PDB Short entry for 1HZA HEADER TRANSCRIPTION 24-JAN-01 1HZA TITLE BACILLUS CALDOLYTICUS COLD-SHOCK PROTEIN MUTANTS TO STUDY DETERMINANTS TITLE 2 OF PROTEIN STABILITY COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLD SHOCK PROTEIN CSPB; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CSPB, BC-CSP; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS CALDOLYTICUS; SOURCE 3 ORGANISM_TAXID: 1394; SOURCE 4 GENE: CSPB; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS BETA BARREL, HOMODIMER, TRANSCRIPTION EXPDTA X-RAY DIFFRACTION AUTHOR H.DELBRUECK,U.MUELLER,D.PERL,F.X.SCHMID,U.HEINEMANN REVDAT 6 09-AUG-23 1HZA 1 REMARK REVDAT 5 27-OCT-21 1HZA 1 SEQADV REVDAT 4 04-APR-18 1HZA 1 REMARK REVDAT 3 24-FEB-09 1HZA 1 VERSN REVDAT 2 01-APR-03 1HZA 1 JRNL REVDAT 1 07-NOV-01 1HZA 0 JRNL AUTH H.DELBRUCK,U.MUELLER,D.PERL,F.X.SCHMID,U.HEINEMANN JRNL TITL CRYSTAL STRUCTURES OF MUTANT FORMS OF THE BACILLUS JRNL TITL 2 CALDOLYTICUS COLD SHOCK PROTEIN DIFFERING IN THERMAL JRNL TITL 3 STABILITY. JRNL REF J.MOL.BIOL. V. 313 359 2001 JRNL REFN ISSN 0022-2836 JRNL PMID 11800562 JRNL DOI 10.1006/JMBI.2001.5051 REMARK 2 REMARK 2 RESOLUTION. 1.80 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 75.9 REMARK 3 NUMBER OF REFLECTIONS : 9838 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : THIN SHELLS 7.5% REMARK 3 R VALUE (WORKING + TEST SET) : 0.206 REMARK 3 R VALUE (WORKING SET) : 0.193 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 744 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1048 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 21.60 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 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) : 0.010 ; NULL REMARK 3 ANGLE DISTANCE (A) : 2.700 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL 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) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; 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 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HZA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 25-JAN-01. REMARK 100 THE DEPOSITION ID IS D_1000012709. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUN-99 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 6.5 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GOEBEL-MIRROR SYSTEM REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9838 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 28.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 75.9 REMARK 200 DATA REDUNDANCY : 2.100 REMARK 200 R MERGE (I) : 0.05100 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 19.1000 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) : 1.82 REMARK 200 COMPLETENESS FOR SHELL (%) : 39.6 REMARK 200 DATA REDUNDANCY IN SHELL : 1.20 REMARK 200 R MERGE FOR SHELL (I) : 0.33900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1C9O REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 800, SODIUM CHLORIDE, CACODYLATE, REMARK 280 PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X,-Y,Z REMARK 290 7555 -Y+1/2,X,Z+3/4 REMARK 290 8555 Y,-X+1/2,Z+1/4 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 38.20900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 38.20900 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 23.73150 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 38.20900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 11.86575 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 38.20900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.59725 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 38.20900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 38.20900 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 23.73150 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 38.20900 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 35.59725 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 38.20900 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 11.86575 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NZ LYS A 7 OE1 GLU B 21 7655 2.09 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 3 CD - NE - CZ ANGL. DEV. = 9.1 DEGREES REMARK 500 GLN A 45 CA - CB - CG ANGL. DEV. = 13.4 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 GLU B 21 96.94 -65.95 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1C9O RELATED DB: PDB REMARK 900 1C9O IS BACILLUS CALDOLYTICUS COLD-SHOCK-PROTEIN REMARK 900 RELATED ID: 1CSP RELATED DB: PDB REMARK 900 1CSP IS BACILLUS SUBTILIS COLD-SHOCK-PROTEIN REMARK 900 RELATED ID: 1HZ9 RELATED DB: PDB REMARK 900 1HZ9 IS SINGLE MUTANT OF 1C9O (E46A) REMARK 900 RELATED ID: 1HZB RELATED DB: PDB REMARK 900 1HZB IS SINGLE MUTANT OF 1C9O (L66E) REMARK 900 RELATED ID: 1HZC RELATED DB: PDB REMARK 900 1HZC IS TRIPLE MUTANT OF 1C9O (R3E/E46A/L66E) DBREF 1HZA A 1 66 UNP P41016 CSPB_BACCL 1 66 DBREF 1HZA B 1 66 UNP P41016 CSPB_BACCL 1 66 SEQADV 1HZA THR A 64 UNP P41016 VAL 64 ENGINEERED MUTATION SEQADV 1HZA GLU A 66 UNP P41016 LEU 66 ENGINEERED MUTATION SEQADV 1HZA ALA A 67 UNP P41016 INSERTION SEQADV 1HZA THR B 64 UNP P41016 VAL 64 ENGINEERED MUTATION SEQADV 1HZA GLU B 66 UNP P41016 LEU 66 ENGINEERED MUTATION SEQADV 1HZA ALA B 67 UNP P41016 INSERTION SEQRES 1 A 67 MET GLN ARG GLY LYS VAL LYS TRP PHE ASN ASN GLU LYS SEQRES 2 A 67 GLY TYR GLY PHE ILE GLU VAL GLU GLY GLY SER ASP VAL SEQRES 3 A 67 PHE VAL HIS PHE THR ALA ILE GLN GLY GLU GLY PHE LYS SEQRES 4 A 67 THR LEU GLU GLU GLY GLN GLU VAL SER PHE GLU ILE VAL SEQRES 5 A 67 GLN GLY ASN ARG GLY PRO GLN ALA ALA ASN VAL THR LYS SEQRES 6 A 67 GLU ALA SEQRES 1 B 67 MET GLN ARG GLY LYS VAL LYS TRP PHE ASN ASN GLU LYS SEQRES 2 B 67 GLY TYR GLY PHE ILE GLU VAL GLU GLY GLY SER ASP VAL SEQRES 3 B 67 PHE VAL HIS PHE THR ALA ILE GLN GLY GLU GLY PHE LYS SEQRES 4 B 67 THR LEU GLU GLU GLY GLN GLU VAL SER PHE GLU ILE VAL SEQRES 5 B 67 GLN GLY ASN ARG GLY PRO GLN ALA ALA ASN VAL THR LYS SEQRES 6 B 67 GLU ALA FORMUL 3 HOH *110(H2 O) HELIX 1 1 THR A 31 ILE A 33 5 3 HELIX 2 2 THR B 31 ILE B 33 5 3 SHEET 1 A 5 VAL A 26 HIS A 29 0 SHEET 2 A 5 TYR A 15 GLU A 19 -1 O GLY A 16 N VAL A 28 SHEET 3 A 5 GLN A 2 ASN A 10 -1 O LYS A 5 N GLU A 19 SHEET 4 A 5 GLU A 46 GLY A 54 -1 N VAL A 47 O GLY A 4 SHEET 5 A 5 GLY A 57 LYS A 65 -1 O GLY A 57 N GLY A 54 SHEET 1 B 6 GLN B 2 ASN B 10 0 SHEET 2 B 6 TYR B 15 VAL B 20 -1 O TYR B 15 N ASN B 10 SHEET 3 B 6 GLY B 23 HIS B 29 -1 N GLY B 23 O VAL B 20 SHEET 4 B 6 GLY B 57 LYS B 65 1 O PRO B 58 N PHE B 27 SHEET 5 B 6 GLU B 46 GLY B 54 -1 O SER B 48 N THR B 64 SHEET 6 B 6 GLN B 2 ASN B 10 -1 N GLN B 2 O PHE B 49 CRYST1 76.418 76.418 47.463 90.00 90.00 90.00 I 41 16 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 0.013086 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013086 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021069 0.00000