HEADER CHAPERONE 15-MAR-10 3M6C TITLE CRYSTAL STRUCTURE OF MYCOBACTERIUM TUBERCULOSIS GROEL1 APICAL DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 60 KDA CHAPERONIN 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 184-377; COMPND 5 SYNONYM: PROTEIN CPN60-1, GROEL PROTEIN 1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM TUBERCULOSIS; SOURCE 3 ORGANISM_TAXID: 83332; SOURCE 4 STRAIN: H37RV; SOURCE 5 GENE: GROEL-1, GROEL1, GROL1, MT3526, MTCY78.12, RV3417C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) RIL; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PPROEX HTB KEYWDS CHAPERONE, ATP-BINDING, NUCLEOTIDE-BINDING EXPDTA X-RAY DIFFRACTION AUTHOR F.T.F.TSAI,B.SIELAFF,K.LEE REVDAT 4 06-SEP-23 3M6C 1 REMARK REVDAT 3 08-NOV-17 3M6C 1 REMARK REVDAT 2 09-FEB-11 3M6C 1 JRNL REVDAT 1 08-DEC-10 3M6C 0 JRNL AUTH B.SIELAFF,K.S.LEE,F.T.TSAI JRNL TITL STRUCTURAL AND FUNCTIONAL CONSERVATION OF MYCOBACTERIUM JRNL TITL 2 TUBERCULOSIS GROEL PARALOGS SUGGESTS THAT GROEL1 IS A JRNL TITL 3 CHAPERONIN. JRNL REF J.MOL.BIOL. V. 405 831 2011 JRNL REFN ISSN 0022-2836 JRNL PMID 21094166 JRNL DOI 10.1016/J.JMB.2010.11.021 REMARK 2 REMARK 2 RESOLUTION. 2.20 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 375010.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 10517 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) : 0.210 REMARK 3 FREE R VALUE : 0.232 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 544 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.010 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) : 2.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.34 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.20 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1458 REMARK 3 BIN R VALUE (WORKING SET) : 0.2500 REMARK 3 BIN FREE R VALUE : 0.2890 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.50 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 68 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.035 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1461 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 65 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.29 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.79000 REMARK 3 B22 (A**2) : -3.87000 REMARK 3 B33 (A**2) : 4.67000 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) : 0.26 REMARK 3 ESD FROM SIGMAA (A) : 0.22 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) : 0.31 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.25 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) : 22.30 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.700 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) : 1.480 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 2.300 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 2.610 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 4.120 ; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.40 REMARK 3 BSOL : 40.12 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 : WATER_REP.PARAM REMARK 3 PARAMETER FILE 3 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : WATER.TOP REMARK 3 TOPOLOGY FILE 3 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: BULK SOLVENT MODEL USED REMARK 4 REMARK 4 3M6C COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-MAR-10. REMARK 100 THE DEPOSITION ID IS D_1000058163. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU FR-E+ SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRRORS VARIMAX HF REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS HTC REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10994 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.300 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.28 REMARK 200 COMPLETENESS FOR SHELL (%) : 91.9 REMARK 200 DATA REDUNDANCY IN SHELL : 2.60 REMARK 200 R MERGE FOR SHELL (I) : 0.36700 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1SJP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.71 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 6000, 0.1M BICINE, PH 9.0, REMARK 280 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 37.73400 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 39.32350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.73400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 39.32350 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 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 223 -159.97 -94.70 REMARK 500 SER A 226 -36.83 -138.60 REMARK 500 LEU A 269 89.90 -159.87 REMARK 500 TYR A 278 -143.93 -92.18 REMARK 500 ASP A 332 73.58 55.25 REMARK 500 REMARK 500 REMARK: NULL DBREF 3M6C A 184 377 UNP P0A518 CH601_MYCTU 184 377 SEQRES 1 A 194 GLU LEU GLU PHE THR GLU GLY ILE GLY PHE ASP LYS GLY SEQRES 2 A 194 PHE LEU SER ALA TYR PHE VAL THR ASP PHE ASP ASN GLN SEQRES 3 A 194 GLN ALA VAL LEU GLU ASP ALA LEU ILE LEU LEU HIS GLN SEQRES 4 A 194 ASP LYS ILE SER SER LEU PRO ASP LEU LEU PRO LEU LEU SEQRES 5 A 194 GLU LYS VAL ALA GLY THR GLY LYS PRO LEU LEU ILE VAL SEQRES 6 A 194 ALA GLU ASP VAL GLU GLY GLU ALA LEU ALA THR LEU VAL SEQRES 7 A 194 VAL ASN ALA ILE ARG LYS THR LEU LYS ALA VAL ALA VAL SEQRES 8 A 194 LYS GLY PRO TYR PHE GLY ASP ARG ARG LYS ALA PHE LEU SEQRES 9 A 194 GLU ASP LEU ALA VAL VAL THR GLY GLY GLN VAL VAL ASN SEQRES 10 A 194 PRO ASP ALA GLY MET VAL LEU ARG GLU VAL GLY LEU GLU SEQRES 11 A 194 VAL LEU GLY SER ALA ARG ARG VAL VAL VAL SER LYS ASP SEQRES 12 A 194 ASP THR VAL ILE VAL ASP GLY GLY GLY THR ALA GLU ALA SEQRES 13 A 194 VAL ALA ASN ARG ALA LYS HIS LEU ARG ALA GLU ILE ASP SEQRES 14 A 194 LYS SER ASP SER ASP TRP ASP ARG GLU LYS LEU GLY GLU SEQRES 15 A 194 ARG LEU ALA LYS LEU ALA GLY GLY VAL ALA VAL ILE FORMUL 2 HOH *65(H2 O) HELIX 1 1 SER A 199 VAL A 203 5 5 HELIX 2 2 SER A 227 GLY A 242 1 16 HELIX 3 3 GLU A 253 ARG A 266 1 14 HELIX 4 4 PHE A 279 GLY A 295 1 17 HELIX 5 5 ASN A 300 GLY A 304 5 5 HELIX 6 6 VAL A 306 VAL A 310 5 5 HELIX 7 7 GLY A 311 LEU A 315 5 5 HELIX 8 8 THR A 336 LYS A 353 1 18 HELIX 9 9 SER A 356 VAL A 374 1 19 SHEET 1 A 6 ILE A 191 PHE A 193 0 SHEET 2 A 6 THR A 328 GLY A 333 -1 O THR A 328 N PHE A 193 SHEET 3 A 6 GLY A 316 VAL A 323 -1 N ARG A 320 O VAL A 331 SHEET 4 A 6 ALA A 211 LEU A 220 -1 N ASP A 215 O ARG A 319 SHEET 5 A 6 LEU A 245 ALA A 249 1 O VAL A 248 N LEU A 219 SHEET 6 A 6 ALA A 271 LYS A 275 1 O VAL A 274 N ILE A 247 SHEET 1 B 2 LYS A 224 ILE A 225 0 SHEET 2 B 2 ASP A 251 VAL A 252 1 O ASP A 251 N ILE A 225 CRYST1 75.468 78.647 34.891 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 0.013251 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012715 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028661 0.00000