HEADER DNA BINDING PROTEIN 12-MAY-16 5JX4 TITLE CRYSTAL STRUCTURE OF E36-G37DEL MUTANT OF THE BACILLUS CALDOLYTICUS TITLE 2 COLD SHOCK PROTEIN. COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLD SHOCK PROTEIN CSPB; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 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: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)C41; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET28B MODIFIED KEYWDS BCCSP, MONOMER, MUTANT, COLD SHOCK PROTEIN., DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.CARVAJAL,V.CASTRO-FERNANDEZ,D.CABREJOS,M.FUENTEALBA,H.M.PEREIRA, AUTHOR 2 G.VALLEJOS,R.CABRERA,R.C.GARRATT,E.A.KOMIVES,C.A.RAMIREZ-SARMIENTO, AUTHOR 3 J.BABUL REVDAT 5 27-SEP-23 5JX4 1 REMARK REVDAT 4 01-NOV-17 5JX4 1 REMARK REVDAT 3 05-JUL-17 5JX4 1 JRNL REVDAT 2 24-MAY-17 5JX4 1 JRNL REVDAT 1 10-MAY-17 5JX4 0 JRNL AUTH A.I.CARVAJAL,G.VALLEJOS,E.A.KOMIVES,V.CASTRO-FERNANDEZ, JRNL AUTH 2 D.A.LEONARDO,R.C.GARRATT,C.A.RAMIREZ-SARMIENTO,J.BABUL JRNL TITL UNUSUAL DIMERIZATION OF A BCCSP MUTANT LEADS TO REDUCED JRNL TITL 2 CONFORMATIONAL DYNAMICS. JRNL REF FEBS J. V. 284 1882 2017 JRNL REFN ISSN 1742-4658 JRNL PMID 28457014 JRNL DOI 10.1111/FEBS.14093 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.4_1496 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 9514 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.152 REMARK 3 R VALUE (WORKING SET) : 0.150 REMARK 3 FREE R VALUE : 0.182 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.860 REMARK 3 FREE R VALUE TEST SET COUNT : 462 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 18.7981 - 2.5931 0.99 3209 121 0.1516 0.1715 REMARK 3 2 2.5931 - 2.0591 0.97 3052 184 0.1512 0.1822 REMARK 3 3 2.0591 - 1.8000 0.89 2791 157 0.1448 0.1975 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 16.600 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 5.86 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 9.23 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 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.013 1093 REMARK 3 ANGLE : 1.335 1471 REMARK 3 CHIRALITY : 0.047 144 REMARK 3 PLANARITY : 0.005 194 REMARK 3 DIHEDRAL : 13.958 388 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5JX4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAY-16. REMARK 100 THE DEPOSITION ID IS D_1000218939. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-AUG-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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 MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9547 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 18.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.6 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 23.6000 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) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 70.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.50 REMARK 200 R MERGE FOR SHELL (I) : 0.11400 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: PHASER REMARK 200 STARTING MODEL: 2HAX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 33.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.84 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, POLY(ETHYLENE REMARK 280 GLYCOL) METHYL ETHER 2000 30%, 0.2 M AMMONIUM SULFATE. PROTEIN REMARK 280 20 MG/ML IN 20 MM SODIUM PHOSPHATE., PH 4.6, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 22.03850 REMARK 290 SMTRY3 2 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 300 REMARK: DIMER CONFIRMED BY GEL FILTRATION 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 880 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 1.0 KCAL/MOL 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 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 -1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CE MET A 1 O HOH A 246 1.54 REMARK 500 O HOH B 275 O HOH B 278 2.04 REMARK 500 O HOH B 301 O HOH B 314 2.07 REMARK 500 NH1 ARG A 3 O HOH A 201 2.15 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 269 O HOH A 287 28510 1.94 REMARK 500 O HOH A 279 O HOH B 266 28410 2.09 REMARK 500 O HOH A 292 O HOH A 303 2859 2.13 REMARK 500 O HOH A 211 O HOH A 248 2849 2.15 REMARK 500 O HOH A 292 O HOH B 288 1554 2.15 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 102 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 103 DBREF 5JX4 A 1 64 UNP P41016 CSPB_BACCL 1 66 DBREF 5JX4 B 1 64 UNP P41016 CSPB_BACCL 1 66 SEQADV 5JX4 GLY A -1 UNP P41016 EXPRESSION TAG SEQADV 5JX4 HIS A 0 UNP P41016 EXPRESSION TAG SEQADV 5JX4 A UNP P41016 GLY 35 DELETION SEQADV 5JX4 A UNP P41016 GLU 36 DELETION SEQADV 5JX4 GLY B -1 UNP P41016 EXPRESSION TAG SEQADV 5JX4 HIS B 0 UNP P41016 EXPRESSION TAG SEQADV 5JX4 B UNP P41016 GLY 35 DELETION SEQADV 5JX4 B UNP P41016 GLU 36 DELETION SEQRES 1 A 66 GLY HIS MET GLN ARG GLY LYS VAL LYS TRP PHE ASN ASN SEQRES 2 A 66 GLU LYS GLY TYR GLY PHE ILE GLU VAL GLU GLY GLY SER SEQRES 3 A 66 ASP VAL PHE VAL HIS PHE THR ALA ILE GLN GLY PHE LYS SEQRES 4 A 66 THR LEU GLU GLU GLY GLN GLU VAL SER PHE GLU ILE VAL SEQRES 5 A 66 GLN GLY ASN ARG GLY PRO GLN ALA ALA ASN VAL VAL LYS SEQRES 6 A 66 LEU SEQRES 1 B 66 GLY HIS MET GLN ARG GLY LYS VAL LYS TRP PHE ASN ASN SEQRES 2 B 66 GLU LYS GLY TYR GLY PHE ILE GLU VAL GLU GLY GLY SER SEQRES 3 B 66 ASP VAL PHE VAL HIS PHE THR ALA ILE GLN GLY PHE LYS SEQRES 4 B 66 THR LEU GLU GLU GLY GLN GLU VAL SER PHE GLU ILE VAL SEQRES 5 B 66 GLN GLY ASN ARG GLY PRO GLN ALA ALA ASN VAL VAL LYS SEQRES 6 B 66 LEU HET SO4 A 101 5 HET SO4 A 102 5 HET SO4 B 101 5 HET SO4 B 102 5 HET SO4 B 103 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 5(O4 S 2-) FORMUL 8 HOH *221(H2 O) HELIX 1 AA1 THR A 31 ILE A 33 5 3 HELIX 2 AA2 THR B 31 ILE B 33 5 3 SHEET 1 AA1 6 GLN A 2 ASN A 10 0 SHEET 2 AA1 6 TYR A 15 GLU A 19 -1 O TYR A 15 N ASN A 10 SHEET 3 AA1 6 VAL A 26 HIS A 29 -1 O VAL A 26 N ILE A 18 SHEET 4 AA1 6 GLY A 55 LYS A 63 1 O ALA A 58 N PHE A 27 SHEET 5 AA1 6 GLU A 44 GLY A 52 -1 N GLY A 52 O GLY A 55 SHEET 6 AA1 6 GLN A 2 ASN A 10 -1 N GLN A 2 O PHE A 47 SHEET 1 AA2 5 VAL B 26 HIS B 29 0 SHEET 2 AA2 5 TYR B 15 GLU B 19 -1 N ILE B 18 O VAL B 26 SHEET 3 AA2 5 GLN B 2 ASN B 10 -1 N LYS B 5 O GLU B 19 SHEET 4 AA2 5 GLU B 44 GLY B 52 -1 O PHE B 47 N GLN B 2 SHEET 5 AA2 5 GLY B 55 LYS B 63 -1 O GLN B 57 N VAL B 50 SITE 1 AC1 7 GLY A 35 PHE A 36 LYS A 37 LYS A 63 SITE 2 AC1 7 HOH A 245 HOH A 247 GLY B -1 SITE 1 AC2 7 HOH A 223 HOH A 249 HOH A 275 GLY B -1 SITE 2 AC2 7 HIS B 0 HOH B 239 HOH B 244 SITE 1 AC3 9 HIS A 0 GLY B 35 PHE B 36 LYS B 37 SITE 2 AC3 9 LYS B 63 HOH B 235 HOH B 249 HOH B 260 SITE 3 AC3 9 HOH B 263 SITE 1 AC4 2 LYS B 37 HOH B 211 SITE 1 AC5 3 HOH B 219 HOH B 233 HOH B 276 CRYST1 34.009 44.077 36.484 90.00 99.28 90.00 P 1 21 1 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 0.029404 0.000000 0.004803 0.00000 SCALE2 0.000000 0.022688 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027773 0.00000