HEADER DNA BINDING PROTEIN 07-DEC-20 7B5U TITLE RCK_C DOMAIN DIMER OF S.AGALACTIAE BUSR IN COMPLEX WITH C-DI-AMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: GNTR FAMILY TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRANSCRIPTIONAL REGULATOR,GNTR FAMILY; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: G133 RESULTS FROM N-TERMINAL TAG SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS AGALACTIAE; SOURCE 3 ORGANISM_TAXID: 1311; SOURCE 4 GENE: BM110_ORF1201, AX245_01365, C6N10_09995, F5043_05515, SOURCE 5 GD434_05225, RDF_1124; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 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 7B5U 1 REMARK REVDAT 3 13-OCT-21 7B5U 1 REMARK REVDAT 2 06-OCT-21 7B5U 1 JRNL REVDAT 1 11-AUG-21 7B5U 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. 1.20 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.67 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.430 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 41497 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.132 REMARK 3 R VALUE (WORKING SET) : 0.131 REMARK 3 FREE R VALUE : 0.155 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.630 REMARK 3 FREE R VALUE TEST SET COUNT : 1923 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 17.6700 - 2.8900 0.98 2930 158 0.1431 0.1530 REMARK 3 2 2.8900 - 2.2900 0.98 2920 158 0.1456 0.1648 REMARK 3 3 2.2900 - 2.0000 0.98 2898 150 0.1345 0.1598 REMARK 3 4 2.0000 - 1.8200 0.98 2897 128 0.1328 0.1418 REMARK 3 5 1.8200 - 1.6900 0.96 2852 125 0.1302 0.1529 REMARK 3 6 1.6900 - 1.5900 0.97 2864 146 0.1240 0.1542 REMARK 3 7 1.5900 - 1.5100 0.96 2837 125 0.1171 0.1445 REMARK 3 8 1.5100 - 1.4500 0.96 2826 135 0.1146 0.1536 REMARK 3 9 1.4500 - 1.3900 0.96 2860 119 0.1134 0.1539 REMARK 3 10 1.3900 - 1.3400 0.95 2847 128 0.1186 0.1519 REMARK 3 11 1.3400 - 1.3000 0.93 2759 135 0.1144 0.1597 REMARK 3 12 1.3000 - 1.2600 0.93 2733 143 0.1149 0.1694 REMARK 3 13 1.2600 - 1.2300 0.94 2732 141 0.1136 0.1693 REMARK 3 14 1.2300 - 1.2000 0.88 2619 132 0.1141 0.1396 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) : 0.070 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 14.940 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.49 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.88 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 7B5U 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_1292112576. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.6 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 : P14 (MX2) REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 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 : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 41497 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 17.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.4 REMARK 200 DATA REDUNDANCY : 6.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 33.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 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) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 14.86 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 7B5T REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 37.25 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NA-ACETATE, 3% (W/V) PEG4000, REMARK 280 PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 30.47350 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 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: 1770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8010 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -16.0 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 B 133 REMARK 465 PRO B 134 REMARK 465 MET B 211 REMARK 465 GLY B 212 REMARK 465 LEU B 213 REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 554 DISTANCE = 6.15 ANGSTROMS REMARK 525 HOH B 423 DISTANCE = 6.28 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 2BA A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7B5T RELATED DB: PDB REMARK 900 FULL LENGTH PROTEIN BUSR REMARK 900 RELATED ID: SASDK74 RELATED DB: SASBDB REMARK 900 SAME MOLECULE BUT WITHOUT LIGAND DBREF 7B5U A 134 213 UNP K0JNC6 K0JNC6_STRAG 134 213 DBREF 7B5U B 134 213 UNP K0JNC6 K0JNC6_STRAG 134 213 SEQADV 7B5U GLY A 133 UNP K0JNC6 EXPRESSION TAG SEQADV 7B5U GLY B 133 UNP K0JNC6 EXPRESSION TAG SEQRES 1 A 81 GLY PRO LEU ALA PRO TYR GLU ILE ILE VAL SER GLU ASP SEQRES 2 A 81 SER GLU HIS LEU GLY LYS SER ILE GLY GLU LEU ASN VAL SEQRES 3 A 81 TRP HIS GLN THR GLY ALA THR ILE VAL ALA ILE GLU HIS SEQRES 4 A 81 GLU GLY LYS PHE ILE VAL SER PRO GLY PRO PHE SER VAL SEQRES 5 A 81 ILE GLU GLN GLY ASP HIS ILE PHE PHE VAL GLY ASP GLU SEQRES 6 A 81 ASP VAL TYR ALA ARG MET LYS THR TYR PHE ASN LEU ARG SEQRES 7 A 81 MET GLY LEU SEQRES 1 B 81 GLY PRO LEU ALA PRO TYR GLU ILE ILE VAL SER GLU ASP SEQRES 2 B 81 SER GLU HIS LEU GLY LYS SER ILE GLY GLU LEU ASN VAL SEQRES 3 B 81 TRP HIS GLN THR GLY ALA THR ILE VAL ALA ILE GLU HIS SEQRES 4 B 81 GLU GLY LYS PHE ILE VAL SER PRO GLY PRO PHE SER VAL SEQRES 5 B 81 ILE GLU GLN GLY ASP HIS ILE PHE PHE VAL GLY ASP GLU SEQRES 6 B 81 ASP VAL TYR ALA ARG MET LYS THR TYR PHE ASN LEU ARG SEQRES 7 B 81 MET GLY LEU HET 2BA A 301 44 HETNAM 2BA (2R,3R,3AS,5R,7AR,9R,10R,10AS,12R,14AR)-2,9-BIS(6- HETNAM 2 2BA AMINO-9H-PURIN-9-YL)OCTAHYDRO-2H,7H-DIFURO[3,2-D:3', HETNAM 3 2BA 2'-J][1,3,7,9,2,8 ]TETRAOXADIPHOSPHACYCLODODECINE-3,5, HETNAM 4 2BA 10,12-TETROL 5,12-DIOXIDE HETSYN 2BA BIS-(3',5')-CYCLIC-DIMERIC-ADENOSINE-MONOPHOSPHATE FORMUL 3 2BA C20 H24 N10 O12 P2 FORMUL 4 HOH *277(H2 O) HELIX 1 AA1 ILE A 153 ASN A 157 1 5 HELIX 2 AA2 ASN A 157 GLY A 163 1 7 HELIX 3 AA3 ASP A 196 PHE A 207 1 12 HELIX 4 AA4 ILE B 153 ASN B 157 1 5 HELIX 5 AA5 ASN B 157 GLY B 163 1 7 HELIX 6 AA6 ASP B 196 PHE B 207 1 12 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 GLU A 170 O HIS A 190 SHEET 4 AA1 4 LYS A 174 VAL A 177 -1 O LYS A 174 N HIS A 171 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 SHEET 1 AA3 4 TYR B 138 ILE B 141 0 SHEET 2 AA3 4 HIS B 190 VAL B 194 -1 O PHE B 193 N TYR B 138 SHEET 3 AA3 4 THR B 165 HIS B 171 -1 N ALA B 168 O PHE B 192 SHEET 4 AA3 4 LYS B 174 VAL B 177 -1 O LYS B 174 N HIS B 171 SHEET 1 AA4 2 LYS B 151 SER B 152 0 SHEET 2 AA4 2 VAL B 184 ILE B 185 -1 O ILE B 185 N LYS B 151 SITE 1 AC1 27 ILE A 153 GLY A 154 ASN A 157 VAL A 158 SITE 2 AC1 27 TRP A 159 HIS A 160 ALA A 164 THR A 165 SITE 3 AC1 27 ILE A 166 PRO A 181 HOH A 420 HOH A 423 SITE 4 AC1 27 HOH A 425 HOH A 430 HOH A 436 HOH A 440 SITE 5 AC1 27 ILE B 153 GLY B 154 ASN B 157 VAL B 158 SITE 6 AC1 27 TRP B 159 HIS B 160 ALA B 164 THR B 165 SITE 7 AC1 27 ILE B 166 PRO B 181 HOH B 341 CRYST1 33.164 60.947 35.714 90.00 101.73 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 0.030153 0.000000 0.006263 0.00000 SCALE2 0.000000 0.016408 0.000000 0.00000 SCALE3 0.000000 0.000000 0.028598 0.00000