PDB Short entry for 4IC2 HEADER LIGASE 09-DEC-12 4IC2 TITLE CRYSTAL STRUCTURE OF THE XIAP RING DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: E3 UBIQUITIN-PROTEIN LIGASE XIAP; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: RING DOMAIN, UNP RESIDUES 429-497; 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, COMPND 7 HIAP3, X-LINKED INHIBITOR OF APOPTOSIS PROTEIN, X-LINKED IAP; COMPND 8 EC: 6.3.2.-; COMPND 9 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: API3, BIR4, IAP3, XIAP; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PGEX6P3 KEYWDS RING DOMAIN, ZINC-FINGER, E3 LIGASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR K.LINKE,Y.NAKATANI,C.L.DAY REVDAT 3 08-NOV-23 4IC2 1 REMARK SEQADV LINK REVDAT 2 10-JUL-13 4IC2 1 JRNL REVDAT 1 19-DEC-12 4IC2 0 JRNL AUTH Y.NAKATANI,T.KLEFFMANN,K.LINKE,S.M.CONDON,M.G.HINDS,C.L.DAY JRNL TITL REGULATION OF UBIQUITIN TRANSFER BY XIAP, A DIMERIC RING E3 JRNL TITL 2 LIGASE JRNL REF BIOCHEM.J. V. 450 629 2013 JRNL REFN ISSN 0264-6021 JRNL PMID 23259674 JRNL DOI 10.1042/BJ20121702 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.1_743) 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 6534 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.810 REMARK 3 FREE R VALUE TEST SET COUNT : 314 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 18.3180 - 2.7707 0.98 3280 155 0.1856 0.2176 REMARK 3 2 2.7707 - 2.2003 0.90 2940 159 0.2002 0.2808 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.00 REMARK 3 SHRINKAGE RADIUS : 0.72 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 48.26 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.590 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.150 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -5.80370 REMARK 3 B22 (A**2) : -4.47500 REMARK 3 B33 (A**2) : 10.27870 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.39910 REMARK 3 B23 (A**2) : 0.00000 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 : 0.009 1028 REMARK 3 ANGLE : 1.191 1379 REMARK 3 CHIRALITY : 0.079 163 REMARK 3 PLANARITY : 0.005 172 REMARK 3 DIHEDRAL : 14.306 403 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 4IC2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-DEC-12. REMARK 100 THE DEPOSITION ID IS D_1000076565. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-SEP-07 REMARK 200 TEMPERATURE (KELVIN) : 113 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : MIRROR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6536 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 18.420 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : 0.06600 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 17.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.32 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.70 REMARK 200 R MERGE FOR SHELL (I) : 0.21300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.100 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 3EB5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.81 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.04 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100MM TRIS-HCL, 20% MME PEG2000, 10MM REMARK 280 NICL2, 1MM TCEP, PH 8.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 24.33600 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: 1870 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 7690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 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 GLY A 424 REMARK 465 PRO A 425 REMARK 465 LEU A 426 REMARK 465 GLY A 427 REMARK 465 SER A 428 REMARK 465 THR A 429 REMARK 465 SER A 430 REMARK 465 LEU A 431 REMARK 465 GLN A 432 REMARK 465 LYS A 433 REMARK 465 GLU A 434 REMARK 465 SER A 497 REMARK 465 GLY B 424 REMARK 465 PRO B 425 REMARK 465 LEU B 426 REMARK 465 GLY B 427 REMARK 465 SER B 428 REMARK 465 THR B 429 REMARK 465 SER B 430 REMARK 465 LEU B 431 REMARK 465 GLN B 432 REMARK 465 LYS B 433 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 A1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 450 SG REMARK 620 2 CYS A 453 SG 107.1 REMARK 620 3 CYS A 471 SG 111.9 114.8 REMARK 620 4 CYS A 474 SG 113.2 107.3 102.5 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 465 SG REMARK 620 2 HIS A 467 ND1 105.4 REMARK 620 3 CYS A 481 SG 105.8 118.5 REMARK 620 4 CYS A 484 SG 104.4 110.6 110.8 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1001 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 450 SG REMARK 620 2 CYS B 453 SG 106.5 REMARK 620 3 CYS B 471 SG 115.9 115.3 REMARK 620 4 CYS B 474 SG 103.4 113.0 102.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B1002 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS B 465 SG REMARK 620 2 HIS B 467 ND1 109.5 REMARK 620 3 CYS B 481 SG 108.3 110.5 REMARK 620 4 CYS B 484 SG 105.6 109.0 113.8 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 1002 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NI B 1003 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4IC3 RELATED DB: PDB DBREF 4IC2 A 429 497 UNP P98170 XIAP_HUMAN 429 497 DBREF 4IC2 B 429 497 UNP P98170 XIAP_HUMAN 429 497 SEQADV 4IC2 GLY A 424 UNP P98170 EXPRESSION TAG SEQADV 4IC2 PRO A 425 UNP P98170 EXPRESSION TAG SEQADV 4IC2 LEU A 426 UNP P98170 EXPRESSION TAG SEQADV 4IC2 GLY A 427 UNP P98170 EXPRESSION TAG SEQADV 4IC2 SER A 428 UNP P98170 EXPRESSION TAG SEQADV 4IC2 GLY B 424 UNP P98170 EXPRESSION TAG SEQADV 4IC2 PRO B 425 UNP P98170 EXPRESSION TAG SEQADV 4IC2 LEU B 426 UNP P98170 EXPRESSION TAG SEQADV 4IC2 GLY B 427 UNP P98170 EXPRESSION TAG SEQADV 4IC2 SER B 428 UNP P98170 EXPRESSION TAG SEQRES 1 A 74 GLY PRO LEU GLY SER THR SER LEU GLN LYS GLU ILE SER SEQRES 2 A 74 THR GLU GLU GLN LEU ARG ARG LEU GLN GLU GLU LYS LEU SEQRES 3 A 74 CYS LYS ILE CYS MET ASP ARG ASN ILE ALA ILE VAL PHE SEQRES 4 A 74 VAL PRO CYS GLY HIS LEU VAL THR CYS LYS GLN CYS ALA SEQRES 5 A 74 GLU ALA VAL ASP LYS CYS PRO MET CYS TYR THR VAL ILE SEQRES 6 A 74 THR PHE LYS GLN LYS ILE PHE MET SER SEQRES 1 B 74 GLY PRO LEU GLY SER THR SER LEU GLN LYS GLU ILE SER SEQRES 2 B 74 THR GLU GLU GLN LEU ARG ARG LEU GLN GLU GLU LYS LEU SEQRES 3 B 74 CYS LYS ILE CYS MET ASP ARG ASN ILE ALA ILE VAL PHE SEQRES 4 B 74 VAL PRO CYS GLY HIS LEU VAL THR CYS LYS GLN CYS ALA SEQRES 5 B 74 GLU ALA VAL ASP LYS CYS PRO MET CYS TYR THR VAL ILE SEQRES 6 B 74 THR PHE LYS GLN LYS ILE PHE MET SER HET ZN A1001 1 HET ZN A1002 1 HET ZN B1001 1 HET ZN B1002 1 HET NI B1003 1 HETNAM ZN ZINC ION HETNAM NI NICKEL (II) ION FORMUL 3 ZN 4(ZN 2+) FORMUL 7 NI NI 2+ FORMUL 8 HOH *43(H2 O) HELIX 1 1 SER A 436 LYS A 448 1 13 HELIX 2 2 GLN A 473 ALA A 477 5 5 HELIX 3 3 SER B 436 GLU B 447 1 12 HELIX 4 4 CYS B 471 GLU B 476 1 6 SHEET 1 A 2 ILE A 460 VAL A 463 0 SHEET 2 A 2 PHE A 490 LYS A 493 -1 O GLN A 492 N VAL A 461 SHEET 1 B 3 LEU B 468 THR B 470 0 SHEET 2 B 3 ILE B 460 VAL B 463 -1 N ILE B 460 O THR B 470 SHEET 3 B 3 PHE B 490 LYS B 493 -1 O PHE B 490 N VAL B 463 LINK SG CYS A 450 ZN ZN A1001 1555 1555 2.47 LINK SG CYS A 453 ZN ZN A1001 1555 1555 2.35 LINK SG CYS A 465 ZN ZN A1002 1555 1555 2.30 LINK ND1 HIS A 467 ZN ZN A1002 1555 1555 2.18 LINK SG CYS A 471 ZN ZN A1001 1555 1555 2.33 LINK SG CYS A 474 ZN ZN A1001 1555 1555 2.26 LINK SG CYS A 481 ZN ZN A1002 1555 1555 2.34 LINK SG CYS A 484 ZN ZN A1002 1555 1555 2.48 LINK SG CYS B 450 ZN ZN B1001 1555 1555 2.38 LINK SG CYS B 453 ZN ZN B1001 1555 1555 2.36 LINK OD1 ASP B 455 NI NI B1003 1555 1555 2.33 LINK SG CYS B 465 ZN ZN B1002 1555 1555 2.36 LINK ND1 HIS B 467 ZN ZN B1002 1555 1555 2.13 LINK SG CYS B 471 ZN ZN B1001 1555 1555 2.42 LINK SG CYS B 474 ZN ZN B1001 1555 1555 2.45 LINK SG CYS B 481 ZN ZN B1002 1555 1555 2.32 LINK SG CYS B 484 ZN ZN B1002 1555 1555 2.35 CISPEP 1 VAL A 463 PRO A 464 0 7.97 CISPEP 2 VAL B 463 PRO B 464 0 9.77 SITE 1 AC1 4 CYS A 450 CYS A 453 CYS A 471 CYS A 474 SITE 1 AC2 4 CYS A 465 HIS A 467 CYS A 481 CYS A 484 SITE 1 AC3 4 CYS B 450 CYS B 453 CYS B 471 CYS B 474 SITE 1 AC4 4 CYS B 465 HIS B 467 CYS B 481 CYS B 484 SITE 1 AC5 1 ASP B 455 CRYST1 35.653 48.672 39.860 90.00 97.24 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 0.028048 0.000000 0.003566 0.00000 SCALE2 0.000000 0.020546 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025290 0.00000