PDB Short entry for 4KMN HEADER LIGASE/LIGASE INHIBITOR 08-MAY-13 4KMN TITLE STRUCTURE OF CIAP1-BIR3 AND INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 260-357; COMPND 5 SYNONYM: C-IAP1, IAP HOMOLOG B, INHIBITOR OF APOPTOSIS PROTEIN 2, COMPND 6 IAP-2, HIAP-2, HIAP2, RING FINGER PROTEIN 48, TNFR2-TRAF-SIGNALING COMPND 7 COMPLEX PROTEIN 2; 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: BIRC2, API1, IAP2, MIHB, RNF48; 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: PET15B KEYWDS APOPTOSIS, CIAP1-BIR3, LIGASE-LIGASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.LI,J.WANG,S.M.CONDON,Y.SHI REVDAT 2 08-NOV-23 4KMN 1 REMARK SEQADV LINK REVDAT 1 14-MAY-14 4KMN 0 JRNL AUTH X.LI,J.WANG,S.M.CONDON,Y.SHI JRNL TITL STRUCTURE OF CIAP1-BIR3 AND INHIBITOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.52 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.5_2) 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) : 1.52 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.5 REMARK 3 NUMBER OF REFLECTIONS : 26069 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.160 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 1321 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 30.2159 - 3.1665 0.97 2978 144 0.1776 0.1998 REMARK 3 2 3.1665 - 2.5137 1.00 2941 148 0.1395 0.2020 REMARK 3 3 2.5137 - 2.1961 1.00 2922 153 0.1267 0.1748 REMARK 3 4 2.1961 - 1.9953 1.00 2898 154 0.1244 0.1605 REMARK 3 5 1.9953 - 1.8523 1.00 2893 151 0.1314 0.1644 REMARK 3 6 1.8523 - 1.7431 1.00 2867 148 0.1412 0.1841 REMARK 3 7 1.7431 - 1.6559 0.99 2854 159 0.1800 0.2092 REMARK 3 8 1.6559 - 1.5838 0.91 2564 168 0.2340 0.3088 REMARK 3 9 1.5838 - 1.5228 0.64 1831 96 0.2666 0.3121 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 : 0.46 REMARK 3 B_SOL : 60.16 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.150 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.380 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.09850 REMARK 3 B22 (A**2) : 2.09850 REMARK 3 B33 (A**2) : -4.19710 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 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 : 0.010 921 REMARK 3 ANGLE : 1.558 1255 REMARK 3 CHIRALITY : 0.069 121 REMARK 3 PLANARITY : 0.007 160 REMARK 3 DIHEDRAL : 18.328 327 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 4KMN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 23-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1000079528. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 31-JAN-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26150 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.520 REMARK 200 RESOLUTION RANGE LOW (A) : 30.210 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: NULL REMARK 200 STARTING MODEL: 1G73 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 67.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.75 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M NA/K PHOSPHATE PH6.9, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 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+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 44.60867 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 22.30433 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 22.30433 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 44.60867 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 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 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 ASN A 295 -126.05 43.74 REMARK 500 ALA A 352 -45.95 159.62 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 501 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 300 SG REMARK 620 2 CYS A 303 SG 108.4 REMARK 620 3 HIS A 320 NE2 99.5 116.5 REMARK 620 4 CYS A 327 SG 114.8 111.0 106.4 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 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 436 A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PO4 A 503 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4KMP RELATED DB: PDB DBREF 4KMN A 254 351 UNP Q13490 BIRC2_HUMAN 260 357 SEQADV 4KMN ALA A 251 UNP Q13490 EXPRESSION TAG SEQADV 4KMN ALA A 252 UNP Q13490 EXPRESSION TAG SEQADV 4KMN ALA A 253 UNP Q13490 EXPRESSION TAG SEQADV 4KMN ALA A 352 UNP Q13490 EXPRESSION TAG SEQADV 4KMN ALA A 353 UNP Q13490 EXPRESSION TAG SEQRES 1 A 103 ALA ALA ALA SER ILE SER ASN LEU SER MET GLN THR HIS SEQRES 2 A 103 ALA ALA ARG MET ARG THR PHE MET TYR TRP PRO SER SER SEQRES 3 A 103 VAL PRO VAL GLN PRO GLU GLN LEU ALA SER ALA GLY PHE SEQRES 4 A 103 TYR TYR VAL GLY ARG ASN ASP ASP VAL LYS CYS PHE CYS SEQRES 5 A 103 CYS ASP GLY GLY LEU ARG CYS TRP GLU SER GLY ASP ASP SEQRES 6 A 103 PRO TRP VAL GLU HIS ALA LYS TRP PHE PRO ARG CYS GLU SEQRES 7 A 103 PHE LEU ILE ARG MET LYS GLY GLN GLU PHE VAL ASP GLU SEQRES 8 A 103 ILE GLN GLY ARG TYR PRO HIS LEU LEU GLU ALA ALA HET ZN A 501 1 HET 436 A 502 58 HET PO4 A 503 5 HETNAM ZN ZINC ION HETNAM 436 (2S)-N-{(2R)-1-[(2R,4S)-2-{[6,6'-DIFLUORO-3'-({(2R,4S)- HETNAM 2 436 4-HYDROXY-1-[(2S)-2-{[(2S)-2-(METHYLAMINO) HETNAM 3 436 PROPANOYL]AMINO}BUTANOYL]PYRROLIDIN-2-YL}METHYL)-1H, HETNAM 4 436 1'H-2,2'-BIINDOL-3-YL]METHYL}-4-HYDROXYPYRROLIDIN-1- HETNAM 5 436 YL]-1-OXOBUTAN-2-YL}-2-(METHYLAMINO)PROPANAMIDE HETNAM PO4 PHOSPHATE ION FORMUL 2 ZN ZN 2+ FORMUL 3 436 C42 H56 F2 N8 O6 FORMUL 4 PO4 O4 P 3- FORMUL 5 HOH *120(H2 O) HELIX 1 1 ASN A 257 GLN A 261 5 5 HELIX 2 2 THR A 262 THR A 269 1 8 HELIX 3 3 PHE A 270 TRP A 273 5 4 HELIX 4 4 GLN A 280 ALA A 287 1 8 HELIX 5 5 ASP A 315 PHE A 324 1 10 HELIX 6 6 CYS A 327 GLY A 335 1 9 HELIX 7 7 GLY A 335 TYR A 346 1 12 SHEET 1 A 3 PHE A 289 TYR A 291 0 SHEET 2 A 3 VAL A 298 CYS A 300 -1 O LYS A 299 N TYR A 290 SHEET 3 A 3 GLY A 306 LEU A 307 -1 O LEU A 307 N VAL A 298 LINK SG CYS A 300 ZN ZN A 501 1555 1555 2.30 LINK SG CYS A 303 ZN ZN A 501 1555 1555 2.27 LINK NE2 HIS A 320 ZN ZN A 501 1555 1555 2.19 LINK SG CYS A 327 ZN ZN A 501 1555 1555 2.26 CISPEP 1 TYR A 346 PRO A 347 0 -6.89 SITE 1 AC1 4 CYS A 300 CYS A 303 HIS A 320 CYS A 327 SITE 1 AC2 14 ARG A 294 LYS A 299 GLY A 306 LEU A 307 SITE 2 AC2 14 ARG A 308 CYS A 309 ASP A 314 GLU A 319 SITE 3 AC2 14 LYS A 322 TRP A 323 PHE A 324 PO4 A 503 SITE 4 AC2 14 HOH A 686 HOH A 714 SITE 1 AC3 5 ARG A 294 LYS A 299 436 A 502 HOH A 674 SITE 2 AC3 5 HOH A 680 CRYST1 67.714 67.714 66.913 90.00 90.00 120.00 P 32 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 0.014768 0.008526 0.000000 0.00000 SCALE2 0.000000 0.017053 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014945 0.00000