HEADER DNA BINDING PROTEIN 07-DEC-20 7B5W TITLE RCK_C DOMAIN OF S.AGALACTIAE BUSR IN LIGAND-FREE STATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GNTR FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: TRANSCRIPTIONAL REGULATOR,GNTR FAMILY; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: N-TERMINAL RESIDUES MAHHHHHHSAALEVLFQG BELONG TO COMPND 7 PURIFICATION TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS AGALACTIAE; SOURCE 3 ORGANISM_TAXID: 1311; SOURCE 4 GENE: BM110_ORF1201, DX05_06300, F5F86_05185, NCTC6175_01043; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS EFFECTOR BINDING DOMAIN, RCK_C, DNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.M.BANDERA,G.WITTE REVDAT 4 31-JAN-24 7B5W 1 REMARK REVDAT 3 13-OCT-21 7B5W 1 REMARK REVDAT 2 06-OCT-21 7B5W 1 JRNL REVDAT 1 11-AUG-21 7B5W 0 JRNL AUTH A.M.BANDERA,J.BARTHO,K.LAMMENS,D.J.DREXLER,J.KLEINSCHWARZER, JRNL AUTH 2 K.P.HOPFNER,G.WITTE JRNL TITL BUSR SENSES BIPARTITE DNA BINDING MOTIFS BY A UNIQUE JRNL TITL 2 MOLECULAR RULER ARCHITECTURE. JRNL REF NUCLEIC ACIDS RES. V. 49 10166 2021 JRNL REFN ESSN 1362-4962 JRNL PMID 34432045 JRNL DOI 10.1093/NAR/GKAB736 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.18.2_3874 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) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 18.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 39372 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.200 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 1906 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 18.0300 - 2.4100 0.99 2742 144 0.1748 0.2091 REMARK 3 2 2.4100 - 1.9100 1.00 2695 152 0.1813 0.2029 REMARK 3 3 1.9100 - 1.6700 0.98 2663 145 0.1967 0.2232 REMARK 3 4 1.6700 - 1.5200 1.00 2709 131 0.1946 0.2236 REMARK 3 5 1.5200 - 1.4100 1.00 2697 119 0.2068 0.2595 REMARK 3 6 1.4100 - 1.3300 0.99 2685 125 0.2139 0.2575 REMARK 3 7 1.3300 - 1.2600 0.99 2656 145 0.2205 0.2345 REMARK 3 8 1.2600 - 1.2100 0.99 2651 145 0.2361 0.2648 REMARK 3 9 1.2100 - 1.1600 1.00 2690 159 0.2383 0.2560 REMARK 3 10 1.1600 - 1.1200 0.98 2659 106 0.2563 0.2352 REMARK 3 11 1.1200 - 1.0800 0.99 2649 137 0.2698 0.3046 REMARK 3 12 1.0800 - 1.0500 1.00 2674 141 0.2844 0.3185 REMARK 3 13 1.0500 - 1.0300 1.00 2665 124 0.2923 0.3081 REMARK 3 14 1.0300 - 1.0000 0.97 2628 133 0.3430 0.3456 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.340 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.40 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 : 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 7B5W COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-DEC-20. REMARK 100 THE DEPOSITION ID IS D_1292112586. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-JUN-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PETRA III, EMBL C/O DESY REMARK 200 BEAMLINE : P13 (MX1) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39372 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 18.030 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : 6.400 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.04 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.30 REMARK 200 R MERGE FOR SHELL (I) : NULL 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: 7B5T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 27.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM BIS-TRIS, 18% (W/V) PEG MME REMARK 280 5000, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 23.13000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.20500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 23.13000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 20.20500 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 10780 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 361 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 393 LIES ON A SPECIAL POSITION. 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 MET A 116 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 LEU A 149 -155.85 -116.47 REMARK 500 ASN A 208 -63.95 -122.64 REMARK 500 ARG A 210 120.01 73.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5B5T RELATED DB: PDB REMARK 900 FULL-LENGTH STRUCTURE OF BUSR REMARK 900 RELATED ID: 7B5U RELATED DB: PDB REMARK 900 RCK_C DOMAIN DIMER WITH C-DI-AMP REMARK 900 RELATED ID: SASDK74 RELATED DB: SASBDB REMARK 900 SAS DATA WITHOUT LIGAND DBREF 7B5W A 134 213 UNP I7JWA3 I7JWA3_STRAG 134 213 SEQADV 7B5W MET A 116 UNP I7JWA3 INITIATING METHIONINE SEQADV 7B5W ALA A 117 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W HIS A 118 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W HIS A 119 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W HIS A 120 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W HIS A 121 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W HIS A 122 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W HIS A 123 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W SER A 124 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W ALA A 125 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W ALA A 126 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W LEU A 127 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W GLU A 128 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W VAL A 129 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W LEU A 130 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W PHE A 131 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W GLN A 132 UNP I7JWA3 EXPRESSION TAG SEQADV 7B5W GLY A 133 UNP I7JWA3 EXPRESSION TAG SEQRES 1 A 98 MET ALA HIS HIS HIS HIS HIS HIS SER ALA ALA LEU GLU SEQRES 2 A 98 VAL LEU PHE GLN GLY PRO LEU ALA PRO TYR GLU ILE ILE SEQRES 3 A 98 VAL SER GLU ASP SER GLU HIS LEU GLY LYS SER ILE GLY SEQRES 4 A 98 GLU LEU ASN VAL TRP HIS GLN THR GLY ALA THR ILE VAL SEQRES 5 A 98 ALA ILE GLU HIS GLU GLY LYS PHE ILE VAL SER PRO GLY SEQRES 6 A 98 PRO PHE SER VAL ILE GLU GLN GLY ASP HIS ILE PHE PHE SEQRES 7 A 98 VAL GLY ASP GLU ASP VAL TYR ALA ARG MET LYS THR TYR SEQRES 8 A 98 PHE ASN LEU ARG MET GLY LEU FORMUL 2 HOH *98(H2 O) HELIX 1 AA1 SER A 124 GLY A 133 1 10 HELIX 2 AA2 ILE A 153 ASN A 157 1 5 HELIX 3 AA3 ASN A 157 GLY A 163 1 7 HELIX 4 AA4 ASP A 196 ASN A 208 1 13 SHEET 1 AA1 4 TYR A 138 ILE A 141 0 SHEET 2 AA1 4 HIS A 190 VAL A 194 -1 O PHE A 193 N TYR A 138 SHEET 3 AA1 4 THR A 165 HIS A 171 -1 N ALA A 168 O PHE A 192 SHEET 4 AA1 4 LYS A 174 VAL A 177 -1 O ILE A 176 N ILE A 169 SHEET 1 AA2 2 LYS A 151 SER A 152 0 SHEET 2 AA2 2 VAL A 184 ILE A 185 -1 O ILE A 185 N LYS A 151 CRYST1 46.260 40.410 41.010 90.00 103.21 90.00 C 1 2 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 0.021617 0.000000 0.005075 0.00000 SCALE2 0.000000 0.024746 0.000000 0.00000 SCALE3 0.000000 0.000000 0.025047 0.00000