HEADER STRUCTURAL PROTEIN 02-OCT-19 6T00 TITLE CRYSTAL STRUCTURE OF COLD SHOCK PROTEIN B (CSP-B) CONTAINING 4-F-PHE TITLE 2 MODIFIED RESIDUES COMPND MOL_ID: 1; COMPND 2 MOLECULE: COLD SHOCK PROTEIN CSPD; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: COLD-SHOCK PROTEIN,COLD-SHOCK PROTEIN CSPB,MAJOR COLD SHOCK COMPND 5 PROTEIN,PUTATIVE COLD-SHOCK DNA-BINDING PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: B4122_0412, B4417_4327, CJ481_22435, DFO69_3150, ETA10_05025, SOURCE 5 ETK61_05130, ETL41_18150, FA024_03420, SC09_CONTIG19ORF00064; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS FLUORINE COLD SHOCK PROTEIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.ZHOU,O.MAYANS REVDAT 2 24-JAN-24 6T00 1 REMARK REVDAT 1 26-FEB-20 6T00 0 JRNL AUTH H.WELTE,T.ZHOU,X.MIHAJLENKO,O.MAYANS,M.KOVERMANN JRNL TITL WHAT DOES FLUORINE DO TO A PROTEIN? THERMODYNAMIC, AND JRNL TITL 2 HIGHLY-RESOLVED STRUCTURAL INSIGHTS INTO FLUORINE-LABELLED JRNL TITL 3 VARIANTS OF THE COLD SHOCK PROTEIN. JRNL REF SCI REP V. 10 2640 2020 JRNL REFN ESSN 2045-2322 JRNL PMID 32060391 JRNL DOI 10.1038/S41598-020-59446-W REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.15.2_3472 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 5518 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.201 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.890 REMARK 3 FREE R VALUE TEST SET COUNT : 270 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 39.7900 - 2.6500 1.00 2697 141 0.1866 0.2373 REMARK 3 2 2.6500 - 2.1000 1.00 2551 129 0.2641 0.3237 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) : 0.278 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.933 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 63.45 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 : 0.010 547 REMARK 3 ANGLE : 1.232 736 REMARK 3 CHIRALITY : 0.058 72 REMARK 3 PLANARITY : 0.006 95 REMARK 3 DIHEDRAL : 14.005 301 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: (CHAIN 'A' AND RESID 1 THROUGH 67) REMARK 3 ORIGIN FOR THE GROUP (A): -7.7812 14.6095 -2.4786 REMARK 3 T TENSOR REMARK 3 T11: 0.3839 T22: 0.3460 REMARK 3 T33: 0.3188 T12: 0.0475 REMARK 3 T13: -0.0221 T23: 0.0197 REMARK 3 L TENSOR REMARK 3 L11: 8.4586 L22: 8.4079 REMARK 3 L33: 9.1371 L12: -0.2112 REMARK 3 L13: -3.0866 L23: 2.1511 REMARK 3 S TENSOR REMARK 3 S11: -0.1274 S12: -0.4808 S13: -0.1547 REMARK 3 S21: 0.6617 S22: -0.0235 S23: -0.3002 REMARK 3 S31: 0.6399 S32: 0.2970 S33: 0.1674 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 6T00 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-OCT-19. REMARK 100 THE DEPOSITION ID IS D_1292104617. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5551 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 39.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.43 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08700 REMARK 200 FOR THE DATA SET : 17.2300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.20 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 2.25200 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: 1CSP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM CHES/ SODIUM HYDROXIDE PH 9.5, REMARK 280 1000 MM SODIUM CITRATE TRIBASIC, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 291K 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 28.85500 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 27.47000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 27.47000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.28250 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 27.47000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 27.47000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 14.42750 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 27.47000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 27.47000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.28250 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 27.47000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 27.47000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 14.42750 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 28.85500 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 380 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 2.0 KCAL/MOL 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU A 3 CG CD OE1 OE2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NHE A 101 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 102 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6SZZ RELATED DB: PDB DBREF1 6T00 A 1 66 UNP A0A063XII3_BACIU DBREF2 6T00 A A0A063XII3 1 66 SEQRES 1 A 66 MET LEU GLU GLY LYS VAL LYS TRP PFF ASN SER GLU LYS SEQRES 2 A 66 GLY PFF GLY PFF ILE GLU VAL GLU GLY GLN ASP ASP VAL SEQRES 3 A 66 PFF VAL HIS PFF SER ALA ILE GLN GLY GLU GLY PFF LYS SEQRES 4 A 66 THR LEU GLU GLU GLY GLN ALA VAL SER PFF GLU ILE VAL SEQRES 5 A 66 GLU GLY ASN ARG GLY PRO GLN ALA ALA ASN VAL THR LYS SEQRES 6 A 66 GLU MODRES 6T00 PFF A 9 PHE MODIFIED RESIDUE MODRES 6T00 PFF A 15 PHE MODIFIED RESIDUE MODRES 6T00 PFF A 17 PHE MODIFIED RESIDUE MODRES 6T00 PFF A 27 PHE MODIFIED RESIDUE MODRES 6T00 PFF A 30 PHE MODIFIED RESIDUE MODRES 6T00 PFF A 38 PHE MODIFIED RESIDUE MODRES 6T00 PFF A 49 PHE MODIFIED RESIDUE HET PFF A 9 12 HET PFF A 15 12 HET PFF A 17 12 HET PFF A 27 12 HET PFF A 30 12 HET PFF A 38 12 HET PFF A 49 12 HET NHE A 101 13 HET GOL A 102 6 HETNAM PFF 4-FLUORO-L-PHENYLALANINE HETNAM NHE 2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID HETNAM GOL GLYCEROL HETSYN NHE N-CYCLOHEXYLTAURINE; CHES HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 PFF 7(C9 H10 F N O2) FORMUL 2 NHE C8 H17 N O3 S FORMUL 3 GOL C3 H8 O3 FORMUL 4 HOH *17(H2 O) HELIX 1 AA1 SER A 31 ILE A 33 5 3 SHEET 1 AA1 5 VAL A 26 HIS A 29 0 SHEET 2 AA1 5 PFF A 15 GLU A 19 -1 N ILE A 18 O VAL A 26 SHEET 3 AA1 5 LEU A 2 ASN A 10 -1 N LYS A 5 O GLU A 19 SHEET 4 AA1 5 ALA A 46 GLY A 54 -1 O PFF A 49 N LEU A 2 SHEET 5 AA1 5 GLY A 57 LYS A 65 -1 O ALA A 61 N GLU A 50 LINK C TRP A 8 N PFF A 9 1555 1555 1.33 LINK C PFF A 9 N ASN A 10 1555 1555 1.33 LINK C GLY A 14 N PFF A 15 1555 1555 1.33 LINK C PFF A 15 N GLY A 16 1555 1555 1.33 LINK C GLY A 16 N PFF A 17 1555 1555 1.33 LINK C PFF A 17 N ILE A 18 1555 1555 1.33 LINK C VAL A 26 N PFF A 27 1555 1555 1.33 LINK C PFF A 27 N VAL A 28 1555 1555 1.33 LINK C HIS A 29 N PFF A 30 1555 1555 1.34 LINK C PFF A 30 N SER A 31 1555 1555 1.33 LINK C GLY A 37 N PFF A 38 1555 1555 1.32 LINK C PFF A 38 N LYS A 39 1555 1555 1.33 LINK C SER A 48 N PFF A 49 1555 1555 1.33 LINK C PFF A 49 N GLU A 50 1555 1555 1.34 SITE 1 AC1 5 SER A 11 GLU A 12 PFF A 15 PFF A 27 SITE 2 AC1 5 HIS A 29 SITE 1 AC2 1 ASN A 55 CRYST1 54.940 54.940 57.710 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 0.018202 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018202 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017328 0.00000