HEADER CHAPERONE 13-DEC-96 1KID TITLE GROEL (HSP60 CLASS) FRAGMENT (APICAL DOMAIN) COMPRISING RESIDUES 191- TITLE 2 376, MUTANT WITH ALA 262 REPLACED WITH LEU AND ILE 267 REPLACED WITH TITLE 3 MET COMPND MOL_ID: 1; COMPND 2 MOLECULE: GROEL (HSP60 CLASS); COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: APICAL DOMAIN, RESIDUES 191 - 376; COMPND 5 SYNONYM: 60 KD CHAPERONIN, PROTEIN CPN60; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: DH5; SOURCE 5 CELLULAR_LOCATION: CYTOPLASM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSET (INVITROGEN) KEYWDS CHAPERONE, HSP60, GROEL, CELL DIVISION, ATP-BINDING, PHOSPHORYLATION EXPDTA X-RAY DIFFRACTION AUTHOR A.M.BUCKLE,A.R.FERSHT REVDAT 4 09-AUG-23 1KID 1 REMARK REVDAT 3 03-NOV-21 1KID 1 REMARK SEQADV REVDAT 2 24-FEB-09 1KID 1 VERSN REVDAT 1 17-SEP-97 1KID 0 JRNL AUTH A.M.BUCKLE,R.ZAHN,A.R.FERSHT JRNL TITL A STRUCTURAL MODEL FOR GROEL-POLYPEPTIDE RECOGNITION. JRNL REF PROC.NATL.ACAD.SCI.USA V. 94 3571 1997 JRNL REFN ISSN 0027-8424 JRNL PMID 9108017 JRNL DOI 10.1073/PNAS.94.8.3571 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 12.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 25290 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.180 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2443 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1440 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 292 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 16.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.13 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.016 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.031 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.035 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.025 ; 0.030 REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.144 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.181 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.269 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.185 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : 4.200 ; 15.000 REMARK 3 STAGGERED (DEGREES) : 15.500; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 27.200; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.435 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.961 ; 3.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.309 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.498 ; 5.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1KID COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000174434. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : EMBL/DESY, HAMBURG REMARK 200 BEAMLINE : X31 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.07 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25290 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 12.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 200 DATA REDUNDANCY : 4.900 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.6 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.21700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: RESIDUES 191 - 345 OF PDB ENTRY 1JON REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.52 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 8.5 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 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 23.86000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 37.55000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 31.90500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 37.55000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.86000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 31.90500 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 300 REMARK: RESIDUES 184 - 190 (PART OF A FUSED N-TERMINAL TAG) BINDS REMARK 300 IN THE PUTATIVE POLYPEPTIDE-BINDING SITE OF A NEIGHBORING REMARK 300 MOLECULE IN THE CRYSTAL LATTICE. THIS "MINI-CHAPERONE - REMARK 300 PEPTIDE COMPLEX" CAN BE GENERATED BY APPLYING THE REMARK 300 TRANSFORMATION 1/2 - X, -Y, 1/2+Z TO THE N-TERMINAL TAG REMARK 300 (RESIDUES 184 - 190) AND COMBINING THE RESULTING REMARK 300 COORDINATES WITH RESIDUES. 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 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 MET A 174 REMARK 465 ARG A 175 REMARK 465 GLY A 176 REMARK 465 SER A 177 REMARK 465 HIS A 178 REMARK 465 HIS A 179 REMARK 465 HIS A 180 REMARK 465 HIS A 181 REMARK 465 HIS A 182 REMARK 465 HIS A 183 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 LYS A 311 CD CE NZ REMARK 470 GLU A 315 CD OE1 OE2 REMARK 470 LYS A 321 CE NZ REMARK 470 GLN A 351 CD OE1 NE2 REMARK 470 GLU A 363 CD OE1 OE2 REMARK 470 GLN A 366 CD OE1 NE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 188 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG A 188 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 PHE A 204 CB - CG - CD2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ARG A 231 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 268 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 268 NE - CZ - NH2 ANGL. DEV. = -6.3 DEGREES REMARK 500 ARG A 285 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 285 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG A 322 CA - CB - CG ANGL. DEV. = 13.2 DEGREES REMARK 500 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 ARG A 362 NE - CZ - NH2 ANGL. DEV. = -4.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 196 45.78 -88.73 REMARK 500 SER A 228 -33.38 -136.49 REMARK 500 ASN A 326 -161.05 -129.59 REMARK 500 REMARK 500 REMARK: NULL DBREF 1KID A 184 376 UNP P0A6F5 CH60_ECOLI 181 375 SEQADV 1KID A UNP P0A6F5 GLN 183 DELETION SEQADV 1KID A UNP P0A6F5 ASP 184 DELETION SEQADV 1KID VAL A 186 UNP P0A6F5 GLU 185 ENGINEERED MUTATION SEQADV 1KID PRO A 187 UNP P0A6F5 LEU 186 ENGINEERED MUTATION SEQADV 1KID ARG A 188 UNP P0A6F5 ASP 187 ENGINEERED MUTATION SEQADV 1KID GLY A 189 UNP P0A6F5 VAL 188 ENGINEERED MUTATION SEQADV 1KID SER A 190 UNP P0A6F5 VAL 189 ENGINEERED MUTATION SEQADV 1KID LEU A 262 UNP P0A6F5 ALA 261 ENGINEERED MUTATION SEQADV 1KID MET A 267 UNP P0A6F5 ILE 266 ENGINEERED MUTATION SEQRES 1 A 203 MET ARG GLY SER HIS HIS HIS HIS HIS HIS GLY LEU VAL SEQRES 2 A 203 PRO ARG GLY SER GLU GLY MET GLN PHE ASP ARG GLY TYR SEQRES 3 A 203 LEU SER PRO TYR PHE ILE ASN LYS PRO GLU THR GLY ALA SEQRES 4 A 203 VAL GLU LEU GLU SER PRO PHE ILE LEU LEU ALA ASP LYS SEQRES 5 A 203 LYS ILE SER ASN ILE ARG GLU MET LEU PRO VAL LEU GLU SEQRES 6 A 203 ALA VAL ALA LYS ALA GLY LYS PRO LEU LEU ILE ILE ALA SEQRES 7 A 203 GLU ASP VAL GLU GLY GLU ALA LEU ALA THR LEU VAL VAL SEQRES 8 A 203 ASN THR MET ARG GLY ILE VAL LYS VAL ALA ALA VAL LYS SEQRES 9 A 203 ALA PRO GLY PHE GLY ASP ARG ARG LYS ALA MET LEU GLN SEQRES 10 A 203 ASP ILE ALA THR LEU THR GLY GLY THR VAL ILE SER GLU SEQRES 11 A 203 GLU ILE GLY MET GLU LEU GLU LYS ALA THR LEU GLU ASP SEQRES 12 A 203 LEU GLY GLN ALA LYS ARG VAL VAL ILE ASN LYS ASP THR SEQRES 13 A 203 THR THR ILE ILE ASP GLY VAL GLY GLU GLU ALA ALA ILE SEQRES 14 A 203 GLN GLY ARG VAL ALA GLN ILE ARG GLN GLN ILE GLU GLU SEQRES 15 A 203 ALA THR SER ASP TYR ASP ARG GLU LYS LEU GLN GLU ARG SEQRES 16 A 203 VAL ALA LYS LEU ALA GLY GLY VAL FORMUL 2 HOH *292(H2 O) HELIX 1 1 PRO A 202 PHE A 204 5 3 HELIX 2 2 ILE A 230 ALA A 243 1 14 HELIX 3 3 GLY A 256 MET A 267 1 12 HELIX 4 4 GLY A 282 THR A 296 1 15 HELIX 5 5 GLU A 303 ILE A 305 5 3 HELIX 6 6 LEU A 309 LYS A 311 5 3 HELIX 7 7 LEU A 314 ASP A 316 5 3 HELIX 8 8 GLU A 339 GLU A 355 1 17 HELIX 9 9 ASP A 359 GLY A 374 1 16 SHEET 1 A 4 MET A 193 PHE A 195 0 SHEET 2 A 4 THR A 330 ILE A 333 -1 N ILE A 332 O MET A 193 SHEET 3 A 4 ARG A 322 ILE A 325 -1 N VAL A 324 O THR A 331 SHEET 4 A 4 VAL A 213 GLU A 216 -1 N LEU A 215 O VAL A 323 SHEET 1 B 3 PHE A 219 LEU A 222 0 SHEET 2 B 3 LEU A 247 ALA A 251 1 N LEU A 248 O PHE A 219 SHEET 3 B 3 VAL A 273 LYS A 277 1 N ALA A 274 O LEU A 247 CRYST1 47.720 63.810 75.100 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 0.020956 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015672 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013316 0.00000