HEADER DNA BINDING PROTEIN 01-SEP-20 7CX5 TITLE CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF BACILLUS SUBTILIS CSSR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATORY PROTEIN CSSR; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS (STRAIN 168); SOURCE 3 ORGANISM_TAXID: 224308; SOURCE 4 STRAIN: 168; SOURCE 5 GENE: CSSR, BSU33010; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PETDEUT-1 KEYWDS TWO-COMPONENT SYSTEM, RESPONSE REGULATOR, DNA BINDING DOMAIN, KEYWDS 2 ENVELOPE STRESS, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR P.DAHAL,D.Y.KIM,E.KWON REVDAT 2 27-MAR-24 7CX5 1 REMARK REVDAT 1 21-APR-21 7CX5 0 JRNL AUTH P.DAHAL,D.Y.KIM,E.KWON JRNL TITL CRYSTAL STRUCTURE OF THE DNA-BINDING DOMAIN OF BACILLUS JRNL TITL 2 SUBTILIS CSSR. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 555 26 2021 JRNL REFN ESSN 1090-2104 JRNL PMID 33812055 JRNL DOI 10.1016/J.BBRC.2021.03.101 REMARK 2 REMARK 2 RESOLUTION. 1.07 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18_3855 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.07 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 40973 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.195 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.980 REMARK 3 FREE R VALUE TEST SET COUNT : 2040 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 39.3200 - 2.6300 0.97 2741 142 0.1996 0.2003 REMARK 3 2 2.6300 - 2.0900 0.98 2640 142 0.1878 0.1911 REMARK 3 3 2.0900 - 1.8200 0.98 2639 129 0.1839 0.1902 REMARK 3 4 1.8200 - 1.6600 0.99 2615 140 0.1760 0.1950 REMARK 3 5 1.6600 - 1.5400 0.98 2599 120 0.1700 0.1759 REMARK 3 6 1.5400 - 1.4500 0.98 2597 132 0.1706 0.1959 REMARK 3 7 1.4500 - 1.3700 0.98 2574 135 0.1764 0.1969 REMARK 3 8 1.3700 - 1.3100 0.99 2582 138 0.1804 0.1979 REMARK 3 9 1.3100 - 1.2600 0.98 2586 127 0.1788 0.2002 REMARK 3 10 1.2600 - 1.2200 0.99 2560 141 0.1860 0.2031 REMARK 3 11 1.2200 - 1.1800 0.99 2568 144 0.2041 0.1964 REMARK 3 12 1.1800 - 1.1500 0.99 2606 141 0.2180 0.2175 REMARK 3 13 1.1500 - 1.1200 0.98 2510 142 0.2490 0.2590 REMARK 3 14 1.1200 - 1.0900 0.98 2557 146 0.2941 0.3792 REMARK 3 15 1.0900 - 1.0700 0.98 2559 121 0.3531 0.3510 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.120 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.890 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.35 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 10.9000 4.2090 8.6359 REMARK 3 T TENSOR REMARK 3 T11: 0.0616 T22: 0.0578 REMARK 3 T33: 0.0573 T12: 0.0053 REMARK 3 T13: 0.0041 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.3109 L22: 0.2153 REMARK 3 L33: 0.4400 L12: -0.0402 REMARK 3 L13: 0.1213 L23: -0.1453 REMARK 3 S TENSOR REMARK 3 S11: -0.0011 S12: -0.0179 S13: -0.0187 REMARK 3 S21: -0.0023 S22: -0.0129 S23: 0.0343 REMARK 3 S31: 0.0481 S32: 0.0189 S33: -0.0072 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 7CX5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018386. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PAL/PLS REMARK 200 BEAMLINE : 11C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41035 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.070 REMARK 200 RESOLUTION RANGE LOW (A) : 39.320 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 5.750 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.07 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.08 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.65500 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: SAD REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.05 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2 M LITHIUM SULFATE, 2% (V/V) PEG400, REMARK 280 AND 0.1 M TRIS/HCL PH 8.5, MICROBATCH, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-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 14.70500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.49500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.37000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.49500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 14.70500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.37000 REMARK 290 SMTRY3 4 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 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: 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 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 131 REMARK 465 SER A 132 REMARK 465 ALA A 133 REMARK 465 VAL A 134 REMARK 465 SER A 135 REMARK 465 SER A 224 REMARK 465 SER A 225 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 O HOH A 334 O HOH A 369 1.89 REMARK 500 O HOH A 391 O HOH A 405 1.90 REMARK 500 OD2 ASP A 162 O HOH A 301 1.93 REMARK 500 O HOH A 308 O HOH A 414 1.96 REMARK 500 O HOH A 316 O HOH A 323 1.98 REMARK 500 O HOH A 301 O HOH A 395 1.98 REMARK 500 O HOH A 419 O HOH A 421 2.00 REMARK 500 O HOH A 344 O HOH A 384 2.02 REMARK 500 O HOH A 377 O HOH A 380 2.03 REMARK 500 O HOH A 332 O HOH A 338 2.04 REMARK 500 O HOH A 307 O HOH A 385 2.09 REMARK 500 O HOH A 409 O HOH A 423 2.12 REMARK 500 O HOH A 308 O HOH A 422 2.13 REMARK 500 NZ LYS A 171 O HOH A 302 2.14 REMARK 500 O HOH A 399 O HOH A 425 2.16 REMARK 500 O HOH A 307 O HOH A 332 2.18 REMARK 500 O HOH A 407 O HOH A 436 2.18 REMARK 500 O HOH A 305 O HOH A 423 2.18 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 333 O HOH A 382 4455 2.02 REMARK 500 O HOH A 359 O HOH A 405 2654 2.04 REMARK 500 O HOH A 319 O HOH A 377 3655 2.13 REMARK 500 REMARK 500 REMARK: NULL 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 HIS A 170 56.58 -141.21 REMARK 500 PHE A 218 -58.06 -135.97 REMARK 500 REMARK 500 REMARK: NULL DBREF 7CX5 A 133 225 UNP O32192 CSSR_BACSU 133 225 SEQADV 7CX5 GLY A 131 UNP O32192 EXPRESSION TAG SEQADV 7CX5 SER A 132 UNP O32192 EXPRESSION TAG SEQRES 1 A 95 GLY SER ALA VAL SER SER TYR ARG VAL ALA GLU ASP ALA SEQRES 2 A 95 ARG GLU VAL TYR ASP GLU ASN GLY ASN ILE ILE ASN LEU SEQRES 3 A 95 THR SER LYS GLU PHE ASP LEU LEU LEU LEU PHE ILE HIS SEQRES 4 A 95 HIS LYS GLY HIS PRO TYR SER ARG GLU ASP ILE LEU LEU SEQRES 5 A 95 LYS VAL TRP GLY HIS ASP TYR PHE GLY THR ASP ARG VAL SEQRES 6 A 95 VAL ASP ASP LEU VAL ARG ARG LEU ARG ARG LYS MET PRO SEQRES 7 A 95 GLU LEU LYS VAL GLU THR ILE TYR GLY PHE GLY TYR ARG SEQRES 8 A 95 MET MET SER SER FORMUL 2 HOH *137(H2 O) HELIX 1 AA1 THR A 157 HIS A 169 1 13 HELIX 2 AA2 ARG A 177 TRP A 185 1 9 HELIX 3 AA3 ASP A 193 MET A 207 1 15 SHEET 1 AA1 3 TYR A 137 ALA A 140 0 SHEET 2 AA1 3 GLU A 145 ASP A 148 -1 O TYR A 147 N ARG A 138 SHEET 3 AA1 3 ILE A 153 ILE A 154 -1 O ILE A 154 N VAL A 146 SHEET 1 AA2 3 TYR A 175 SER A 176 0 SHEET 2 AA2 3 GLY A 219 MET A 222 -1 O TYR A 220 N TYR A 175 SHEET 3 AA2 3 VAL A 212 ILE A 215 -1 N ILE A 215 O GLY A 219 CRYST1 29.410 52.740 58.990 90.00 90.00 90.00 P 21 21 21 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 0.034002 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018961 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016952 0.00000