PDB Short entry for 1QX3 HEADER HYDROLASE 04-SEP-03 1QX3 TITLE CONFORMATIONAL RESTRICTIONS IN THE ACTIVE SITE OF UNLIGANDED HUMAN TITLE 2 CASPASE-3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: APOPAIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CYSTEINE PROTEASE CPP32, YAMA PROTEIN, CPP-32, CASPASE-3, COMPND 5 CASP-3, SREBP CLEAVAGE ACTIVITY 1, SCA-1; COMPND 6 EC: 3.4.22.-; COMPND 7 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: CASP3 OR CPP32; 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: PET21B KEYWDS CASPASE-3, ACTIVE SITE, CYSTEINE PROTEASE, APOPTOSIS, CELL DEATH, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR C.-Z.NI,C.LI,J.C.WU,A.P.SPADA,K.R.ELY REVDAT 4 11-OCT-17 1QX3 1 REMARK REVDAT 3 13-JUL-11 1QX3 1 VERSN REVDAT 2 24-FEB-09 1QX3 1 VERSN REVDAT 1 07-OCT-03 1QX3 0 JRNL AUTH C.-Z.NI,C.LI,J.C.WU,A.P.SPADA,K.R.ELY JRNL TITL CONFORMATIONAL RESTRICTIONS IN THE ACTIVE SITE OF UNLIGANDED JRNL TITL 2 HUMAN CASPASE-3 JRNL REF J.MOL.RECOG. V. 16 121 2003 JRNL REFN ISSN 0952-3499 JRNL PMID 12833566 JRNL DOI 10.1002/JMR.615 REMARK 2 REMARK 2 RESOLUTION. 1.90 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 81.9 REMARK 3 NUMBER OF REFLECTIONS : 19881 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.249 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 970 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 : 3 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.93 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 3.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.4890 REMARK 3 BIN FREE R VALUE : 0.5170 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : 42 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 : 1881 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 147 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.90 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.74000 REMARK 3 B22 (A**2) : 11.92000 REMARK 3 B33 (A**2) : -19.66000 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 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.30 REMARK 3 ESD FROM SIGMAA (A) : 0.43 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.32 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.40 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.50 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.710 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 1QX3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-SEP-03. REMARK 100 THE DEPOSITION ID IS D_1000020173. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 98 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL7-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9200 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21234 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.5 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.31800 REMARK 200 <I/SIGMA(I)> FOR SHELL : 13.50 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1CP3 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.22 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4-6% PEG 8000, 5-7% ISOPROPANOL, PH REMARK 280 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X+1/2,Y+1/2,-Z REMARK 290 4555 X+1/2,-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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 35.13000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.09500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.13000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.09500 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 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: PQS 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 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 96.19000 REMARK 350 BIOMT3 2 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 SER A 29 REMARK 465 GLY A 30 REMARK 465 ILE A 31 REMARK 465 SER A 32 REMARK 465 LEU A 33 REMARK 465 ASP A 34 REMARK 465 THR A 174 REMARK 465 ASP A 175 REMARK 465 SER A 176 REMARK 465 GLY A 177 REMARK 465 VAL A 178 REMARK 465 ASP A 179 REMARK 465 ASP A 180 REMARK 465 ASP A 181 REMARK 465 MET A 182 REMARK 465 ALA A 183 REMARK 465 CYS A 184 REMARK 465 LEU A 278 REMARK 465 GLU A 279 REMARK 465 HIS A 280 REMARK 465 HIS A 281 REMARK 465 HIS A 282 REMARK 465 HIS A 283 REMARK 465 HIS A 284 REMARK 465 HIS A 285 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 LYS A 82 31.26 74.00 REMARK 500 ASP A 90 73.13 37.39 REMARK 500 SER A 120 -166.48 176.10 REMARK 500 SER A 209 -9.06 -55.68 REMARK 500 LYS A 229 -65.10 -136.75 REMARK 500 PHE A 275 31.80 -82.29 REMARK 500 REMARK 500 REMARK: NULL DBREF 1QX3 A 29 277 UNP P42574 CASP3_HUMAN 29 277 SEQADV 1QX3 LEU A 278 UNP P42574 EXPRESSION TAG SEQADV 1QX3 GLU A 279 UNP P42574 EXPRESSION TAG SEQADV 1QX3 HIS A 280 UNP P42574 EXPRESSION TAG SEQADV 1QX3 HIS A 281 UNP P42574 EXPRESSION TAG SEQADV 1QX3 HIS A 282 UNP P42574 EXPRESSION TAG SEQADV 1QX3 HIS A 283 UNP P42574 EXPRESSION TAG SEQADV 1QX3 HIS A 284 UNP P42574 EXPRESSION TAG SEQADV 1QX3 HIS A 285 UNP P42574 EXPRESSION TAG SEQRES 1 A 257 SER GLY ILE SER LEU ASP ASN SER TYR LYS MET ASP TYR SEQRES 2 A 257 PRO GLU MET GLY LEU CYS ILE ILE ILE ASN ASN LYS ASN SEQRES 3 A 257 PHE HIS LYS SER THR GLY MET THR SER ARG SER GLY THR SEQRES 4 A 257 ASP VAL ASP ALA ALA ASN LEU ARG GLU THR PHE ARG ASN SEQRES 5 A 257 LEU LYS TYR GLU VAL ARG ASN LYS ASN ASP LEU THR ARG SEQRES 6 A 257 GLU GLU ILE VAL GLU LEU MET ARG ASP VAL SER LYS GLU SEQRES 7 A 257 ASP HIS SER LYS ARG SER SER PHE VAL CYS VAL LEU LEU SEQRES 8 A 257 SER HIS GLY GLU GLU GLY ILE ILE PHE GLY THR ASN GLY SEQRES 9 A 257 PRO VAL ASP LEU LYS LYS ILE THR ASN PHE PHE ARG GLY SEQRES 10 A 257 ASP ARG CYS ARG SER LEU THR GLY LYS PRO LYS LEU PHE SEQRES 11 A 257 ILE ILE GLN ALA CYS ARG GLY THR GLU LEU ASP CYS GLY SEQRES 12 A 257 ILE GLU THR ASP SER GLY VAL ASP ASP ASP MET ALA CYS SEQRES 13 A 257 HIS LYS ILE PRO VAL ASP ALA ASP PHE LEU TYR ALA TYR SEQRES 14 A 257 SER THR ALA PRO GLY TYR TYR SER TRP ARG ASN SER LYS SEQRES 15 A 257 ASP GLY SER TRP PHE ILE GLN SER LEU CYS ALA MET LEU SEQRES 16 A 257 LYS GLN TYR ALA ASP LYS LEU GLU PHE MET HIS ILE LEU SEQRES 17 A 257 THR ARG VAL ASN ARG LYS VAL ALA THR GLU PHE GLU SER SEQRES 18 A 257 PHE SER PHE ASP ALA THR PHE HIS ALA LYS LYS GLN ILE SEQRES 19 A 257 PRO CYS ILE VAL SER MET LEU THR LYS GLU LEU TYR PHE SEQRES 20 A 257 TYR HIS LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *147(H2 O) HELIX 1 1 HIS A 56 GLY A 60 5 5 HELIX 2 2 GLY A 66 LEU A 81 1 16 HELIX 3 3 THR A 92 LYS A 105 1 14 HELIX 4 4 LEU A 136 PHE A 142 1 7 HELIX 5 5 CYS A 148 THR A 152 5 5 HELIX 6 6 TRP A 214 ALA A 227 1 14 HELIX 7 7 GLU A 231 PHE A 247 1 17 SHEET 1 A 6 GLU A 84 ASN A 89 0 SHEET 2 A 6 GLU A 43 ASN A 51 1 N ASN A 51 O LYS A 88 SHEET 3 A 6 ARG A 111 LEU A 119 1 O VAL A 117 N ILE A 48 SHEET 4 A 6 LYS A 156 GLN A 161 1 O LEU A 157 N PHE A 114 SHEET 5 A 6 PHE A 193 TYR A 197 1 O LEU A 194 N PHE A 158 SHEET 6 A 6 CYS A 264 SER A 267 -1 O VAL A 266 N TYR A 195 SHEET 1 B 3 GLY A 122 GLU A 123 0 SHEET 2 B 3 ILE A 126 PHE A 128 -1 O ILE A 126 N GLU A 123 SHEET 3 B 3 PRO A 133 ASP A 135 -1 O VAL A 134 N ILE A 127 SHEET 1 C 2 ARG A 207 ASN A 208 0 SHEET 2 C 2 GLY A 212 SER A 213 -1 O GLY A 212 N ASN A 208 CRYST1 70.260 96.190 44.170 90.00 90.00 90.00 P 21 21 2 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 0.014233 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010396 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022640 0.00000