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 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 MASTER 254 0 5 2 11 0 9 6 0 0 0 12 END