HEADER CHAPERONE 09-OCT-12 3VZ7 TITLE CRYSTAL STRUCTURE ANALYSIS OF THE MINI-CHAPERONIN VARIANT WITH PRO 187 TITLE 2 GLY COMPND MOL_ID: 1; COMPND 2 MOLECULE: 60 KDA CHAPERONIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: APICAL DOMAIN, UNP RESIDUES 191-376; COMPND 5 SYNONYM: GROEL PROTEIN, PROTEIN CPN60; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: GROL, GROEL, MOPA, B4143, JW4103; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS CHAPERONIN, HSP60, GROEL, CELL DIVISION, ATP-BINDING, KEYWDS 2 PHOSPHOLYRATION, CHAPERONE EXPDTA X-RAY DIFFRACTION AUTHOR S.SAIJO,T.SATO REVDAT 2 08-NOV-23 3VZ7 1 SEQADV REVDAT 1 13-NOV-13 3VZ7 0 JRNL AUTH S.SAIJO,T.SATO JRNL TITL BINDING ENERGY(BE) FROM CRYSTAL PACKING OF MINI-CHAPERONES JRNL TITL 2 (MCPN) PROVIDED INSIGHTS INTO THE ALLOSTERIC INTERACTION OF JRNL TITL 3 GROEL/ES COMPLEX JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.3 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1217562.690 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 21847 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) : 0.227 REMARK 3 FREE R VALUE : 0.249 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1094 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.008 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.91 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.60 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 3410 REMARK 3 BIN R VALUE (WORKING SET) : 0.2710 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 155 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.024 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1454 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 15.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 18.80 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -3.96000 REMARK 3 B22 (A**2) : 3.43000 REMARK 3 B33 (A**2) : 0.53000 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) : 0.24 REMARK 3 ESD FROM SIGMAA (A) : 0.12 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) : 0.27 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.19 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.300 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.00 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.750 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED 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 : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 36.35 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : DNA-RNA_REP.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : CARBOHYDRATE.PARAM REMARK 3 PARAMETER FILE 6 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-RNA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : CARBOHYDRATE.TOP REMARK 3 TOPOLOGY FILE 6 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3VZ7 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 16-OCT-12. REMARK 100 THE DEPOSITION ID IS D_1000095684. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-AUG-00 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : BL-6A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21847 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: 1KID REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.07 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M TRIS-HCL, 1M NACL, 3.75% REMARK 280 GLYCEROL, PH 7.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 288K 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 37.99500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 42.40500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.99500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 42.40500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 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 ASN A 326 -167.63 -123.42 REMARK 500 ASP A 334 73.18 53.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3VZ6 RELATED DB: PDB REMARK 900 RELATED ID: 3VZ8 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 RESIDUES 184-190 ARE HETEROLOGOUS FUSION TAG DBREF 3VZ7 A 191 376 UNP P0A6F5 CH60_ECOLI 191 376 SEQADV 3VZ7 HIS A 178 UNP P0A6F5 EXPRESSION TAG SEQADV 3VZ7 HIS A 179 UNP P0A6F5 EXPRESSION TAG SEQADV 3VZ7 HIS A 180 UNP P0A6F5 EXPRESSION TAG SEQADV 3VZ7 HIS A 181 UNP P0A6F5 EXPRESSION TAG SEQADV 3VZ7 HIS A 182 UNP P0A6F5 EXPRESSION TAG SEQADV 3VZ7 HIS A 183 UNP P0A6F5 EXPRESSION TAG SEQADV 3VZ7 GLY A 184 UNP P0A6F5 SEE REMARK 999 SEQADV 3VZ7 LEU A 185 UNP P0A6F5 SEE REMARK 999 SEQADV 3VZ7 VAL A 186 UNP P0A6F5 SEE REMARK 999 SEQADV 3VZ7 GLY A 187 UNP P0A6F5 SEE REMARK 999 SEQADV 3VZ7 ARG A 188 UNP P0A6F5 SEE REMARK 999 SEQADV 3VZ7 GLY A 189 UNP P0A6F5 SEE REMARK 999 SEQADV 3VZ7 SER A 190 UNP P0A6F5 SEE REMARK 999 SEQRES 1 A 199 HIS HIS HIS HIS HIS HIS GLY LEU VAL GLY ARG GLY SER SEQRES 2 A 199 GLU GLY MET GLN PHE ASP ARG GLY TYR LEU SER PRO TYR SEQRES 3 A 199 PHE ILE ASN LYS PRO GLU THR GLY ALA VAL GLU LEU GLU SEQRES 4 A 199 SER PRO PHE ILE LEU LEU ALA ASP LYS LYS ILE SER ASN SEQRES 5 A 199 ILE ARG GLU MET LEU PRO VAL LEU GLU ALA VAL ALA LYS SEQRES 6 A 199 ALA GLY LYS PRO LEU LEU ILE ILE ALA GLU ASP VAL GLU SEQRES 7 A 199 GLY GLU ALA LEU ALA THR LEU VAL VAL ASN THR MET ARG SEQRES 8 A 199 GLY ILE VAL LYS VAL ALA ALA VAL LYS ALA PRO GLY PHE SEQRES 9 A 199 GLY ASP ARG ARG LYS ALA MET LEU GLN ASP ILE ALA THR SEQRES 10 A 199 LEU THR GLY GLY THR VAL ILE SER GLU GLU ILE GLY MET SEQRES 11 A 199 GLU LEU GLU LYS ALA THR LEU GLU ASP LEU GLY GLN ALA SEQRES 12 A 199 LYS ARG VAL VAL ILE ASN LYS ASP THR THR THR ILE ILE SEQRES 13 A 199 ASP GLY VAL GLY GLU GLU ALA ALA ILE GLN GLY ARG VAL SEQRES 14 A 199 ALA GLN ILE ARG GLN GLN ILE GLU GLU ALA THR SER ASP SEQRES 15 A 199 TYR ASP ARG GLU LYS LEU GLN GLU ARG VAL ALA LYS LEU SEQRES 16 A 199 ALA GLY GLY VAL FORMUL 2 HOH *139(H2 O) HELIX 1 1 SER A 201 ILE A 205 5 5 HELIX 2 2 LYS A 207 GLY A 211 5 5 HELIX 3 3 ASN A 229 GLU A 232 5 4 HELIX 4 4 MET A 233 GLY A 244 1 12 HELIX 5 5 GLU A 255 ARG A 268 1 14 HELIX 6 6 PHE A 281 GLY A 297 1 17 HELIX 7 7 GLU A 308 ALA A 312 5 5 HELIX 8 8 THR A 313 LEU A 317 5 5 HELIX 9 9 GLU A 338 ALA A 356 1 19 HELIX 10 10 SER A 358 GLY A 375 1 18 SHEET 1 A 4 MET A 193 PHE A 195 0 SHEET 2 A 4 THR A 330 GLY A 335 -1 O ILE A 332 N MET A 193 SHEET 3 A 4 GLY A 318 ILE A 325 -1 N ARG A 322 O ILE A 333 SHEET 4 A 4 VAL A 213 GLU A 216 -1 N VAL A 213 O 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 O ILE A 332 N MET A 193 SHEET 3 B 6 GLY A 318 ILE A 325 -1 N ARG A 322 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 ILE A 250 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 CRYST1 75.990 84.810 35.270 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 0.013160 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011791 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028353 0.00000