10 20 30 40 50 60 70 80 1JBK - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER CHAPERONE 05-JUN-01 1JBK
TITLE CRYSTAL STRUCTURE OF THE FIRST NUCELOTIDE BINDING DOMAIN OF TITLE 2 CLPB
COMPND MOL_ID: 1; COMPND 2 MOLECULE: CLPB PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: FIRST NUCLEOTIDE BINDING DOMAIN (RESIDUES 159- COMPND 5 351); COMPND 6 SYNONYM: HEAT SHOCK PROTEIN F84.1; COMPND 7 ENGINEERED: YES
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B
KEYWDS BETA BARREL, CHAPERONE
EXPDTA X-RAY DIFFRACTION
AUTHOR L.JINGZHI,S.BINGDONG
REVDAT 3 24-FEB-09 1JBK 1 VERSN REVDAT 2 01-APR-03 1JBK 1 JRNL REVDAT 1 05-JUN-02 1JBK 0
JRNL AUTH J.LI,B.SHA JRNL TITL CRYSTAL STRUCTURE OF E. COLI HSP100 CLPB JRNL TITL 2 NUCLEOTIDE-BINDING DOMAIN 1 (NBD1) AND MECHANISTIC JRNL TITL 3 STUDIES ON CLPB ATPASE ACTIVITY. JRNL REF J.MOL.BIOL. V. 318 1127 2002 JRNL REFN ISSN 0022-2836 JRNL PMID 12054807 JRNL DOI 10.1016/S0022-2836(02)00188-2
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 13559 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 SET) : 0.222 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1107 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL 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 : 1475 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 296 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.21 REMARK 3 ESD FROM SIGMAA (A) : 0.10 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) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.30 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.40 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.71 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 1JBK COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUN-01. REMARK 100 THE RCSB ID CODE IS RCSB013589.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-01; NULL REMARK 200 TEMPERATURE (KELVIN) : 100; NULL REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : APS; APS REMARK 200 BEAMLINE : 14-BM-C; 14-BM-D REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; NULL REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786, 0.9784, 0.9632, REMARK 200 0.9941; 1.0 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111); REMARK 200 NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : SCALE REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19159 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 32.6000 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) : 1.88 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.20 REMARK 200 R MERGE FOR SHELL (I) : 0.14200 REMARK 200 R SYM FOR SHELL (I) : 0.14200 REMARK 200 <I/SIGMA(I)> FOR SHELL : 11.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: MAD; NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MADSYS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.32 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, PH 7.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K
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 19.24400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 39.54350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 32.84300 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 39.54350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.24400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 32.84300 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 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 GLY A 287 REMARK 465 LYS A 288 REMARK 465 ALA A 289 REMARK 465 ASP A 290 REMARK 465 GLY A 291 REMARK 465 ALA A 292
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 GLU A 227 44.12 -85.38 REMARK 500 LYS A 250 -48.75 63.80 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 515 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH A 519 DISTANCE = 8.35 ANGSTROMS REMARK 525 HOH A 535 DISTANCE = 6.85 ANGSTROMS REMARK 525 HOH A 537 DISTANCE = 6.71 ANGSTROMS REMARK 525 HOH A 539 DISTANCE = 6.97 ANGSTROMS REMARK 525 HOH A 590 DISTANCE = 7.38 ANGSTROMS REMARK 525 HOH A 605 DISTANCE = 8.21 ANGSTROMS REMARK 525 HOH A 606 DISTANCE = 8.20 ANGSTROMS REMARK 525 HOH A 610 DISTANCE = 5.88 ANGSTROMS REMARK 525 HOH A 646 DISTANCE = 5.20 ANGSTROMS
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 1
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NBD RELATED DB: PDB REMARK 900 1NBD BELONGS TO THE AAA ATPASE FAMILY
DBREF 1JBK A 159 351 UNP P63284 CLPB_ECOLI 159 351
SEQADV 1JBK HIS A 157 UNP P63284 EXPRESSION TAG SEQADV 1JBK MET A 158 UNP P63284 EXPRESSION TAG
SEQRES 1 A 195 HIS MET GLN ALA LEU LYS LYS TYR THR ILE ASP LEU THR SEQRES 2 A 195 GLU ARG ALA GLU GLN GLY LYS LEU ASP PRO VAL ILE GLY SEQRES 3 A 195 ARG ASP GLU GLU ILE ARG ARG THR ILE GLN VAL LEU GLN SEQRES 4 A 195 ARG ARG THR LYS ASN ASN PRO VAL LEU ILE GLY GLU PRO SEQRES 5 A 195 GLY VAL GLY LYS THR ALA ILE VAL GLU GLY LEU ALA GLN SEQRES 6 A 195 ARG ILE ILE ASN GLY GLU VAL PRO GLU GLY LEU LYS GLY SEQRES 7 A 195 ARG ARG VAL LEU ALA LEU ASP MET GLY ALA LEU VAL ALA SEQRES 8 A 195 GLY ALA LYS TYR ARG GLY GLU PHE GLU GLU ARG LEU LYS SEQRES 9 A 195 GLY VAL LEU ASN ASP LEU ALA LYS GLN GLU GLY ASN VAL SEQRES 10 A 195 ILE LEU PHE ILE ASP GLU LEU HIS THR MET VAL GLY ALA SEQRES 11 A 195 GLY LYS ALA ASP GLY ALA MET ASP ALA GLY ASN MET LEU SEQRES 12 A 195 LYS PRO ALA LEU ALA ARG GLY GLU LEU HIS CYS VAL GLY SEQRES 13 A 195 ALA THR THR LEU ASP GLU TYR ARG GLN TYR ILE GLU LYS SEQRES 14 A 195 ASP ALA ALA LEU GLU ARG ARG PHE GLN LYS VAL PHE VAL SEQRES 15 A 195 ALA GLU PRO SER VAL GLU ASP THR ILE ALA ILE LEU ARG
HET MG A 1 1
HETNAM MG MAGNESIUM ION
FORMUL 2 MG MG 2+ FORMUL 3 HOH *296(H2 O)
HELIX 1 1 MET A 158 TYR A 164 1 7 HELIX 2 2 LEU A 168 GLN A 174 1 7 HELIX 3 3 ARG A 183 GLN A 195 1 13 HELIX 4 4 GLY A 211 GLY A 226 1 16 HELIX 5 5 PRO A 229 LYS A 233 5 5 HELIX 6 6 ASP A 241 ALA A 247 1 7 HELIX 7 7 TYR A 251 GLN A 269 1 19 HELIX 8 8 LEU A 280 VAL A 284 5 5 HELIX 9 9 ALA A 295 ARG A 305 1 11 HELIX 10 10 THR A 315 ILE A 323 1 9 HELIX 11 11 ASP A 326 ARG A 331 1 6 HELIX 12 12 SER A 342 ALA A 348 1 7
SHEET 1 A 6 THR A 165 ASP A 167 0 SHEET 2 A 6 ARG A 236 LEU A 240 -1 N ALA A 239 O ILE A 166 SHEET 3 A 6 VAL A 273 ASP A 278 1 N ILE A 274 O ARG A 236 SHEET 4 A 6 CYS A 310 THR A 314 1 O VAL A 311 N ILE A 277 SHEET 5 A 6 ASN A 201 ILE A 205 1 O PRO A 202 N GLY A 312 SHEET 6 A 6 PHE A 333 PHE A 337 1 O GLN A 334 N VAL A 203
SITE 1 AC1 3 GLY A 209 GLY A 211 LYS A 212
CRYST1 38.488 65.686 79.087 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 0.025982 0.000000 0.000000 0.00000
SCALE2 0.000000 0.015224 0.000000 0.00000
SCALE3 0.000000 0.000000 0.012644 0.00000