HEADER ANTIVIRAL PROTEIN 10-DEC-20 7KZH TITLE ZINC FINGER ANTIVIRAL PROTEIN (ZAP) CENTRAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC FINGER CCCH-TYPE ANTIVIRAL PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: ADP-RIBOSYLTRANSFERASE DIPHTHERIA TOXIN-LIKE 13,ARTD13, COMPND 5 INACTIVE POLY [ADP-RIBOSE] POLYMERASE 13,PARP13,ZINC FINGER CCCH COMPND 6 DOMAIN-CONTAINING PROTEIN 2,ZINC FINGER ANTIVIRAL PROTEIN,ZAP; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: ZC3HAV1, ZC3HDC2, PRO1677; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RESTRICTION FACTOR, ANTIVIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR O.P.PORNILLOS REVDAT 2 11-JAN-23 7KZH 1 JRNL REVDAT 1 15-DEC-21 7KZH 0 JRNL AUTH G.XUE,K.BRACZYK,D.GONCALVES-CARNEIRO,D.M.DAWIDZIAK, JRNL AUTH 2 K.SANCHEZ,H.ONG,Y.WAN,K.K.ZADROZNY,B.K.GANSER-PORNILLOS, JRNL AUTH 3 P.D.BIENIASZ,O.PORNILLOS JRNL TITL POLY(ADP-RIBOSE) POTENTIATES ZAP ANTIVIRAL ACTIVITY. JRNL REF PLOS PATHOG. V. 18 09202 2022 JRNL REFN ESSN 1553-7374 JRNL PMID 35130321 JRNL DOI 10.1371/JOURNAL.PPAT.1009202 REMARK 2 REMARK 2 RESOLUTION. 2.49 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18_3845 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.49 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 8724 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.226 REMARK 3 FREE R VALUE : 0.263 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.910 REMARK 3 FREE R VALUE TEST SET COUNT : 428 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 38.8100 - 3.6000 0.97 2808 142 0.2090 0.2589 REMARK 3 2 3.5900 - 2.8500 1.00 2758 145 0.2375 0.2542 REMARK 3 3 2.8500 - 2.4900 0.98 2730 141 0.2602 0.2943 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) : 0.305 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.509 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 35.61 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 41.92 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 : 0.003 1489 REMARK 3 ANGLE : 0.530 2023 REMARK 3 CHIRALITY : 0.044 215 REMARK 3 PLANARITY : 0.003 255 REMARK 3 DIHEDRAL : 16.563 532 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 7KZH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1000253462. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8-6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8779 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 48.00 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 24.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 24.00 REMARK 200 R MERGE FOR SHELL (I) : 1.00000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHENIX 1.18_3845 REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.63 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.8-1.1 M SODIUM NITRATE 0.1 M SODIUM REMARK 280 ACETATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 3 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z REMARK 290 6555 -X,-X+Y,-Z 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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 0.00000 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 0.00000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 SER A 498 REMARK 465 THR A 499 REMARK 465 THR A 500 REMARK 465 SER A 501 REMARK 465 SER A 502 REMARK 465 ARG A 503 REMARK 465 VAL A 504 REMARK 465 ASP A 505 REMARK 465 ASP A 506 REMARK 465 HIS A 507 REMARK 465 ASP A 508 REMARK 465 GLU A 624 REMARK 465 LYS A 625 REMARK 465 ASP A 626 REMARK 465 LYS A 627 REMARK 465 ARG A 628 REMARK 465 LYS A 629 REMARK 465 GLY A 697 REMARK 465 PRO A 698 REMARK 465 ASP A 699 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 ASN A 524 CG OD1 ND2 REMARK 470 LYS A 544 CG CD CE NZ REMARK 470 SER A 571 OG REMARK 470 TYR A 572 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASP A 582 CG OD1 OD2 REMARK 470 SER A 583 OG REMARK 470 PHE A 584 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU A 614 CG CD OE1 OE2 REMARK 470 ARG A 647 CG CD NE CZ NH1 NH2 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 CYS A 518 -112.00 -104.45 REMARK 500 ASN A 524 -137.31 51.72 REMARK 500 HIS A 551 73.76 -104.30 REMARK 500 SER A 583 -39.82 82.76 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 701 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 513 SG REMARK 620 2 CYS A 521 SG 111.0 REMARK 620 3 CYS A 527 SG 116.0 107.8 REMARK 620 4 HIS A 531 NE2 113.5 108.0 99.8 REMARK 620 N 1 2 3 DBREF 7KZH A 498 699 UNP Q7Z2W4 ZCCHV_HUMAN 498 699 SEQRES 1 A 202 SER THR THR SER SER ARG VAL ASP ASP HIS ASP SER GLU SEQRES 2 A 202 GLU ILE CYS LEU ASP HIS LEU CYS LYS GLY CYS PRO LEU SEQRES 3 A 202 ASN GLY SER CYS SER LYS VAL HIS PHE HIS LEU PRO TYR SEQRES 4 A 202 ARG TRP GLN MSE LEU ILE GLY LYS THR TRP THR ASP PHE SEQRES 5 A 202 GLU HIS MSE GLU THR ILE GLU LYS GLY TYR CYS ASN PRO SEQRES 6 A 202 GLY ILE HIS LEU CYS SER VAL GLY SER TYR THR ILE ASN SEQRES 7 A 202 PHE ARG VAL MSE SER CYS ASP SER PHE PRO ILE ARG ARG SEQRES 8 A 202 LEU SER THR PRO SER SER VAL THR LYS PRO ALA ASN SER SEQRES 9 A 202 VAL PHE THR THR LYS TRP ILE TRP TYR TRP LYS ASN GLU SEQRES 10 A 202 SER GLY THR TRP ILE GLN TYR GLY GLU GLU LYS ASP LYS SEQRES 11 A 202 ARG LYS ASN SER ASN VAL ASP SER SER TYR LEU GLU SER SEQRES 12 A 202 LEU TYR GLN SER CYS PRO ARG GLY VAL VAL PRO PHE GLN SEQRES 13 A 202 ALA GLY SER ARG ASN TYR GLU LEU SER PHE GLN GLY MSE SEQRES 14 A 202 ILE GLN THR ASN ILE ALA SER LYS THR GLN LYS ASP VAL SEQRES 15 A 202 ILE ARG ARG PRO THR PHE VAL PRO GLN TRP TYR VAL GLN SEQRES 16 A 202 GLN MSE LYS ARG GLY PRO ASP MODRES 7KZH MSE A 540 MET MODIFIED RESIDUE MODRES 7KZH MSE A 552 MET MODIFIED RESIDUE MODRES 7KZH MSE A 579 MET MODIFIED RESIDUE MODRES 7KZH MSE A 666 MET MODIFIED RESIDUE MODRES 7KZH MSE A 694 MET MODIFIED RESIDUE HET MSE A 540 17 HET MSE A 552 17 HET MSE A 579 17 HET MSE A 666 17 HET MSE A 694 17 HET ZN A 701 1 HETNAM MSE SELENOMETHIONINE HETNAM ZN ZINC ION FORMUL 1 MSE 5(C5 H11 N O2 SE) FORMUL 2 ZN ZN 2+ FORMUL 3 HOH *33(H2 O) HELIX 1 AA1 CYS A 513 CYS A 518 1 6 HELIX 2 AA2 LEU A 523 CYS A 527 5 5 HELIX 3 AA3 HIS A 551 ASN A 561 1 11 HELIX 4 AA4 SER A 593 LYS A 597 5 5 HELIX 5 AA5 ASP A 634 CYS A 645 1 12 HELIX 6 AA6 PRO A 687 ARG A 696 1 10 SHEET 1 AA1 6 THR A 545 ASP A 548 0 SHEET 2 AA1 6 TYR A 536 ILE A 542 -1 N ILE A 542 O THR A 545 SHEET 3 AA1 6 PHE A 584 SER A 590 -1 O PRO A 585 N LEU A 541 SHEET 4 AA1 6 SER A 580 CYS A 581 -1 N CYS A 581 O PHE A 584 SHEET 5 AA1 6 TYR A 572 ASN A 575 -1 N ASN A 575 O SER A 580 SHEET 6 AA1 6 LEU A 566 VAL A 569 -1 N CYS A 567 O ILE A 574 SHEET 1 AA2 6 TRP A 618 GLN A 620 0 SHEET 2 AA2 6 TRP A 607 LYS A 612 -1 N TRP A 611 O ILE A 619 SHEET 3 AA2 6 GLN A 676 PRO A 683 -1 O ARG A 682 N ILE A 608 SHEET 4 AA2 6 ILE A 667 ASN A 670 -1 N GLN A 668 O LYS A 677 SHEET 5 AA2 6 ARG A 657 SER A 662 -1 N SER A 662 O ILE A 667 SHEET 6 AA2 6 VAL A 649 ALA A 654 -1 N PHE A 652 O TYR A 659 LINK C GLN A 539 N MSE A 540 1555 1555 1.33 LINK C MSE A 540 N LEU A 541 1555 1555 1.33 LINK C HIS A 551 N MSE A 552 1555 1555 1.33 LINK C MSE A 552 N GLU A 553 1555 1555 1.33 LINK C VAL A 578 N MSE A 579 1555 1555 1.33 LINK C MSE A 579 N SER A 580 1555 1555 1.33 LINK C GLY A 665 N MSE A 666 1555 1555 1.33 LINK C MSE A 666 N ILE A 667 1555 1555 1.33 LINK C GLN A 693 N MSE A 694 1555 1555 1.33 LINK C MSE A 694 N LYS A 695 1555 1555 1.34 LINK SG CYS A 513 ZN ZN A 701 1555 1555 2.32 LINK SG CYS A 521 ZN ZN A 701 1555 1555 2.31 LINK SG CYS A 527 ZN ZN A 701 1555 1555 2.33 LINK NE2 HIS A 531 ZN ZN A 701 1555 1555 2.03 CRYST1 89.637 89.637 53.055 90.00 90.00 120.00 P 3 2 1 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 0.011156 0.006441 0.000000 0.00000 SCALE2 0.000000 0.012882 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018848 0.00000