HEADER STRUCTURAL PROTEIN 02-OCT-19 6SZZ TITLE CRYSTAL STRUCTURE OF COLD SHOCK PROTEIN B (CSPB) CONTAINING THE TITLE 2 MODIFIED RESIDUE 4-F-TRP 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 DOMAIN, STRUCTURAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.ZHOU,O.MAYANS REVDAT 2 24-JAN-24 6SZZ 1 REMARK REVDAT 1 26-FEB-20 6SZZ 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. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.64 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 5879 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.210 REMARK 3 R VALUE (WORKING SET) : 0.208 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 306 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 39.6400 - 2.5800 1.00 2850 175 0.1962 0.2227 REMARK 3 2 2.5800 - 2.0500 1.00 2723 131 0.2775 0.3036 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) : 0.246 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 32.956 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 50.99 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 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 : 0.008 538 REMARK 3 ANGLE : 0.922 719 REMARK 3 CHIRALITY : 0.050 72 REMARK 3 PLANARITY : 0.005 96 REMARK 3 DIHEDRAL : 13.502 306 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): 15.5960 7.7835 11.6199 REMARK 3 T TENSOR REMARK 3 T11: 0.3770 T22: 0.3815 REMARK 3 T33: 0.4252 T12: -0.0316 REMARK 3 T13: 0.1096 T23: 0.0533 REMARK 3 L TENSOR REMARK 3 L11: 9.5491 L22: 8.7312 REMARK 3 L33: 8.9417 L12: 0.0100 REMARK 3 L13: 1.9669 L23: 1.9993 REMARK 3 S TENSOR REMARK 3 S11: -0.1333 S12: -1.0717 S13: -0.4506 REMARK 3 S21: 0.7017 S22: -0.0672 S23: 0.2363 REMARK 3 S31: 0.5723 S32: -0.3802 S33: 0.1480 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 6SZZ 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_1292104584. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 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 : X06DA 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 PILATUS 2M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 5913 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 39.640 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 24.75 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.07500 REMARK 200 FOR THE DATA SET : 28.8900 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 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) : 2.73500 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 (%): 58.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.93 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PROPANE PH 7.0,1.2 M REMARK 280 SODIUM CITRATE TRIBASIC DIHYDRATE, 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 27.56000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.02500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.02500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 41.34000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.02500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.02500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 13.78000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.02500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.02500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 41.34000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.02500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.02500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 13.78000 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 27.56000 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: 400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 4650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 21 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 GOL 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 DBREF1 6SZZ A 1 67 UNP A0A063XII3_BACIU DBREF2 6SZZ A A0A063XII3 1 67 SEQRES 1 A 67 MET LEU GLU GLY LYS VAL LYS 4FW PHE ASN SER GLU LYS SEQRES 2 A 67 GLY PHE GLY PHE ILE GLU VAL GLU GLY GLN ASP ASP VAL SEQRES 3 A 67 PHE VAL HIS PHE SER ALA ILE GLN GLY GLU GLY PHE LYS SEQRES 4 A 67 THR LEU GLU GLU GLY GLN ALA VAL SER PHE GLU ILE VAL SEQRES 5 A 67 GLU GLY ASN ARG GLY PRO GLN ALA ALA ASN VAL THR LYS SEQRES 6 A 67 GLU ALA MODRES 6SZZ 4FW A 8 TRP MODIFIED RESIDUE HET 4FW A 8 15 HET GOL A 101 6 HET GOL A 102 6 HETNAM 4FW 4-FLUOROTRYPTOPHANE HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 4FW C11 H11 F N2 O2 FORMUL 2 GOL 2(C3 H8 O3) FORMUL 4 HOH *18(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 PHE 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 PHE A 49 N LEU A 2 SHEET 5 AA1 5 GLY A 57 LYS A 65 -1 O THR A 64 N SER A 48 LINK C LYS A 7 N 4FW A 8 1555 1555 1.33 LINK C 4FW A 8 N PHE A 9 1555 1555 1.33 SITE 1 AC1 3 GLU A 12 PHE A 38 GLN A 59 SITE 1 AC2 3 LYS A 7 4FW A 8 ASP A 25 CRYST1 56.050 56.050 55.120 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 0.017841 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017841 0.000000 0.00000 SCALE3 0.000000 0.000000 0.018142 0.00000