ALA SEQRES 6 A 777 GLY ARG VAL LEU SER LYS ARG SER SER SER SER ALA LEU SEQRES 7 A 777 MET PHE ILE ASP LEU HIS ASP SER GLN THR LYS LEU GLN SEQRES 8 A 777 ILE MET LEU ASN LYS SER ALA TYR GLU ASN LYS GLU ASP SEQRES 9 A 777 PHE VAL SER LEU THR LYS MET ILE TYR ARG GLY ASP ILE SEQRES 10 A 777 CYS GLY PHE THR GLY HIS PRO THR ARG THR LYS THR GLY SEQRES 11 A 777 GLU LEU SER LEU ILE PRO ILE SER GLY MET ILE LEU SER SEQRES 12 A 777 PRO CYS LEU HIS MET LEU PRO SER MET HIS TYR GLY LEU SEQRES 13 A 777 GLY ASP GLN GLU THR ARG PHE ARG LYS ARG TYR LEU ASP SEQRES 14 A 777 LEU ILE VAL ASN PRO GLU SER VAL LYS ASN PHE VAL LEU SEQRES 15 A 777 ARG THR LYS VAL VAL LYS ALA VAL ARG LYS TYR LEU ASP SEQRES 16 A 777 ASP LYS GLY PHE LEU GLU VAL GLU THR PRO ILE LEU ASN SEQRES 17 A 777 THR ILE PRO GLY GLY ALA THR ALA ARG PRO PHE ILE THR SEQRES 18 A 777 HIS HIS ASN GLN LEU ASP ILE GLN MET TYR MET ARG ILE SEQRES 19 A 777 ALA PRO GLU LEU TYR LEU LYS GLU LEU VAL VAL GLY GLY SEQRES 20 A 777 ILE ASN ARG VAL TYR GLU ILE GLY ARG LEU PHE ARG ASN SEQRES 21 A 777 GLU GLY ILE ASP GLN THR HIS ASN PRO GLU PHE THR THR SEQRES 22 A 777 CYS GLU PHE TYR MET ALA TYR ALA ASP TYR ASN ASP ILE SEQRES 23 A 777 MET LYS MET THR GLU GLU LEU LEU GLY ASN MET VAL LYS SEQRES 24 A 777 ASP ILE THR GLY GLY SER THR LYS LEU GLU ILE LYS ASP SEQRES 25 A 777 ARG LEU MET ASP ILE ASN ASN GLU GLU ASP ILE LYS MET SEQRES 26 A 777 LEU GLU LYS PHE PHE LYS GLU PRO ILE PRO ARG PRO PHE SEQRES 27 A 777 ASN SER ALA GLU CYS SER LYS VAL ILE GLU LYS HIS CYS SEQRES 28 A 777 THR GLU LEU ASN TYR TYR TYR ASP GLY ASN ASN GLU LYS SEQRES 29 A 777 ALA MET LYS LYS LEU PHE ALA ASP PHE VAL THR GLU LYS SEQRES 30 A 777 LYS MET VAL LEU ASP PHE THR ALA PRO PHE LYS ARG ILE SEQRES 31 A 777 SER TYR VAL HIS ALA LEU GLU GLU LYS PHE GLY GLU LYS SEQRES 32 A 777 ILE PRO ARG PRO LEU ASP GLY PRO GLU ALA LEU THR PHE SEQRES 33 A 777 LEU LYS LYS GLN ALA ILE ARG PHE ASN ALA ILE CYS ALA SEQRES 34 A 777 GLU PRO GLN THR THR ALA ARG VAL MET ASP LYS LEU PHE SEQRES 35 A 777 GLY ASP LEU ILE GLU VAL ASP LEU VAL GLN PRO THR PHE SEQRES 36 A 777 VAL CYS ASP GLN PRO GLN LEU MET SER PRO LEU ALA LYS SEQRES 37 A 777 TYR HIS ARG SER GLU PRO GLU LEU THR GLU ARG PHE GLU SEQRES 38 A 777 LEU PHE ILE LEU LYS ARG GLU ILE ALA ASN ALA TYR THR SEQRES 39 A 777 GLU LEU ASN ASN PRO ILE VAL GLN ARG SER ASN PHE GLU SEQRES 40 A 777 GLN GLN ALA LYS ASP LYS ALA ALA GLY ASP ASP GLU ALA SEQRES 41 A 777 GLN LEU VAL ASP GLU VAL PHE LEU ASP ALA ILE GLU HIS SEQRES 42 A 777 ALA PHE PRO PRO THR GLY GLY TRP GLY LEU GLY ILE ASP SEQRES 43 A 777 ARG LEU ALA MET LEU LEU ALA ASP VAL ASP ASN ILE LYS SEQRES 44 A 777 GLU VAL ILE LEU PHE PRO THR MET ARG PRO GLU ASP GLU SEQRES 45 A 777 LEU GLU LYS LYS ALA ARG GLU ALA LYS GLU ASP ALA MET SEQRES 46 A 777 VAL ALA GLN GLU LYS ALA ALA THR GLU GLU LYS GLY GLY SEQRES 47 A 777 LYS LYS VAL VAL LYS PRO LYS ALA ASN LYS GLN GLN PRO SEQRES 48 A 777 VAL LYS GLU VAL LEU ASP GLY PHE GLN LEU GLU ILE ARG SEQRES 49 A 777 VAL GLY LYS ILE VAL GLU ALA GLY PRO HIS PRO ASN SER SEQRES 50 A 777 GLU HIS LEU LEU ALA LEU LYS VAL ASP VAL GLY GLU GLU SEQRES 51 A 777 LYS PRO ARG SER VAL VAL ALA GLY LEU ALA GLU HIS TYR SEQRES 52 A 777 LYS PRO GLU GLU LEU LEU ASN GLN LYS ALA THR PHE VAL SEQRES 53 A 777 CYS ASN LEU LYS PRO SER LYS LEU ARG GLY VAL ALA SER SEQRES 54 A 777 GLU ALA MET ILE LEU ALA ALA THR SER LEU ASP GLY THR SEQRES 55 A 777 LYS VAL LYS PHE CYS HIS PRO SER ALA ASP ALA ALA ILE SEQRES 56 A 777 GLY ALA GLN VAL ILE PRO LYS GLU GLY LYS VAL THR ILE SEQRES 57 A 777 SER ALA LYS LYS ILE SER ILE ASP VAL VAL GLY LYS MET SEQRES 58 A 777 ASN LEU ALA LEU LYS GLY GLY LEU VAL ARG THR ASN ASP SEQRES 59 A 777 VAL PRO LEU ILE VAL LYS ASP THR GLU LEU THR VAL THR SEQRES 60 A 777 VAL ASP GLU VAL ILE ASP GLY THR VAL ARG HET ANP A1584 31 HETNAM ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER FORMUL 2 ANP C10 H17 N6 O12 P3 HELIX 1 1 HIS A -1 ALA A 19 1 21 HELIX 2 2 THR A 33 SER A 42 1 10 HELIX 3 3 SER A 89 TYR A 91 5 3 HELIX 4 4 ASN A 93 ILE A 104 1 12 HELIX 5 5 ASP A 150 LYS A 157 1 8 HELIX 6 6 LYS A 157 ASN A 165 1 9 HELIX 7 7 SER A 168 ASP A 188 1 21 HELIX 8 8 PRO A 228 GLY A 238 1 11 HELIX 9 9 ASP A 274 GLY A 295 1 22 HELIX 10 10 TYR A 384 GLY A 393 1 10 HELIX 11 11 GLY A 402 PHE A 416 1 15 HELIX 12 12 THR A 425 ILE A 438 1 14 HELIX 13 13 ASN A 490 ALA A 506 1 17 HELIX 14 14 ASP A 516 HIS A 525 1 10 HELIX 15 15 ILE A 537 ASP A 546 1 10 HELIX 16 16 ASN A 549 ILE A 554 5 6 HELIX 17 17 ASP A 563 ALA A 583 1 21 SHEET 1 AA 7 GLN A 48 VAL A 49 0 SHEET 2 AA 7 ILE A 109 ARG A 118 -1 N ARG A 118 O GLN A 48 SHEET 3 AA 7 LEU A 124 SER A 135 -1 O SER A 125 N THR A 117 SHEET 4 AA 7 THR A 80 ASN A 87 1 O GLN A 83 N LEU A 126 SHEET 5 AA 7 LEU A 70 ASP A 77 -1 O MET A 71 N LEU A 86 SHEET 6 AA 7 VAL A 54 SER A 65 -1 O ARG A 59 N HIS A 76 SHEET 7 AA 7 GLN A 48 VAL A 49 0 SHEET 1 AB 8 LEU A 192 GLU A 193 0 SHEET 2 AB 8 ARG A 242 PHE A 250 1 O ARG A 242 N LEU A 192 SHEET 3 AB 8 GLU A 262 ALA A 271 -1 O PHE A 263 N LEU A 249 SHEET 4 AB 8 THR A 530 GLY A 536 -1 O GLY A 531 N MET A 270 SHEET 5 AB 8 ARG A 479 THR A 486 -1 O ILE A 481 N GLY A 536 SHEET 6 AB 8 ARG A 471 ILE A 476 -1 O PHE A 472 N ALA A 484 SHEET 7 AB 8 THR A 446 CYS A 449 -1 O THR A 446 N PHE A 475 SHEET 8 AB 8 LYS A 380 SER A 383 1 O LYS A 380 N PHE A 447 SHEET 1 AC 3 LEU A 199 ASN A 200 0 SHEET 2 AC 3 ILE A 220 MET A 224 -1 O TYR A 223 N ASN A 200 SHEET 3 AC 3 ILE A 212 HIS A 215 -1 O THR A 213 N MET A 222 SHEET 1 AD 2 THR A 298 ILE A 302 0 SHEET 2 AD 2 LYS A 370 ASP A 374 -1 O MET A 371 N GLU A 301 CISPEP 1 MET A 144 HIS A 145 0 1.30 CISPEP 2 LEU A 148 GLY A 149 0 2.29 CISPEP 3 ALA A 377 PRO A 378 0 -1.78 CISPEP 4 GLU A 422 PRO A 423 0 0.22 CISPEP 5 VAL A 440 ASP A 441 0 -0.09 SITE 1 AC1 7 ARG A 251 THR A 258 HIS A 259 ASN A 260 SITE 2 AC1 7 PHE A 263 ARG A 539 ILE A 550 CRYST1 156.820 156.820 94.132 90.00 90.00 120.00 P 62 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.006377 0.003682 0.000000 0.00000 SCALE2 0.000000 0.007363 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010623 0.00000