HEADER APOPTOSIS 31-AUG-99 1CY5 TITLE CRYSTAL STRUCTURE OF THE APAF-1 CARD COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (APOPTOTIC PROTEASE ACTIVATING FACTOR 1); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: CASPASE RECRUITMENT DOMAIN; COMPND 5 SYNONYM: APAF-1 CARD; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_COMMON: BACTERIA KEYWDS CASPASE RECRUITMENT DOMAIN, DEATH FOLD, SIX ALPHA-HELIX KEYWDS 2 BUNDLE, GREEK KEY TOPOLOGY, APOPTOSIS EXPDTA X-RAY DIFFRACTION AUTHOR D.E.VAUGHN,L.JOSHUA-TOR REVDAT 3 01-APR-03 1CY5 1 JRNL REVDAT 2 01-DEC-99 1CY5 1 JRNL REVDAT 1 13-SEP-99 1CY5 0 JRNL AUTH D.E.VAUGHN,J.RODRIGUEZ,Y.LAZEBNIK,L.JOSHUA-TOR JRNL TITL CRYSTAL STRUCTURE OF APAF-1 CASPASE RECRUITMENT JRNL TITL 2 DOMAIN: AN ALPHA-HELICAL GREEK KEY FOLD FOR JRNL TITL 3 APOPTOTIC SIGNALING. JRNL REF J.MOL.BIOL. V. 293 439 1999 JRNL REFN ASTM JMOBAK UK ISSN 0022-2836 REMARK 1 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 6.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 87.0 REMARK 3 CROSS-VALIDATION METHOD : FREE-R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.169 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3918 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 39179 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.159 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.188 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 3111 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 31310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 745 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 106 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 853.00 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 741.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 7764 REMARK 3 NUMBER OF RESTRAINTS : 13719 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 ANGLE DISTANCES (A) : 0.019 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.032 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.021 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.030 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : NULL REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.004 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.068 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.095 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1CY5 COMPLIES WITH FORMAT V. 3.0, 1-DEC-2006 REMARK 4 REMARK 4 THIS IS THE REMEDIATED VERSION OF THIS PDB ENTRY. REMARK 4 REMEDIATED DATA FILE REVISION 3.100 (2007-03-16) REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB . REMARK 100 THE RCSB ID CODE IS RCSB009622. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-FEB-1999 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.00 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X26C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.10 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 24113 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -9.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.02600 REMARK 200 FOR THE DATA SET : 35.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.23000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD PROGRAM PACKAGE REMARK 200 USED (IF ANY) : SHARP STARTING MODEL FOR MOLECULAR REMARK 200 REPLACEMENT: NONE REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: RESIDUES 93-97 ARE DISORDERED AND NOT MODELED. SEE REMARK 200 JOURNAL REFERENCE FOR PHASING DETAILS REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HANGING DROP VAPOR DIFFUSION WITH REMARK 280 EQUAL VOLUMES OF PROTEIN AND RESERVOIR SOLUTIONS. PROTEIN REMARK 280 SOLUTION: 5-20 MG/ML PROTEIN IN 0.02 MOLAR TRIS (PH 8.0-8.5) , REMARK 280 0.1-0.2 MOLAR SODIUM CHLORIDE. 0.005 MOLAR 2-MERCAPTOETHANOL REMARK 280 RESERVOIR SOLUTION: 8-20% (W/V) PEG 8000, 0.2 MOLAR TRIS (PH REMARK 280 7.5-8.0), 0.05-0.2 MOLAR ZINC ACETATE., VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 17K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 1/2-X,-Y,1/2+Z REMARK 290 3555 -X,1/2+Y,1/2-Z REMARK 290 4555 1/2+X,1/2-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 -1.000000 0.000000 0.000000 18.17500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 27.17500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.45500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 27.17500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 18.17500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.45500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT REMARK 300 WHICH CONSISTS OF 1 CHAIN(S). SEE REMARK 350 FOR REMARK 300 INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). REMARK 350 REMARK 350 GENERATING THE BIOMOLECULE 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 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 VAL A 94 REMARK 465 SER A 95 REMARK 465 SER A 96 REMARK 465 SER A 97 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 VAL A 93 CA C O CB CG1 CG2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI REMARK 500 O HOH 286 O HOH 289 1.31 REMARK 500 O HOH 221 O HOH 282 1.98 REMARK 500 CB ASP A 66 O HOH 273 2.10 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD2 ASP A 66 O HOH 290 3545 2.09 REMARK 500 CG ASP A 66 O HOH 290 3545 2.18 REMARK 500 O HOH 229 O HOH 271 3545 2.18 REMARK 525 REMARK 525 SOLVENT REMARK 525 THE FOLLOWING SOLVENT MOLECULES LIE FARTHER THAN EXPECTED REMARK 525 FROM THE PROTEIN OR NUCLEIC ACID MOLECULE AND MAY BE REMARK 525 ASSOCIATED WITH A SYMMETRY RELATED MOLECULE (M=MODEL REMARK 525 NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH 281 DISTANCE = 5.26 ANGSTROMS DBREF 1CY5 A 1 97 UNP O14727 APAF_HUMAN 1 97 SEQRES 1 A 97 MET ASP ALA LYS ALA ARG ASN CYS LEU LEU GLN HIS ARG SEQRES 2 A 97 GLU ALA LEU GLU LYS ASP ILE LYS THR SER TYR ILE MET SEQRES 3 A 97 ASP HIS MET ILE SER ASP GLY PHE LEU THR ILE SER GLU SEQRES 4 A 97 GLU GLU LYS VAL ARG ASN GLU PRO THR GLN GLN GLN ARG SEQRES 5 A 97 ALA ALA MET LEU ILE LYS MET ILE LEU LYS LYS ASP ASN SEQRES 6 A 97 ASP SER TYR VAL SER PHE TYR ASN ALA LEU LEU HIS GLU SEQRES 7 A 97 GLY TYR LYS ASP LEU ALA ALA LEU LEU HIS ASP GLY ILE SEQRES 8 A 97 PRO VAL VAL SER SER SER HET ZN A 101 2 HET ZN A 102 1 HET ZN A 103 1 HET ZN A 104 1 HET ZN A 105 1 HET BME 99 4 HETNAM ZN ZINC ION HETNAM BME BETA-MERCAPTOETHANOL FORMUL 2 ZN 5(ZN 2+) FORMUL 7 BME C2 H6 O S FORMUL 8 HOH *106(H2 O) HELIX 1 H1 ASP A 2 ILE A 20 1KINKED 77 DEGREES AT HIS-12 19 HELIX 2 H2 THR A 22 GLY A 33 1 12 HELIX 3 H3 THR A 36 GLU A 46 1 11 HELIX 4 H4 THR A 48 LYS A 63 1 16 HELIX 5 H5 ASP A 64 GLU A 78 1 15 HELIX 6 H6A TYR A 80 HIS A 88 1 9 HELIX 7 H6B LEU A 87 ILE A 91 5 5 LINK ZN ZN A 101 OE1 GLU A 17 LINK ZN ZN A 104 OE2 GLU A 41 LINK S2 BME 99 SG CYS A 8 CRYST1 36.350 46.910 54.350 90.00 90.00 90.00 P 21 21 21 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 0.027510 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021317 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018399 0.00000