HEADER TRANSCRIPTION 26-OCT-09 3KEO TITLE CRYSTAL STRUCTURE OF A REX-FAMILY TRANSCRIPTIONAL REGULATORY PROTEIN TITLE 2 FROM STREPTOCOCCUS AGALACTIAE COMPLEXED WITH NAD+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: REDOX-SENSING TRANSCRIPTIONAL REPRESSOR REX; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STREPTOCOCCUS AGALACTIAE SEROGROUP III; SOURCE 3 ORGANISM_TAXID: 216495; SOURCE 4 STRAIN: NEM316; SOURCE 5 GENE: GBS1167, REX; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: TUNER (DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET101 KEYWDS DNA BINDING PROTEIN, WINGED HELIX, ROSSMANN FOLD, NAD+, REPRESSOR, KEYWDS 2 TRANSCRIPTION, TRANSCRIPTION REGULATION, REDOX SENSING EXPDTA X-RAY DIFFRACTION AUTHOR S.THIYAGARAJAN,D.LOGAN,C.VON WACHENFELDT REVDAT 4 01-NOV-23 3KEO 1 REMARK REVDAT 3 08-SEP-21 3KEO 1 JRNL REMARK LINK REVDAT 2 16-MAY-18 3KEO 1 REMARK REVDAT 1 10-NOV-10 3KEO 0 JRNL AUTH T.FRANZA,A.ROGSTAM,S.THIYAGARAJAN,M.J.SULLIVAN, JRNL AUTH 2 A.DERRE-BOBILLOT,M.C.BAUER,K.G.K.GOH,V.DA CUNHA,P.GLASER, JRNL AUTH 3 D.T.LOGAN,G.C.ULETT,C.VON WACHENFELDT,P.GAUDU JRNL TITL NAD+ POOL DEPLETION AS A SIGNAL FOR THE REX REGULON INVOLVED JRNL TITL 2 IN STREPTOCOCCUS AGALACTIAE VIRULENCE. JRNL REF PLOS PATHOG. V. 17 09791 2021 JRNL REFN ESSN 1553-7374 JRNL PMID 34370789 JRNL DOI 10.1371/JOURNAL.PPAT.1009791 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0072 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.07 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 58774 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.178 REMARK 3 R VALUE (WORKING SET) : 0.175 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3147 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3920 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.22 REMARK 3 BIN R VALUE (WORKING SET) : 0.2480 REMARK 3 BIN FREE R VALUE SET COUNT : 208 REMARK 3 BIN FREE R VALUE : 0.3680 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3258 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 96 REMARK 3 SOLVENT ATOMS : 544 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 11.49 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : 0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.108 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.092 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.061 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.624 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.946 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3360 ; 0.025 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2212 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4568 ; 2.038 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5382 ; 1.101 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 416 ; 5.406 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 146 ;39.295 ;24.384 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 557 ;13.137 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;21.740 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 531 ; 0.137 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3698 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 681 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2051 ; 2.190 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 845 ; 0.944 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3304 ; 3.176 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1309 ; 4.639 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1261 ; 6.375 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 5572 ; 2.268 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 552 ;10.687 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 5506 ; 4.262 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 6 A 85 REMARK 3 ORIGIN FOR THE GROUP (A): 26.6554 29.7728 26.4765 REMARK 3 T TENSOR REMARK 3 T11: 0.0495 T22: 0.0182 REMARK 3 T33: 0.0552 T12: -0.0241 REMARK 3 T13: -0.0075 T23: 0.0027 REMARK 3 L TENSOR REMARK 3 L11: 0.4768 L22: 0.8682 REMARK 3 L33: 0.7917 L12: -0.1853 REMARK 3 L13: -0.0710 L23: 0.4207 REMARK 3 S TENSOR REMARK 3 S11: -0.0146 S12: 0.0276 S13: -0.0708 REMARK 3 S21: -0.0536 S22: 0.0274 S23: 0.0355 REMARK 3 S31: 0.0913 S32: -0.0779 S33: -0.0128 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 6 B 85 REMARK 3 ORIGIN FOR THE GROUP (A): 44.9523 29.2147 46.2330 REMARK 3 T TENSOR REMARK 3 T11: 0.0439 T22: 0.0147 REMARK 3 T33: 0.0393 T12: 0.0194 REMARK 3 T13: -0.0034 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.6604 L22: 0.8317 REMARK 3 L33: 1.0697 L12: 0.2118 REMARK 3 L13: -0.3147 L23: -0.6913 REMARK 3 S TENSOR REMARK 3 S11: -0.0126 S12: -0.0593 S13: -0.0705 REMARK 3 S21: 0.0258 S22: 0.0099 S23: -0.0180 REMARK 3 S31: 0.0650 S32: 0.0590 S33: 0.0027 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 95 A 190 REMARK 3 ORIGIN FOR THE GROUP (A): 25.3532 53.2419 44.5917 REMARK 3 T TENSOR REMARK 3 T11: 0.0204 T22: 0.0497 REMARK 3 T33: 0.0612 T12: 0.0132 REMARK 3 T13: -0.0018 T23: -0.0464 REMARK 3 L TENSOR REMARK 3 L11: 1.8041 L22: 0.6768 REMARK 3 L33: 1.1502 L12: 0.3583 REMARK 3 L13: -0.0074 L23: 0.5343 REMARK 3 S TENSOR REMARK 3 S11: -0.0291 S12: -0.2504 S13: 0.2289 REMARK 3 S21: -0.0512 S22: -0.0646 S23: 0.0458 REMARK 3 S31: -0.0498 S32: -0.0976 S33: 0.0937 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 95 B 190 REMARK 3 ORIGIN FOR THE GROUP (A): 46.8837 53.5905 26.7065 REMARK 3 T TENSOR REMARK 3 T11: 0.0126 T22: 0.0162 REMARK 3 T33: 0.0524 T12: -0.0006 REMARK 3 T13: 0.0052 T23: 0.0216 REMARK 3 L TENSOR REMARK 3 L11: 1.0535 L22: 0.6742 REMARK 3 L33: 1.5814 L12: -0.0895 REMARK 3 L13: -0.3090 L23: -0.0992 REMARK 3 S TENSOR REMARK 3 S11: 0.0242 S12: 0.1132 S13: 0.1184 REMARK 3 S21: -0.0205 S22: -0.0337 S23: -0.0418 REMARK 3 S31: -0.0327 S32: -0.0005 S33: 0.0095 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 196 A 212 REMARK 3 ORIGIN FOR THE GROUP (A): 47.7978 38.2946 32.5138 REMARK 3 T TENSOR REMARK 3 T11: 0.0370 T22: 0.0209 REMARK 3 T33: 0.0654 T12: -0.0132 REMARK 3 T13: 0.0101 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 1.8102 L22: 0.7858 REMARK 3 L33: 1.7764 L12: -0.9837 REMARK 3 L13: -0.7892 L23: 0.0095 REMARK 3 S TENSOR REMARK 3 S11: -0.0445 S12: -0.0146 S13: 0.0231 REMARK 3 S21: 0.0003 S22: 0.0098 S23: -0.0361 REMARK 3 S31: 0.0397 S32: 0.0930 S33: 0.0347 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 196 B 212 REMARK 3 ORIGIN FOR THE GROUP (A): 23.7743 38.6574 39.4772 REMARK 3 T TENSOR REMARK 3 T11: 0.0168 T22: 0.0154 REMARK 3 T33: 0.0511 T12: 0.0058 REMARK 3 T13: 0.0100 T23: 0.0101 REMARK 3 L TENSOR REMARK 3 L11: 3.2897 L22: 2.1938 REMARK 3 L33: 3.1421 L12: 1.9954 REMARK 3 L13: -2.0745 L23: -0.7970 REMARK 3 S TENSOR REMARK 3 S11: -0.0361 S12: -0.0191 S13: 0.0168 REMARK 3 S21: -0.0196 S22: 0.0228 S23: 0.0721 REMARK 3 S31: 0.0464 S32: -0.1028 S33: 0.0133 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 3KEO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 28-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055897. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : MAX II REMARK 200 BEAMLINE : I911-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0379 REMARK 200 MONOCHROMATOR : BENT SI (111) CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62064 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 27.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.50 REMARK 200 R MERGE FOR SHELL (I) : 0.52800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.260 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: PDB ENTRY 2DT5 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.83 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 6000, 175MM MAGNESIUM REMARK 280 CHLORIDE, 100MM HEPES, PH 7.0, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 46.20500 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: 9780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18900 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -121.0 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 MET A 1 REMARK 465 ILE A 2 REMARK 465 MET A 3 REMARK 465 ASP A 4 REMARK 465 LYS A 5 REMARK 465 ILE A 145 REMARK 465 MET B 1 REMARK 465 ILE B 2 REMARK 465 MET B 3 REMARK 465 ASP B 4 REMARK 465 LYS B 5 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 SER A 6 OG REMARK 480 ARG A 61 CB CG CD NE CZ NH1 NH2 REMARK 480 LYS A 69 CG CD CE NZ REMARK 480 ARG A 103 CG CD NE CZ NH1 NH2 REMARK 480 ASP A 122 CG OD1 OD2 REMARK 480 LYS A 126 CD CE NZ REMARK 480 THR A 128 OG1 REMARK 480 LYS A 170 CG CD CE NZ REMARK 480 LYS A 188 CG CD CE NZ REMARK 480 LEU B 59 CG CD1 CD2 REMARK 480 ARG B 61 CG CD NE CZ NH1 NH2 REMARK 480 LYS B 69 CD CE NZ REMARK 480 ARG B 103 CG CD NE CZ NH1 NH2 REMARK 480 ARG B 107 CD NE CZ NH1 NH2 REMARK 480 ASP B 146 CB CG OD1 OD2 REMARK 480 LYS B 170 CG CD CE NZ REMARK 480 LYS B 188 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 SER A 6 CB SER A 6 OG -0.266 REMARK 500 ARG A 14 CZ ARG A 14 NH2 -0.097 REMARK 500 ARG A 61 CA ARG A 61 CB 0.136 REMARK 500 VAL A 87 CB VAL A 87 CG2 -0.203 REMARK 500 ARG A 103 CB ARG A 103 CG -0.176 REMARK 500 LYS A 126 CG LYS A 126 CD -0.208 REMARK 500 THR A 128 CB THR A 128 OG1 -0.131 REMARK 500 LYS A 170 CB LYS A 170 CG -0.165 REMARK 500 VAL B 87 CB VAL B 87 CG2 -0.168 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 14 NE - CZ - NH1 ANGL. DEV. = 8.1 DEGREES REMARK 500 ARG A 14 NE - CZ - NH2 ANGL. DEV. = -8.5 DEGREES REMARK 500 ARG A 51 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 103 CA - CB - CG ANGL. DEV. = 21.0 DEGREES REMARK 500 LYS A 188 CA - CB - CG ANGL. DEV. = 13.6 DEGREES REMARK 500 ARG B 14 NE - CZ - NH1 ANGL. DEV. = 10.4 DEGREES REMARK 500 ARG B 14 NE - CZ - NH2 ANGL. DEV. = -10.2 DEGREES REMARK 500 ARG B 212 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES 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 CYS B 92 57.30 -102.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 215 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 355 O REMARK 620 2 HOH B 288 O 141.4 REMARK 620 3 HOH B 411 O 100.3 110.9 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD A 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 216 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 217 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 218 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NAD B 213 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 214 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 215 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 216 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VT3 RELATED DB: PDB REMARK 900 STRUCTURE AND FUNCTIONAL PROPERTIES OF THE BACILLUS SUBTILIS REMARK 900 TRANSCRIPTIONAL REPRESSOR REX REMARK 900 RELATED ID: 2DT5 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF TTHA1657 (AT-RICH DNA-BINDING PROTEIN) FROM REMARK 900 THERMUS THERMOPHILUS HB8 REMARK 900 RELATED ID: 3KEQ RELATED DB: PDB REMARK 900 STRUCTURE AND FUNCTIONAL PROPERTIES OF THE STREPTOCOCCUS AGALACTIAE REMARK 900 TRANSCRIPTIONAL REPRESSOR REX REMARK 900 RELATED ID: 3KET RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A REX-FAMILY TRANSCRIPTIONAL REGULATORY REMARK 900 PROTEIN FROM STREPTOCOCCUS AGALACTIAE BOUND TO A PALINDROMIC REMARK 900 OPERATOR DBREF 3KEO A 1 212 UNP Q8E565 REX_STRA3 1 212 DBREF 3KEO B 1 212 UNP Q8E565 REX_STRA3 1 212 SEQRES 1 A 212 MET ILE MET ASP LYS SER ILE PRO LYS ALA THR ALA LYS SEQRES 2 A 212 ARG LEU SER LEU TYR TYR ARG ILE PHE LYS ARG PHE ASN SEQRES 3 A 212 THR ASP GLY ILE GLU LYS ALA SER SER LYS GLN ILE ALA SEQRES 4 A 212 ASP ALA LEU GLY ILE ASP SER ALA THR VAL ARG ARG ASP SEQRES 5 A 212 PHE SER TYR PHE GLY GLU LEU GLY ARG ARG GLY PHE GLY SEQRES 6 A 212 TYR ASP VAL LYS LYS LEU MET ASN PHE PHE ALA GLU ILE SEQRES 7 A 212 LEU ASN ASP HIS SER THR THR ASN VAL MET LEU VAL GLY SEQRES 8 A 212 CYS GLY ASN ILE GLY ARG ALA LEU LEU HIS TYR ARG PHE SEQRES 9 A 212 HIS ASP ARG ASN LYS MET GLN ILE SER MET ALA PHE ASP SEQRES 10 A 212 LEU ASP SER ASN ASP LEU VAL GLY LYS THR THR GLU ASP SEQRES 11 A 212 GLY ILE PRO VAL TYR GLY ILE SER THR ILE ASN ASP HIS SEQRES 12 A 212 LEU ILE ASP SER ASP ILE GLU THR ALA ILE LEU THR VAL SEQRES 13 A 212 PRO SER THR GLU ALA GLN GLU VAL ALA ASP ILE LEU VAL SEQRES 14 A 212 LYS ALA GLY ILE LYS GLY ILE LEU SER PHE SER PRO VAL SEQRES 15 A 212 HIS LEU THR LEU PRO LYS ASP ILE ILE VAL GLN TYR VAL SEQRES 16 A 212 ASP LEU THR SER GLU LEU GLN THR LEU LEU TYR PHE MET SEQRES 17 A 212 ASN GLN GLN ARG SEQRES 1 B 212 MET ILE MET ASP LYS SER ILE PRO LYS ALA THR ALA LYS SEQRES 2 B 212 ARG LEU SER LEU TYR TYR ARG ILE PHE LYS ARG PHE ASN SEQRES 3 B 212 THR ASP GLY ILE GLU LYS ALA SER SER LYS GLN ILE ALA SEQRES 4 B 212 ASP ALA LEU GLY ILE ASP SER ALA THR VAL ARG ARG ASP SEQRES 5 B 212 PHE SER TYR PHE GLY GLU LEU GLY ARG ARG GLY PHE GLY SEQRES 6 B 212 TYR ASP VAL LYS LYS LEU MET ASN PHE PHE ALA GLU ILE SEQRES 7 B 212 LEU ASN ASP HIS SER THR THR ASN VAL MET LEU VAL GLY SEQRES 8 B 212 CYS GLY ASN ILE GLY ARG ALA LEU LEU HIS TYR ARG PHE SEQRES 9 B 212 HIS ASP ARG ASN LYS MET GLN ILE SER MET ALA PHE ASP SEQRES 10 B 212 LEU ASP SER ASN ASP LEU VAL GLY LYS THR THR GLU ASP SEQRES 11 B 212 GLY ILE PRO VAL TYR GLY ILE SER THR ILE ASN ASP HIS SEQRES 12 B 212 LEU ILE ASP SER ASP ILE GLU THR ALA ILE LEU THR VAL SEQRES 13 B 212 PRO SER THR GLU ALA GLN GLU VAL ALA ASP ILE LEU VAL SEQRES 14 B 212 LYS ALA GLY ILE LYS GLY ILE LEU SER PHE SER PRO VAL SEQRES 15 B 212 HIS LEU THR LEU PRO LYS ASP ILE ILE VAL GLN TYR VAL SEQRES 16 B 212 ASP LEU THR SER GLU LEU GLN THR LEU LEU TYR PHE MET SEQRES 17 B 212 ASN GLN GLN ARG HET NAD A 213 44 HET MG A 214 1 HET MG A 215 1 HET MG A 216 1 HET MG A 217 1 HET CL A 218 1 HET NAD B 213 44 HET MG B 214 1 HET MG B 215 1 HET MG B 216 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION FORMUL 3 NAD 2(C21 H27 N7 O14 P2) FORMUL 4 MG 7(MG 2+) FORMUL 8 CL CL 1- FORMUL 13 HOH *544(H2 O) HELIX 1 1 PRO A 8 LYS A 13 1 6 HELIX 2 2 ARG A 14 ASP A 28 1 15 HELIX 3 3 SER A 34 GLY A 43 1 10 HELIX 4 4 ASP A 45 TYR A 55 1 11 HELIX 5 5 PHE A 56 GLY A 60 5 5 HELIX 6 6 VAL A 68 LEU A 79 1 12 HELIX 7 7 GLY A 93 LEU A 100 1 8 HELIX 8 8 THR A 139 LEU A 144 1 6 HELIX 9 9 PRO A 157 THR A 159 5 3 HELIX 10 10 GLU A 160 GLY A 172 1 13 HELIX 11 11 ASP A 196 ARG A 212 1 17 HELIX 12 12 PRO B 8 LYS B 13 1 6 HELIX 13 13 ARG B 14 ASP B 28 1 15 HELIX 14 14 SER B 34 GLY B 43 1 10 HELIX 15 15 ASP B 45 TYR B 55 1 11 HELIX 16 16 VAL B 68 LEU B 79 1 12 HELIX 17 17 GLY B 93 LEU B 100 1 8 HELIX 18 18 THR B 139 ILE B 145 1 7 HELIX 19 19 PRO B 157 THR B 159 5 3 HELIX 20 20 GLU B 160 GLY B 172 1 13 HELIX 21 21 ASP B 196 ARG B 212 1 17 SHEET 1 A 2 LYS A 32 ALA A 33 0 SHEET 2 A 2 TYR A 66 ASP A 67 -1 O TYR A 66 N ALA A 33 SHEET 1 B 6 VAL A 134 GLY A 136 0 SHEET 2 B 6 MET A 110 ASP A 117 1 N ALA A 115 O TYR A 135 SHEET 3 B 6 THR A 85 VAL A 90 1 N VAL A 87 O GLN A 111 SHEET 4 B 6 THR A 151 LEU A 154 1 O ILE A 153 N VAL A 90 SHEET 5 B 6 GLY A 175 SER A 178 1 O LEU A 177 N LEU A 154 SHEET 6 B 6 ILE A 191 TYR A 194 1 O GLN A 193 N ILE A 176 SHEET 1 C 2 LYS B 32 ALA B 33 0 SHEET 2 C 2 TYR B 66 ASP B 67 -1 O TYR B 66 N ALA B 33 SHEET 1 D 6 VAL B 134 GLY B 136 0 SHEET 2 D 6 MET B 110 ASP B 117 1 N ALA B 115 O TYR B 135 SHEET 3 D 6 THR B 85 VAL B 90 1 N VAL B 87 O SER B 113 SHEET 4 D 6 THR B 151 LEU B 154 1 O ILE B 153 N VAL B 90 SHEET 5 D 6 GLY B 175 SER B 178 1 O LEU B 177 N LEU B 154 SHEET 6 D 6 ILE B 191 TYR B 194 1 O GLN B 193 N ILE B 176 LINK MG MG A 214 O HOH B 414 1555 1555 2.91 LINK O HOH A 355 MG MG B 215 1555 1555 2.74 LINK OD1 ASP B 81 MG MG B 214 1555 1555 2.90 LINK MG MG B 215 O HOH B 288 1555 1555 2.64 LINK MG MG B 215 O HOH B 411 1555 1555 2.71 LINK MG MG B 216 O HOH B 344 1555 1555 2.66 SITE 1 AC1 29 GLY A 91 CYS A 92 GLY A 93 ASN A 94 SITE 2 AC1 29 ILE A 95 ASP A 117 LEU A 118 ASN A 121 SITE 3 AC1 29 ILE A 137 THR A 155 VAL A 156 PRO A 157 SITE 4 AC1 29 SER A 158 VAL A 164 PHE A 179 SER A 180 SITE 5 AC1 29 PRO A 181 LEU A 197 HOH A 225 HOH A 235 SITE 6 AC1 29 HOH A 309 HOH A 371 HOH A 374 HOH A 396 SITE 7 AC1 29 HOH A 402 HOH A 423 ALA B 98 LEU B 99 SITE 8 AC1 29 TYR B 102 SITE 1 AC2 4 TYR A 102 ARG A 103 NAD B 213 HOH B 414 SITE 1 AC3 3 ARG A 14 HOH A 336 ARG B 14 SITE 1 AC4 3 GLU A 77 ARG A 212 HOH A 512 SITE 1 AC5 3 HIS A 105 ASP A 106 HOH A 331 SITE 1 AC6 3 ARG A 14 HOH B 218 HOH B 378 SITE 1 AC7 31 ALA A 98 LEU A 99 TYR A 102 MG A 214 SITE 2 AC7 31 GLY B 91 CYS B 92 GLY B 93 ASN B 94 SITE 3 AC7 31 ILE B 95 ASP B 117 LEU B 118 ILE B 137 SITE 4 AC7 31 THR B 155 VAL B 156 PRO B 157 SER B 158 SITE 5 AC7 31 VAL B 164 PHE B 179 SER B 180 PRO B 181 SITE 6 AC7 31 LEU B 197 HOH B 227 HOH B 269 HOH B 324 SITE 7 AC7 31 HOH B 333 HOH B 337 HOH B 382 HOH B 390 SITE 8 AC7 31 HOH B 392 HOH B 399 HOH B 414 SITE 1 AC8 4 GLN A 202 ASP B 81 HIS B 105 MET B 110 SITE 1 AC9 6 LEU A 42 GLY A 43 HOH A 355 LYS B 13 SITE 2 AC9 6 HOH B 288 HOH B 411 SITE 1 BC1 3 ASP B 119 SER B 120 HOH B 344 CRYST1 46.270 92.410 47.190 90.00 91.26 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 0.021612 0.000000 0.000475 0.00000 SCALE2 0.000000 0.010821 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021196 0.00000