HEADER TRANSFERASE 25-AUG-23 8W5A TITLE CRYSTAL STRUCTURE OF THE RING DOMAIN OF HUMAN XIAP COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE XIAP; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RING DOMAIN; COMPND 5 SYNONYM: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4,IAP-LIKE COMPND 6 PROTEIN,ILP,HILP,INHIBITOR OF APOPTOSIS PROTEIN 3,IAP-3,HIAP-3,HIAP3, COMPND 7 RING-TYPE E3 UBIQUITIN TRANSFERASE XIAP,X-LINKED INHIBITOR OF COMPND 8 APOPTOSIS PROTEIN,X-LINKED IAP; COMPND 9 EC: 2.3.2.27; COMPND 10 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: XIAP, API3, BIRC4, IAP3; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RING DOMAIN, XIAP, LIGASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR Q.ZHANG,H.SUN,X.HU,M.WANG REVDAT 3 25-OCT-23 8W5A 1 AUTHOR REVDAT 2 04-OCT-23 8W5A 1 KEYWDS REVDAT 1 27-SEP-23 8W5A 0 JRNL AUTH Q.ZHANG,H.SUN JRNL TITL CRYSTAL STRUCTURE OF THE RING DOMAIN OF HUMAN XIAP JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.0 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 16111 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.217 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.210 REMARK 3 FREE R VALUE TEST SET COUNT : 840 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 39.3200 - 3.0000 0.99 2581 145 0.1853 0.2302 REMARK 3 2 3.0000 - 2.3800 0.99 2562 128 0.2162 0.2291 REMARK 3 3 2.3800 - 2.0800 0.99 2542 136 0.2088 0.2229 REMARK 3 4 2.0800 - 1.8900 0.99 2526 155 0.2269 0.2500 REMARK 3 5 1.8900 - 1.7600 0.99 2529 148 0.2803 0.3182 REMARK 3 6 1.7600 - 1.6500 0.99 2531 128 0.2931 0.3512 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.230 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.008 1007 REMARK 3 ANGLE : 1.024 1350 REMARK 3 CHIRALITY : 0.061 162 REMARK 3 PLANARITY : 0.008 168 REMARK 3 DIHEDRAL : 6.773 133 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 8W5A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-SEP-23. REMARK 100 THE DEPOSITION ID IS D_1300035289. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-SEP-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97915 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16111 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 REMARK 200 RESOLUTION RANGE LOW (A) : 39.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 200 DATA REDUNDANCY : 8.400 REMARK 200 R MERGE (I) : 0.32300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 0.2170 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.65 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 39.32 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.32300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1 MM TCEP, 30-32% PEG 3350, 100 MM REMARK 280 TRIS-HCL, PH 7.4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y+1/2,-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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 24.37100 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1860 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 GLU A 434 REMARK 465 SER A 497 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 PHE A 490 CG CD1 CD2 CE1 CE2 CZ REMARK 470 GLU B 446 CG CD OE1 OE2 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 MET B 454 22.67 48.24 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 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 450 SG REMARK 620 2 CYS A 453 SG 106.4 REMARK 620 3 CYS A 471 SG 113.4 116.6 REMARK 620 4 CYS A 474 SG 108.9 108.8 102.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 465 SG REMARK 620 2 HIS A 467 ND1 106.7 REMARK 620 3 CYS A 481 SG 107.5 114.5 REMARK 620 4 CYS A 484 SG 108.6 106.8 112.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 502 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 450 SG REMARK 620 2 CYS B 453 SG 107.5 REMARK 620 3 CYS B 471 SG 113.0 113.3 REMARK 620 4 CYS B 474 SG 104.7 114.3 103.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA B 501 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 455 OD1 REMARK 620 2 HOH B 601 O 85.3 REMARK 620 3 HOH B 616 O 84.5 168.3 REMARK 620 4 HOH B 620 O 93.8 95.5 91.0 REMARK 620 5 HOH B 622 O 97.9 88.1 87.5 168.1 REMARK 620 6 HOH B 624 O 172.6 92.6 98.2 79.3 89.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 465 SG REMARK 620 2 HIS B 467 ND1 109.6 REMARK 620 3 CYS B 481 SG 109.7 110.3 REMARK 620 4 CYS B 484 SG 106.8 109.0 111.4 REMARK 620 N 1 2 3 DBREF 8W5A A 434 497 UNP P98170 XIAP_HUMAN 434 497 DBREF 8W5A B 434 497 UNP P98170 XIAP_HUMAN 434 497 SEQRES 1 A 64 GLU ILE SER THR GLU GLU GLN LEU ARG ARG LEU GLN GLU SEQRES 2 A 64 GLU LYS LEU CYS LYS ILE CYS MET ASP ARG ASN ILE ALA SEQRES 3 A 64 ILE VAL PHE VAL PRO CYS GLY HIS LEU VAL THR CYS LYS SEQRES 4 A 64 GLN CYS ALA GLU ALA VAL ASP LYS CYS PRO MET CYS TYR SEQRES 5 A 64 THR VAL ILE THR PHE LYS GLN LYS ILE PHE MET SER SEQRES 1 B 64 GLU ILE SER THR GLU GLU GLN LEU ARG ARG LEU GLN GLU SEQRES 2 B 64 GLU LYS LEU CYS LYS ILE CYS MET ASP ARG ASN ILE ALA SEQRES 3 B 64 ILE VAL PHE VAL PRO CYS GLY HIS LEU VAL THR CYS LYS SEQRES 4 B 64 GLN CYS ALA GLU ALA VAL ASP LYS CYS PRO MET CYS TYR SEQRES 5 B 64 THR VAL ILE THR PHE LYS GLN LYS ILE PHE MET SER HET ZN A 501 1 HET ZN A 502 1 HET CA B 501 1 HET ZN B 502 1 HET ZN B 503 1 HETNAM ZN ZINC ION HETNAM CA CALCIUM ION FORMUL 3 ZN 4(ZN 2+) FORMUL 5 CA CA 2+ FORMUL 8 HOH *37(H2 O) HELIX 1 AA1 SER A 436 LYS A 448 1 13 HELIX 2 AA2 GLN A 473 VAL A 478 5 6 HELIX 3 AA3 SER B 436 GLU B 447 1 12 HELIX 4 AA4 CYS B 471 GLU B 476 1 6 SHEET 1 AA1 2 ILE A 460 VAL A 463 0 SHEET 2 AA1 2 PHE A 490 LYS A 493 -1 O PHE A 490 N VAL A 463 SHEET 1 AA2 2 ILE B 460 VAL B 463 0 SHEET 2 AA2 2 PHE B 490 LYS B 493 -1 O PHE B 490 N VAL B 463 LINK SG CYS A 450 ZN ZN A 502 1555 1555 2.34 LINK SG CYS A 453 ZN ZN A 502 1555 1555 2.31 LINK SG CYS A 465 ZN ZN A 501 1555 1555 2.33 LINK ND1 HIS A 467 ZN ZN A 501 1555 1555 2.02 LINK SG CYS A 471 ZN ZN A 502 1555 1555 2.35 LINK SG CYS A 474 ZN ZN A 502 1555 1555 2.35 LINK SG CYS A 481 ZN ZN A 501 1555 1555 2.28 LINK SG CYS A 484 ZN ZN A 501 1555 1555 2.31 LINK SG CYS B 450 ZN ZN B 502 1555 1555 2.36 LINK SG CYS B 453 ZN ZN B 502 1555 1555 2.33 LINK OD1 ASP B 455 CA CA B 501 1555 1555 2.18 LINK SG CYS B 465 ZN ZN B 503 1555 1555 2.31 LINK ND1 HIS B 467 ZN ZN B 503 1555 1555 1.99 LINK SG CYS B 471 ZN ZN B 502 1555 1555 2.30 LINK SG CYS B 474 ZN ZN B 502 1555 1555 2.31 LINK SG CYS B 481 ZN ZN B 503 1555 1555 2.33 LINK SG CYS B 484 ZN ZN B 503 1555 1555 2.27 LINK CA CA B 501 O HOH B 601 1555 1555 2.01 LINK CA CA B 501 O HOH B 616 1555 1555 2.14 LINK CA CA B 501 O HOH B 620 1555 1555 2.28 LINK CA CA B 501 O HOH B 622 1555 1555 2.24 LINK CA CA B 501 O HOH B 624 1555 1555 2.39 CISPEP 1 VAL A 463 PRO A 464 0 7.90 CISPEP 2 VAL B 463 PRO B 464 0 5.23 CRYST1 35.696 48.742 39.639 90.00 97.28 90.00 P 1 21 1 4 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 0.028014 0.000000 0.003579 0.00000 SCALE2 0.000000 0.020516 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025433 0.00000