HEADER APOPTOSIS ACTIVATOR 30-JAN-07 2OPY
TITLE SMAC MIMIC BOUND TO BIR3-XIAP
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: BACULOVIRAL IAP REPEAT-CONTAINING PROTEIN 4;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: INHIBITOR OF APOPTOSIS PROTEIN 3, X-LINKED INHIBITOR OF
COMPND 5 APOPTOSIS PROTEIN, X-LINKED IAP, IAP-LIKE PROTEIN, HILP;
COMPND 6 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: BIRC4, API3, IAP3, XIAP;
SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21;
SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693;
SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21;
SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID;
SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCOOL
KEYWDS PEPTIDE MIMIC, BIR3, APOPTOSIS ACTIVATOR
EXPDTA X-RAY DIFFRACTION
AUTHOR A.D.WIST,G.LU,S.J.RIEDL,Y.SHI,G.L.MCLENDON
REVDAT 4 27-DEC-23 2OPY 1 REMARK LINK
REVDAT 3 24-FEB-09 2OPY 1 VERSN
REVDAT 2 03-APR-07 2OPY 1 JRNL
REVDAT 1 20-FEB-07 2OPY 0
JRNL AUTH A.D.WIST,L.GU,S.J.RIEDL,Y.SHI,G.L.MCLENDON
JRNL TITL STRUCTURE-ACTIVITY BASED STUDY OF THE SMAC-BINDING POCKET
JRNL TITL 2 WITHIN THE BIR3 DOMAIN OF XIAP.
JRNL REF BIOORG.MED.CHEM. V. 15 2935 2007
JRNL REFN ISSN 0968-0896
JRNL PMID 17336535
JRNL DOI 10.1016/J.BMC.2007.02.010
REMARK 2
REMARK 2 RESOLUTION. 2.80 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : CNS
REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE-
REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU,
REMARK 3 : READ,RICE,SIMONSON,WARREN
REMARK 3
REMARK 3 REFINEMENT TARGET : ENGH & HUBER
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00
REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000
REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL
REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL
REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.2
REMARK 3 NUMBER OF REFLECTIONS : 6502
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 CROSS-VALIDATION METHOD : NULL
REMARK 3 FREE R VALUE TEST SET SELECTION : NULL
REMARK 3 R VALUE (WORKING SET) : 0.213
REMARK 3 FREE R VALUE : 0.235
REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL
REMARK 3
REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN.
REMARK 3 TOTAL NUMBER OF BINS USED : NULL
REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80
REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.90
REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0
REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL
REMARK 3 BIN R VALUE (WORKING SET) : NULL
REMARK 3 BIN FREE R VALUE : NULL
REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL
REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL
REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL
REMARK 3
REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT.
REMARK 3 PROTEIN ATOMS : 866
REMARK 3 NUCLEIC ACID ATOMS : 0
REMARK 3 HETEROGEN ATOMS : 33
REMARK 3 SOLVENT ATOMS : 64
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 ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.34
REMARK 3 ESD FROM SIGMAA (A) : NULL
REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL
REMARK 3
REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR.
REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL
REMARK 3 ESD FROM C-V SIGMAA (A) : NULL
REMARK 3
REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES.
REMARK 3 BOND LENGTHS (A) : NULL
REMARK 3 BOND ANGLES (DEGREES) : NULL
REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL
REMARK 3 IMPROPER ANGLES (DEGREES) : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL MODEL : NULL
REMARK 3
REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA
REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL
REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL
REMARK 3
REMARK 3 BULK SOLVENT MODELING.
REMARK 3 METHOD USED : NULL
REMARK 3 KSOL : NULL
REMARK 3 BSOL : NULL
REMARK 3
REMARK 3 NCS MODEL : NULL
REMARK 3
REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT
REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL
REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL
REMARK 3
REMARK 3 PARAMETER FILE 1 : NULL
REMARK 3 TOPOLOGY FILE 1 : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 2OPY COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-FEB-07.
REMARK 100 THE DEPOSITION ID IS D_1000041442.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : NULL
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 : NSLS
REMARK 200 BEAMLINE : X12C
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418,1.5621,1.7321
REMARK 200 MONOCHROMATOR : GRAPHITE
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : NULL
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6502
REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800
REMARK 200 RESOLUTION RANGE LOW (A) : 20.000
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 97.2
REMARK 200 DATA REDUNDANCY : NULL
REMARK 200 R MERGE (I) : NULL
REMARK 200 R SYM (I) : 0.07600
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 35.7000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90
REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0
REMARK 200 DATA REDUNDANCY IN SHELL : NULL
REMARK 200 R MERGE FOR SHELL (I) : NULL
REMARK 200 R SYM FOR SHELL (I) : 0.44700
REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.800
REMARK 200
REMARK 200 DIFFRACTION PROTOCOL: MAD
REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER, PHASES
REMARK 200 STARTING MODEL: NULL
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 77.33
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.43
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, 4.3 M NACL, PH 7.5, VAPOR
REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 2 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y,X,Z+1/4
REMARK 290 4555 Y,-X,Z+3/4
REMARK 290 5555 -X,Y,-Z
REMARK 290 6555 X,-Y,-Z+1/2
REMARK 290 7555 Y,X,-Z+3/4
REMARK 290 8555 -Y,-X,-Z+1/4
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 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 52.55000
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 26.27500
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 78.82500
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 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 52.55000
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 78.82500
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 26.27500
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 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 -71.20000
REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000
REMARK 350 BIOMT3 2 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 ASP A 296 37.13 -97.60
REMARK 500 PRO A 312 -70.03 -35.96
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 102 ZN
REMARK 620 N RES CSSEQI ATOM
REMARK 620 1 CYS A 300 SG
REMARK 620 2 CYS A 303 SG 109.4
REMARK 620 3 HIS A 320 NE2 94.4 113.8
REMARK 620 4 CYS A 327 SG 121.0 109.7 107.9
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 102
REMARK 800
REMARK 800 SITE_IDENTIFIER: AC2
REMARK 800 EVIDENCE_CODE: SOFTWARE
REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CO9 A 101
REMARK 900
REMARK 900 RELATED ENTRIES
REMARK 900 RELATED ID: 1G3F RELATED DB: PDB
REMARK 900 NMR STRUCTURE OF A 9 RESIDUE PEPTIDE FROM SMAC/DIABLO COMPLEXED TO
REMARK 900 THE BIR3 DOMAIN OF XIAP
REMARK 900 RELATED ID: 1G73 RELATED DB: PDB
REMARK 900 CRYSTAL STRUCTURE OF SMAC BOUND TO XIAP-BIR3 DOMAIN
REMARK 900 RELATED ID: 2I3H RELATED DB: PDB
REMARK 900 STRUCTURE OF AN ML-IAP/XIAP CHIMERA BOUND TO A 4-MER PEPTIDE (AVPW)
REMARK 900 RELATED ID: 2OPZ RELATED DB: PDB
DBREF 2OPY A 249 354 UNP P98170 BIRC4_HUMAN 249 354
SEQRES 1 A 106 ASN PHE PRO ASN SER THR ASN LEU PRO ARG ASN PRO SER
SEQRES 2 A 106 MET ALA ASP TYR GLU ALA ARG ILE PHE THR PHE GLY THR
SEQRES 3 A 106 TRP ILE TYR SER VAL ASN LYS GLU GLN LEU ALA ARG ALA
SEQRES 4 A 106 GLY PHE TYR ALA LEU GLY GLU GLY ASP LYS VAL LYS CYS
SEQRES 5 A 106 PHE HIS CYS GLY GLY GLY LEU THR ASP TRP LYS PRO SER
SEQRES 6 A 106 GLU ASP PRO TRP GLU GLN HIS ALA LYS TRP TYR PRO GLY
SEQRES 7 A 106 CYS LYS TYR LEU LEU GLU GLN LYS GLY GLN GLU TYR ILE
SEQRES 8 A 106 ASN ASN ILE HIS LEU THR HIS SER LEU GLU GLU CYS LEU
SEQRES 9 A 106 VAL ARG
HET ZN A 102 1
HET CO9 A 101 32
HETNAM ZN ZINC ION
HETNAM CO9 1-({2-[(1S)-1-AMINOETHYL]-1,3-OXAZOL-4-YL}CARBONYL)-L-
HETNAM 2 CO9 PROLYL-L-TRYPTOPHAN
FORMUL 2 ZN ZN 2+
FORMUL 3 CO9 C22 H25 N5 O5
FORMUL 4 HOH *64(H2 O)
HELIX 1 1 ASN A 259 ALA A 263 5 5
HELIX 2 2 ASP A 264 GLY A 273 1 10
HELIX 3 3 ASN A 280 ALA A 287 1 8
HELIX 4 4 ASP A 315 TYR A 324 1 10
HELIX 5 5 CYS A 327 ARG A 354 1 28
SHEET 1 A 3 PHE A 289 ALA 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 ZN ZN A 102 SG CYS A 300 1555 1555 2.33
LINK ZN ZN A 102 SG CYS A 303 1555 1555 2.39
LINK ZN ZN A 102 NE2 HIS A 320 1555 1555 2.18
LINK ZN ZN A 102 SG CYS A 327 1555 1555 2.39
SITE 1 AC1 4 CYS A 300 CYS A 303 HIS A 320 CYS A 327
SITE 1 AC2 15 HOH A 4 HOH A 29 HOH A 41 HOH A 48
SITE 2 AC2 15 HOH A 57 LEU A 292 VAL A 298 GLY A 306
SITE 3 AC2 15 LEU A 307 THR A 308 ASP A 309 GLU A 314
SITE 4 AC2 15 GLN A 319 TRP A 323 TYR A 324
CRYST1 71.200 71.200 105.100 90.00 90.00 90.00 P 41 2 2 8
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 0.014045 0.000000 0.000000 0.00000
SCALE2 0.000000 0.014045 0.000000 0.00000
SCALE3 0.000000 0.000000 0.009515 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
