HEADER TRANSCRIPTION 26-OCT-09 3KEQ 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 3KEQ 1 REMARK REVDAT 3 08-SEP-21 3KEQ 1 JRNL REMARK REVDAT 2 16-MAY-18 3KEQ 1 REMARK REVDAT 1 10-NOV-10 3KEQ 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 28.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 17958 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) : 0.227 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.292 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 978 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1290 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.40 REMARK 3 BIN R VALUE (WORKING SET) : 0.3550 REMARK 3 BIN FREE R VALUE SET COUNT : 63 REMARK 3 BIN FREE R VALUE : 0.3310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3147 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 64.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 60.85 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.15000 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): 0.412 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.298 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.229 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.742 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.901 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3116 ; 0.017 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2003 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4232 ; 1.678 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): 4875 ; 1.008 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 395 ; 6.630 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 128 ;40.211 ;24.688 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 493 ;19.000 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;26.323 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 499 ; 0.096 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3464 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 616 ; 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): 1967 ; 0.796 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 813 ; 0.156 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3148 ; 1.466 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1149 ; 2.169 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1084 ; 3.342 ; 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): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 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 211 REMARK 3 ORIGIN FOR THE GROUP (A): 8.7435 -13.9607 -18.7483 REMARK 3 T TENSOR REMARK 3 T11: 0.1471 T22: 0.2315 REMARK 3 T33: 0.5127 T12: 0.0918 REMARK 3 T13: 0.1515 T23: 0.1696 REMARK 3 L TENSOR REMARK 3 L11: 2.7905 L22: 3.2627 REMARK 3 L33: 1.7811 L12: -1.4363 REMARK 3 L13: -0.0473 L23: 1.3746 REMARK 3 S TENSOR REMARK 3 S11: -0.4215 S12: -0.4735 S13: -0.5008 REMARK 3 S21: 0.3475 S22: 0.2929 S23: 1.1331 REMARK 3 S31: 0.0174 S32: -0.2226 S33: 0.1286 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 211 REMARK 3 ORIGIN FOR THE GROUP (A): 17.5197 -1.6929 -21.1824 REMARK 3 T TENSOR REMARK 3 T11: 0.1280 T22: 0.1661 REMARK 3 T33: 0.1255 T12: 0.0360 REMARK 3 T13: 0.0103 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 2.2997 L22: 3.6564 REMARK 3 L33: 4.1446 L12: 0.4112 REMARK 3 L13: -1.3459 L23: 0.4166 REMARK 3 S TENSOR REMARK 3 S11: -0.1789 S12: -0.3203 S13: 0.0260 REMARK 3 S21: 0.0300 S22: 0.1880 S23: 0.3255 REMARK 3 S31: -0.4822 S32: 0.2881 S33: -0.0091 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 3KEQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 29-OCT-09. REMARK 100 THE DEPOSITION ID IS D_1000055899. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JUL-09 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 : 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 : 18880 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 28.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.000 REMARK 200 R MERGE (I) : 0.04200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 27.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.46 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.10 REMARK 200 R MERGE FOR SHELL (I) : 0.53200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.650 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 3KEO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.46 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 17% PEG 3350, 175 MM SODIUM FLUORIDE, REMARK 280 100 MM BISTRISPROPANE, PH 6.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 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 28.83500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.94000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.73500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.94000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.83500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.73500 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 300 REMARK: ASYMMETRIC UNIT IS THE BIOLOGICAL UNIT 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: 5780 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19680 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 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 LEU A 59 REMARK 465 GLY A 60 REMARK 465 ARG A 61 REMARK 465 ARG A 62 REMARK 465 GLY A 63 REMARK 465 PHE A 64 REMARK 465 GLY A 65 REMARK 465 ASP A 81 REMARK 465 HIS A 82 REMARK 465 SER A 83 REMARK 465 ARG A 212 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 465 ILE B 145 REMARK 465 ASP B 146 REMARK 465 ARG B 212 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 LYS A 70 CG CD CE NZ 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 ARG A 24 CG CD NE CZ NH1 NH2 REMARK 480 GLU A 31 CB CG CD OE1 OE2 REMARK 480 LYS A 32 CB CG CD CE NZ REMARK 480 LYS A 36 CB CG CD CE NZ REMARK 480 GLN A 37 CG CD OE1 NE2 REMARK 480 LYS A 69 CG CD CE NZ REMARK 480 ASN A 73 CB CG OD1 ND2 REMARK 480 GLU A 77 CB CG CD OE1 OE2 REMARK 480 ARG A 103 CG CD NE CZ NH1 NH2 REMARK 480 ASP A 106 CB CG OD1 OD2 REMARK 480 ARG A 107 CB CG CD NE CZ NH1 NH2 REMARK 480 LYS A 109 CB CG CD CE NZ REMARK 480 GLN A 111 CB CG CD OE1 NE2 REMARK 480 GLU A 129 CG CD OE1 OE2 REMARK 480 LYS A 170 CG CD CE NZ REMARK 480 LYS A 174 CD CE NZ REMARK 480 LYS A 188 CG CD CE NZ REMARK 480 ILE B 7 CG2 REMARK 480 LYS B 36 CG CD CE NZ REMARK 480 ARG B 51 CG CD NE CZ NH1 NH2 REMARK 480 GLU B 58 CG CD OE1 OE2 REMARK 480 ARG B 61 CG CD NE CZ NH1 NH2 REMARK 480 ARG B 97 CG CD NE CZ NH1 NH2 REMARK 480 ARG B 103 CG CD NE CZ NH1 NH2 REMARK 480 SER B 120 CB OG REMARK 480 LYS B 126 CG CD CE NZ REMARK 480 SER B 138 CB OG REMARK 480 ASP B 142 CB CG OD1 OD2 REMARK 480 LYS B 188 CB CG CD CE NZ 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 B 24 NE - CZ - NH1 ANGL. DEV. = -5.1 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 LYS A 36 -70.63 -52.07 REMARK 500 CYS A 92 53.00 -92.11 REMARK 500 ASP A 106 -88.47 -70.40 REMARK 500 ASN A 108 80.96 -61.71 REMARK 500 ASP A 146 -32.52 173.95 REMARK 500 PHE B 56 31.90 -95.95 REMARK 500 CYS B 92 47.50 -94.57 REMARK 500 ASN B 94 -82.13 -88.89 REMARK 500 LYS B 126 178.09 -59.43 REMARK 500 SER B 158 -47.64 -27.74 REMARK 500 PRO B 187 158.23 -49.02 REMARK 500 REMARK 500 REMARK: NULL 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 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KEO RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A REX-FAMILY TRANSCRIPTIONAL REGULATORY REMARK 900 PROTEIN FROM STREPTOCOCCUS AGALACTIAE COMPLEXED WITH NAD+ 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 DBREF 3KEQ A 1 212 UNP Q8E565 REX_STRA3 1 212 DBREF 3KEQ 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 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE FORMUL 3 NAD C21 H27 N7 O14 P2 FORMUL 4 HOH *59(H2 O) HELIX 1 1 PRO A 8 GLY A 29 1 22 HELIX 2 2 SER A 34 GLY A 43 1 10 HELIX 3 3 ASP A 45 TYR A 55 1 11 HELIX 4 4 ASP A 67 ASN A 80 1 14 HELIX 5 5 GLY A 93 LEU A 100 1 8 HELIX 6 6 THR A 139 ILE A 145 1 7 HELIX 7 7 PRO A 157 THR A 159 5 3 HELIX 8 8 GLU A 160 ALA A 171 1 12 HELIX 9 9 ASP A 196 GLN A 211 1 16 HELIX 10 10 PRO B 8 LYS B 13 1 6 HELIX 11 11 ARG B 14 ASP B 28 1 15 HELIX 12 12 SER B 34 GLY B 43 1 10 HELIX 13 13 ASP B 45 SER B 54 1 10 HELIX 14 14 PHE B 56 ARG B 61 1 6 HELIX 15 15 VAL B 68 ASN B 80 1 13 HELIX 16 16 GLY B 93 TYR B 102 1 10 HELIX 17 17 HIS B 105 ASN B 108 5 4 HELIX 18 18 SER B 138 ASN B 141 5 4 HELIX 19 19 GLU B 160 GLY B 172 1 13 HELIX 20 20 ASP B 196 GLN B 210 1 15 SHEET 1 A 6 VAL A 134 GLY A 136 0 SHEET 2 A 6 MET A 110 ASP A 117 1 N ALA A 115 O TYR A 135 SHEET 3 A 6 THR A 85 VAL A 90 1 N VAL A 87 O GLN A 111 SHEET 4 A 6 THR A 151 LEU A 154 1 O ILE A 153 N MET A 88 SHEET 5 A 6 GLY A 175 SER A 178 1 O LEU A 177 N ALA A 152 SHEET 6 A 6 ILE A 191 TYR A 194 1 O GLN A 193 N SER A 178 SHEET 1 B 2 LYS B 32 ALA B 33 0 SHEET 2 B 2 TYR B 66 ASP B 67 -1 O TYR B 66 N ALA B 33 SHEET 1 C 6 VAL B 134 GLY B 136 0 SHEET 2 C 6 MET B 110 ASP B 117 1 N ALA B 115 O TYR B 135 SHEET 3 C 6 THR B 85 VAL B 90 1 N LEU B 89 O MET B 114 SHEET 4 C 6 THR B 151 LEU B 154 1 O ILE B 153 N VAL B 90 SHEET 5 C 6 GLY B 175 SER B 178 1 O LEU B 177 N ALA B 152 SHEET 6 C 6 ILE B 191 TYR B 194 1 O GLN B 193 N SER B 178 SITE 1 AC1 21 GLY A 91 CYS A 92 GLY A 93 ASN A 94 SITE 2 AC1 21 ILE A 95 ASP A 117 LEU A 118 ILE A 137 SITE 3 AC1 21 THR A 155 VAL A 156 PRO A 157 SER A 158 SITE 4 AC1 21 VAL A 164 PHE A 179 SER A 180 PRO A 181 SITE 5 AC1 21 HOH A 217 HOH A 242 ALA B 98 LEU B 99 SITE 6 AC1 21 TYR B 102 CRYST1 57.670 71.470 113.880 90.00 90.00 90.00 P 21 21 21 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 0.017340 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013992 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008781 0.00000