PDB Short entry for 2I5L HEADER GENE REGULATION 25-AUG-06 2I5L TITLE CRYSTAL STRUCTURE OF BACILLUS SUBTILIS COLD SHOCK PROTEIN VARIANT BS- TITLE 2 CSPB M1R/E3K/K65I COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLD SHOCK PROTEIN CSPB; COMPND 3 CHAIN: X; COMPND 4 SYNONYM: MAJOR COLD SHOCK PROTEIN; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: CSPB, CSPA; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET11 KEYWDS OLIGONUCLEOTIDE/OLIGOSACCHARIDE BINDING FOLD, COLD SHOCK DOMAIN, KEYWDS 2 BETA-BARREL, DNA BINDING PROTEIN, EXPRESSION REGULATOR, GENE KEYWDS 3 REGULATION EXPDTA X-RAY DIFFRACTION AUTHOR K.E.A.MAX,U.HEINEMANN REVDAT 6 30-AUG-23 2I5L 1 REMARK REVDAT 5 20-OCT-21 2I5L 1 SEQADV REVDAT 4 18-OCT-17 2I5L 1 REMARK REVDAT 3 24-FEB-09 2I5L 1 VERSN REVDAT 2 12-JUN-07 2I5L 1 JRNL REVDAT 1 22-MAY-07 2I5L 0 JRNL AUTH K.E.MAX,M.WUNDERLICH,Y.ROSKE,F.X.SCHMID,U.HEINEMANN JRNL TITL OPTIMIZED VARIANTS OF THE COLD SHOCK PROTEIN FROM IN VITRO JRNL TITL 2 SELECTION: STRUCTURAL BASIS OF THEIR HIGH THERMOSTABILITY. JRNL REF J.MOL.BIOL. V. 369 1087 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17481655 JRNL DOI 10.1016/J.JMB.2007.04.016 REMARK 2 REMARK 2 RESOLUTION. 2.55 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 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 3071 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 + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.227 REMARK 3 FREE R VALUE : 0.244 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.400 REMARK 3 FREE R VALUE TEST SET COUNT : 134 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.62 REMARK 3 REFLECTION IN BIN (WORKING SET) : 206 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3960 REMARK 3 BIN FREE R VALUE SET COUNT : 7 REMARK 3 BIN FREE R VALUE : 0.3420 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 523 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 10 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 49.58 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.67000 REMARK 3 B22 (A**2) : 0.67000 REMARK 3 B33 (A**2) : -1.33000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.485 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.270 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.200 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.525 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.933 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.899 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 537 ; 0.016 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 469 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 720 ; 1.717 ; 1.924 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1097 ; 0.927 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 66 ; 5.749 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 30 ;31.264 ;25.667 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 92 ;16.890 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 2 ; 9.925 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 73 ; 0.112 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 618 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 115 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 91 ; 0.216 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 444 ; 0.215 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 268 ; 0.193 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 326 ; 0.102 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 18 ; 0.139 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 3 ; 0.146 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 29 ; 0.306 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.057 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 435 ; 2.375 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 144 ; 0.312 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 520 ; 2.868 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 274 ; 4.645 ; 4.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 200 ; 5.473 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2I5L COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-AUG-06. REMARK 100 THE DEPOSITION ID IS D_1000039165. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9537 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL MONOCHROMATOR, SI REMARK 200 -111 CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION JUNE 2005 REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 3223 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 9.720 REMARK 200 R MERGE (I) : 0.08800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.1400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.60 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.6 REMARK 200 DATA REDUNDANCY IN SHELL : 9.36 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 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 1CSQ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.48 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION: 20 MM TRIS PH 7.5, REMARK 280 50 MM SODIUM CHLORIDE, 3 MM MAGNESIUM CHLORIDE, 20.4 MG/ML REMARK 280 PROTEIN. CRYSTALLIZATION BUFFER: 25 % PEG 3350, 0.2 M SODIUM REMARK 280 CARBONATE, 0.1 M TRIS HCL PH 8.5. CRYSTALLIZATION SETUP: 0.8 REMARK 280 MICROLITER PROTEIN SOLUTION:0.8 MICROLITER RESERVOIR SOLUTION, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 27.73500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.75000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.75000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.60250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.75000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.75000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 13.86750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.75000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.75000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.60250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.75000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.75000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.86750 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 27.73500 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: X 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 VAL X 6 107.54 -59.75 REMARK 500 GLN X 45 133.50 -38.48 REMARK 500 GLU X 66 141.22 142.60 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1CSP RELATED DB: PDB REMARK 900 RELATED ID: 1CSQ RELATED DB: PDB REMARK 900 RELATED ID: 2ES2 RELATED DB: PDB REMARK 900 RELATED ID: 2I5M RELATED DB: PDB DBREF 2I5L X 1 67 UNP P32081 CSPB_BACSU 1 67 SEQADV 2I5L ARG X 1 UNP P32081 MET 1 ENGINEERED MUTATION SEQADV 2I5L LYS X 3 UNP P32081 GLU 3 ENGINEERED MUTATION SEQADV 2I5L ILE X 65 UNP P32081 LYS 65 ENGINEERED MUTATION SEQRES 1 X 67 ARG LEU LYS GLY LYS VAL LYS TRP PHE ASN SER GLU LYS SEQRES 2 X 67 GLY PHE GLY PHE ILE GLU VAL GLU GLY GLN ASP ASP VAL SEQRES 3 X 67 PHE VAL HIS PHE SER ALA ILE GLN GLY GLU GLY PHE LYS SEQRES 4 X 67 THR LEU GLU GLU GLY GLN ALA VAL SER PHE GLU ILE VAL SEQRES 5 X 67 GLU GLY ASN ARG GLY PRO GLN ALA ALA ASN VAL THR ILE SEQRES 6 X 67 GLU ALA FORMUL 2 HOH *10(H2 O) HELIX 1 1 SER X 31 ILE X 33 5 3 SHEET 1 A 5 VAL X 26 HIS X 29 0 SHEET 2 A 5 PHE X 15 GLU X 19 -1 N ILE X 18 O VAL X 26 SHEET 3 A 5 LEU X 2 PHE X 9 -1 N LYS X 5 O GLU X 19 SHEET 4 A 5 ALA X 46 GLY X 54 -1 O PHE X 49 N LEU X 2 SHEET 5 A 5 GLY X 57 ILE X 65 -1 O GLN X 59 N VAL X 52 CRYST1 55.500 55.500 55.470 90.00 90.00 90.00 P 43 21 2 8 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 0.018018 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018018 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018028 0.00000