HEADER CHAPERONE 28-SEP-00 1FYA TITLE CRYSTAL STRUCTURE OF THE HEXA-SUBSTITUTED MUTANT OF THE MOLECULAR TITLE 2 CHAPERONIN GROEL APICAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 60 KD CHAPERONIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: APICAL DOMAIN (RESIDUES 191-376); COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PRSET A KEYWDS CHAPERONE, STABILIZING MUTANT EXPDTA X-RAY DIFFRACTION AUTHOR Q.WANG,A.M.BUCKLE,A.R.FERSHT REVDAT 6 25-OCT-23 1FYA 1 REMARK REVDAT 5 10-NOV-21 1FYA 1 REMARK SEQADV REVDAT 4 13-JUL-11 1FYA 1 VERSN REVDAT 3 24-FEB-09 1FYA 1 VERSN REVDAT 2 31-DEC-02 1FYA 1 REMARK REVDAT 1 22-NOV-00 1FYA 0 JRNL AUTH Q.WANG,A.M.BUCKLE,A.R.FERSHT JRNL TITL STABILIZATION OF GROEL MINICHAPERONES BY CORE AND SURFACE JRNL TITL 2 MUTATIONS. JRNL REF J.MOL.BIOL. V. 298 917 2000 JRNL REFN ISSN 0022-2836 JRNL PMID 10801358 JRNL DOI 10.1006/JMBI.2000.3716 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH Q.WANG,A.M.BUCKLE,N.W.FOSTER,C.M.JOHNSON,A.R.FERSHT REMARK 1 TITL DESIGN OF HIGHLY STABLE FUNCTIONAL GROEL MINICHAPERONES REMARK 1 REF PROTEIN SCI. V. 8 2186 1999 REMARK 1 REFN ISSN 0961-8368 REMARK 2 REMARK 2 RESOLUTION. 2.20 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 10757 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.237 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.279 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 558 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1412 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 149 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.10 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.40 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): 0.350 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.250 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.190 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.800 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.005 ; 0.020 REMARK 3 ANGLE DISTANCE (A) : 0.022 ; 0.040 REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : 0.018 ; 0.050 REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : 0.015 ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : 0.077 ; 0.150 REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : 0.179 ; 0.300 REMARK 3 MULTIPLE TORSION (A) : 0.238 ; 0.300 REMARK 3 H-BOND (X...Y) (A) : 0.179 ; 0.300 REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : 0.000 ; 15.000 REMARK 3 PLANAR (DEGREES) : 2.100 ; 3.000 REMARK 3 STAGGERED (DEGREES) : 15.500; 15.000 REMARK 3 TRANSVERSE (DEGREES) : 27.100; 20.000 REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 1.029 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 1.651 ; 5.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.919 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 3.958 ; 8.000 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1FYA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-OCT-00. REMARK 100 THE DEPOSITION ID IS D_1000012009. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-NOV-98 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 6.50 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LURE REMARK 200 BEAMLINE : DW32 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9630 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 : 10757 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 38.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 5.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.34 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.90 REMARK 200 R MERGE FOR SHELL (I) : 0.39800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.400 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MR REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: GROEL(191-376) (PDB: 1KID) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.75-0.9 M SODIUM POTASSIUM TARTRATE, REMARK 280 50 MM MES SODIUM, PH 6.50, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 290K 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 37.96500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.97000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.96500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.97000 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: 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 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 186 CG2 REMARK 470 ARG A 188 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 207 CD CE NZ REMARK 470 GLU A 209 CG CD OE1 OE2 REMARK 470 ASN A 229 CG OD1 ND2 REMARK 470 ARG A 231 CD NE CZ NH1 NH2 REMARK 470 GLU A 257 CG CD OE1 OE2 REMARK 470 LYS A 272 CD CE NZ REMARK 470 LYS A 308 CE NZ REMARK 470 GLU A 315 CD OE1 OE2 REMARK 470 LYS A 321 CD CE NZ REMARK 470 ARG A 322 CZ NH1 NH2 REMARK 470 GLN A 351 CD OE1 NE2 REMARK 470 GLU A 363 CD OE1 OE2 REMARK 470 GLN A 366 CG CD OE1 NE2 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 DISTANCE REMARK 500 OD1 ASP A 359 NH1 ARG A 362 2.17 REMARK 500 REMARK 500 REMARK: NULL 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 350 CD - NE - CZ ANGL. DEV. = 11.8 DEGREES REMARK 500 ARG A 350 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 362 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1FY9 RELATED DB: PDB REMARK 900 1FY9 CONTAINS THE APICAL DOMAIN OF 60 KD CHAPERONIN (A212E/A223V/ REMARK 900 M233L/I305L/E308K/N326T). REMARK 900 RELATED ID: 1KID RELATED DB: PDB REMARK 900 1KID CONTAINS THE APICAL DOMAIN OF 60 KD WILD-TYPE CHAPERONIN. DBREF 1FYA A 184 376 UNP P0A6F5 CH60_ECOLI 184 376 SEQADV 1FYA GLY A 184 UNP P0A6F5 GLN 184 CLONING ARTIFACT SEQADV 1FYA LEU A 185 UNP P0A6F5 ASP 185 CLONING ARTIFACT SEQADV 1FYA VAL A 186 UNP P0A6F5 GLU 186 CLONING ARTIFACT SEQADV 1FYA PRO A 187 UNP P0A6F5 LEU 187 CLONING ARTIFACT SEQADV 1FYA ARG A 188 UNP P0A6F5 ASP 188 CLONING ARTIFACT SEQADV 1FYA GLY A 189 UNP P0A6F5 VAL 189 CLONING ARTIFACT SEQADV 1FYA SER A 190 UNP P0A6F5 VAL 190 CLONING ARTIFACT SEQADV 1FYA GLU A 212 UNP P0A6F5 ALA 212 ENGINEERED MUTATION SEQADV 1FYA THR A 223 UNP P0A6F5 ALA 223 ENGINEERED MUTATION SEQADV 1FYA LEU A 233 UNP P0A6F5 MET 233 ENGINEERED MUTATION SEQADV 1FYA LEU A 305 UNP P0A6F5 ILE 305 ENGINEERED MUTATION SEQADV 1FYA LYS A 308 UNP P0A6F5 GLU 308 ENGINEERED MUTATION SEQADV 1FYA THR A 326 UNP P0A6F5 ASN 326 ENGINEERED MUTATION SEQRES 1 A 193 GLY LEU VAL PRO ARG GLY SER GLU GLY MET GLN PHE ASP SEQRES 2 A 193 ARG GLY TYR LEU SER PRO TYR PHE ILE ASN LYS PRO GLU SEQRES 3 A 193 THR GLY GLU VAL GLU LEU GLU SER PRO PHE ILE LEU LEU SEQRES 4 A 193 THR ASP LYS LYS ILE SER ASN ILE ARG GLU LEU LEU PRO SEQRES 5 A 193 VAL LEU GLU ALA VAL ALA LYS ALA GLY LYS PRO LEU LEU SEQRES 6 A 193 ILE ILE ALA GLU ASP VAL GLU GLY GLU ALA LEU ALA THR SEQRES 7 A 193 LEU VAL VAL ASN THR MET ARG GLY ILE VAL LYS VAL ALA SEQRES 8 A 193 ALA VAL LYS ALA PRO GLY PHE GLY ASP ARG ARG LYS ALA SEQRES 9 A 193 MET LEU GLN ASP ILE ALA THR LEU THR GLY GLY THR VAL SEQRES 10 A 193 ILE SER GLU GLU LEU GLY MET LYS LEU GLU LYS ALA THR SEQRES 11 A 193 LEU GLU ASP LEU GLY GLN ALA LYS ARG VAL VAL ILE THR SEQRES 12 A 193 LYS ASP THR THR THR ILE ILE ASP GLY VAL GLY GLU GLU SEQRES 13 A 193 ALA ALA ILE GLN GLY ARG VAL ALA GLN ILE ARG GLN GLN SEQRES 14 A 193 ILE GLU GLU ALA THR SER ASP TYR ASP ARG GLU LYS LEU SEQRES 15 A 193 GLN GLU ARG VAL ALA LYS LEU ALA GLY GLY VAL HET GOL A 401 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 GOL C3 H8 O3 FORMUL 3 HOH *149(H2 O) HELIX 1 1 SER A 201 ILE A 205 5 5 HELIX 2 2 LEU A 233 GLY A 244 1 12 HELIX 3 3 GLU A 255 ARG A 268 1 14 HELIX 4 4 PHE A 281 GLY A 297 1 17 HELIX 5 5 LYS A 308 ALA A 312 5 5 HELIX 6 6 GLU A 338 ALA A 356 1 19 HELIX 7 7 SER A 358 VAL A 376 1 19 SHEET 1 A 4 MET A 193 PHE A 195 0 SHEET 2 A 4 THR A 330 GLY A 335 -1 N THR A 330 O PHE A 195 SHEET 3 A 4 GLY A 318 ILE A 325 -1 N LYS A 321 O ILE A 333 SHEET 4 A 4 VAL A 213 GLU A 216 -1 O VAL A 213 N ILE A 325 SHEET 1 B 6 MET A 193 PHE A 195 0 SHEET 2 B 6 THR A 330 GLY A 335 -1 N THR A 330 O PHE A 195 SHEET 3 B 6 GLY A 318 ILE A 325 -1 N LYS A 321 O ILE A 333 SHEET 4 B 6 PHE A 219 LEU A 222 -1 N ILE A 220 O GLY A 318 SHEET 5 B 6 LEU A 247 ALA A 251 1 O LEU A 248 N LEU A 221 SHEET 6 B 6 VAL A 273 LYS A 277 1 O ALA A 274 N ILE A 249 SHEET 1 C 2 LYS A 226 ILE A 227 0 SHEET 2 C 2 ASP A 253 VAL A 254 1 O ASP A 253 N ILE A 227 SITE 1 AC1 7 HOH A 74 PHE A 195 ASP A 196 ARG A 284 SITE 2 AC1 7 LYS A 364 GLU A 367 LYS A 371 CRYST1 75.930 83.940 35.300 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 0.013170 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011910 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028330 0.00000