HEADER TRANSCRIPTION/DNA 26-OCT-09 3KET TITLE CRYSTAL STRUCTURE OF A REX-FAMILY TRANSCRIPTIONAL REGULATORY PROTEIN TITLE 2 FROM STREPTOCOCCUS AGALACTIAE BOUND TO A PALINDROMIC OPERATOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: REDOX-SENSING TRANSCRIPTIONAL REPRESSOR REX; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*AP*AP*TP*TP*GP*TP*GP*AP*AP*AP*T)-3'); COMPND 7 CHAIN: B; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (5'-D(P*AP*TP*TP*TP*CP*AP*CP*AP*AP*TP*T)-3'); COMPND 11 CHAIN: C; COMPND 12 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; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 14 ORGANISM_TAXID: 32630; SOURCE 15 OTHER_DETAILS: NUCLEOTIDE SYNTHESIS; SOURCE 16 MOL_ID: 3; SOURCE 17 SYNTHETIC: YES; SOURCE 18 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 19 ORGANISM_TAXID: 32630; SOURCE 20 OTHER_DETAILS: NUCLEOTIDE SYNTHESIS KEYWDS PROTEIN-DNA COMPLEX, WINGED HELIX, ROSSMANN FOLD, NAD+, REPRESSOR, KEYWDS 2 TRANSCRIPTION, TRANSCRIPTION REGULATION, REDOX SENSING, KEYWDS 3 TRANSCRIPTION-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.THIYAGARAJAN,D.LOGAN,C.VON WACHENFELDT REVDAT 4 01-NOV-23 3KET 1 REMARK REVDAT 3 08-SEP-21 3KET 1 JRNL REMARK REVDAT 2 16-MAY-18 3KET 1 SOURCE REMARK REVDAT 1 10-NOV-10 3KET 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) : 29.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.2 REMARK 3 NUMBER OF REFLECTIONS : 14638 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) : 0.198 REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 784 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) : 1089 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2880 REMARK 3 BIN FREE R VALUE SET COUNT : 70 REMARK 3 BIN FREE R VALUE : 0.3790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1613 REMARK 3 NUCLEIC ACID ATOMS : 431 REMARK 3 HETEROGEN ATOMS : 45 REMARK 3 SOLVENT ATOMS : 119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.43 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.03000 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): 0.298 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.238 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.164 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.041 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.902 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2171 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1315 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3029 ; 2.203 ; 2.242 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3230 ; 1.095 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 204 ; 6.560 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 74 ;40.311 ;24.054 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 293 ;17.457 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;22.275 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 348 ; 0.151 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2058 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 386 ; 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): 1015 ; 0.869 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 418 ; 0.190 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1642 ; 1.675 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1156 ; 2.362 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1387 ; 3.450 ; 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 : 5 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 80 REMARK 3 ORIGIN FOR THE GROUP (A): 13.1175 14.3014 35.3959 REMARK 3 T TENSOR REMARK 3 T11: 0.1068 T22: 0.0977 REMARK 3 T33: 0.1473 T12: -0.0609 REMARK 3 T13: -0.0619 T23: -0.0128 REMARK 3 L TENSOR REMARK 3 L11: 1.7538 L22: 6.8909 REMARK 3 L33: 6.1974 L12: -0.2425 REMARK 3 L13: -0.9813 L23: 2.9620 REMARK 3 S TENSOR REMARK 3 S11: 0.1946 S12: -0.0637 S13: 0.1661 REMARK 3 S21: 0.4178 S22: 0.0318 S23: -0.6702 REMARK 3 S31: -0.1416 S32: 0.1881 S33: -0.2264 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 1 B 11 REMARK 3 ORIGIN FOR THE GROUP (A): 8.3304 16.3633 50.7757 REMARK 3 T TENSOR REMARK 3 T11: 0.5122 T22: 0.1495 REMARK 3 T33: 0.0378 T12: -0.2270 REMARK 3 T13: -0.0567 T23: -0.0078 REMARK 3 L TENSOR REMARK 3 L11: 3.5737 L22: 5.6965 REMARK 3 L33: 1.1023 L12: 2.3481 REMARK 3 L13: 0.4519 L23: 2.3596 REMARK 3 S TENSOR REMARK 3 S11: 0.4917 S12: -0.4420 S13: 0.0004 REMARK 3 S21: 1.0896 S22: -0.4698 S23: -0.0828 REMARK 3 S31: 0.3652 S32: -0.1163 S33: -0.0219 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 : C 34 C 44 REMARK 3 ORIGIN FOR THE GROUP (A): 7.1203 14.5145 51.0010 REMARK 3 T TENSOR REMARK 3 T11: 0.4776 T22: 0.1208 REMARK 3 T33: 0.0446 T12: -0.1970 REMARK 3 T13: 0.0067 T23: -0.0231 REMARK 3 L TENSOR REMARK 3 L11: 4.0971 L22: 7.4421 REMARK 3 L33: 2.5173 L12: 3.5936 REMARK 3 L13: 0.7357 L23: 1.9259 REMARK 3 S TENSOR REMARK 3 S11: 0.3182 S12: -0.4139 S13: 0.0717 REMARK 3 S21: 1.0384 S22: -0.4690 S23: 0.0603 REMARK 3 S31: 0.3611 S32: -0.2683 S33: 0.1508 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 : A 90 A 190 REMARK 3 ORIGIN FOR THE GROUP (A): 10.6165 -8.8623 14.7141 REMARK 3 T TENSOR REMARK 3 T11: 0.0283 T22: 0.1242 REMARK 3 T33: 0.0367 T12: 0.0455 REMARK 3 T13: 0.0132 T23: -0.0124 REMARK 3 L TENSOR REMARK 3 L11: 2.3287 L22: 1.8304 REMARK 3 L33: 1.8939 L12: 0.5364 REMARK 3 L13: -0.4538 L23: -0.3020 REMARK 3 S TENSOR REMARK 3 S11: -0.0409 S12: 0.1216 S13: -0.2178 REMARK 3 S21: -0.1515 S22: -0.0531 S23: -0.1521 REMARK 3 S31: 0.1225 S32: 0.1842 S33: 0.0939 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 191 A 210 REMARK 3 ORIGIN FOR THE GROUP (A): -7.3710 -1.4910 27.7880 REMARK 3 T TENSOR REMARK 3 T11: 0.0607 T22: 0.1447 REMARK 3 T33: 0.0294 T12: -0.0096 REMARK 3 T13: 0.0372 T23: -0.0115 REMARK 3 L TENSOR REMARK 3 L11: 3.6414 L22: 3.8708 REMARK 3 L33: 0.6391 L12: -2.3427 REMARK 3 L13: -0.1343 L23: -0.5589 REMARK 3 S TENSOR REMARK 3 S11: -0.0448 S12: -0.1803 S13: -0.0768 REMARK 3 S21: 0.3187 S22: 0.0594 S23: 0.2831 REMARK 3 S31: -0.0027 S32: -0.0756 S33: -0.0146 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 3KET 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_1000055902. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.0 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 : 16157 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 29.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 4.670 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.2000 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 (%) : 97.9 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 0.46000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.040 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: 3KEO AND A FIBER MODEL DOUBLE STRANDED B-DNA OF REMARK 200 LENGTH 11 BASE PAIRS REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 22 % PEG 1500, 50MM MIB, PH 5.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 24.36000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 53.51500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 76.97500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 24.36000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 53.51500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 76.97500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 24.36000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 53.51500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 76.97500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 24.36000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 53.51500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 76.97500 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24130 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 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 GLN A 211 REMARK 465 ARG A 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 DT C 44 O5' C5' C4' O4' C3' O3' C2' REMARK 470 DT C 44 C1' N1 C2 O2 N3 C4 O4 REMARK 470 DT C 44 C5 C7 C6 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 O3' DT B 11 P DA C 34 2555 1.56 REMARK 500 REMARK 500 REMARK: NULL 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 DT B 11 O3' DT B 11 C3' -0.044 REMARK 500 DT C 35 O3' DT C 35 C3' -0.044 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 20 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 ARG A 20 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 DA B 1 O4' - C1' - N9 ANGL. DEV. = 4.3 DEGREES REMARK 500 DA B 1 C2 - N3 - C4 ANGL. DEV. = -3.1 DEGREES REMARK 500 DA B 1 C4 - C5 - N7 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA B 1 C5 - N7 - C8 ANGL. DEV. = -4.4 DEGREES REMARK 500 DA B 1 N7 - C8 - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA B 2 O5' - P - OP1 ANGL. DEV. = 9.6 DEGREES REMARK 500 DA B 2 O5' - P - OP2 ANGL. DEV. = -6.7 DEGREES REMARK 500 DA B 2 C1' - O4' - C4' ANGL. DEV. = -6.5 DEGREES REMARK 500 DT B 4 C6 - N1 - C2 ANGL. DEV. = -3.1 DEGREES REMARK 500 DT B 4 N3 - C4 - O4 ANGL. DEV. = 3.8 DEGREES REMARK 500 DG B 5 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 DG B 5 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 DT B 6 O3' - P - O5' ANGL. DEV. = -22.9 DEGREES REMARK 500 DT B 6 O3' - P - OP1 ANGL. DEV. = -22.0 DEGREES REMARK 500 DT B 6 O5' - P - OP1 ANGL. DEV. = 12.3 DEGREES REMARK 500 DT B 6 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT B 6 N3 - C2 - O2 ANGL. DEV. = -4.8 DEGREES REMARK 500 DA B 10 C3' - C2' - C1' ANGL. DEV. = -4.8 DEGREES REMARK 500 DT B 11 O4' - C1' - N1 ANGL. DEV. = 3.2 DEGREES REMARK 500 DT B 11 C4 - C5 - C7 ANGL. DEV. = 5.5 DEGREES REMARK 500 DT B 11 C6 - C5 - C7 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT C 36 O4' - C1' - N1 ANGL. DEV. = -8.6 DEGREES REMARK 500 DT C 37 C4 - C5 - C7 ANGL. DEV. = 4.4 DEGREES REMARK 500 DC C 38 O4' - C1' - N1 ANGL. DEV. = -5.5 DEGREES REMARK 500 DC C 38 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DA C 39 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 DA C 39 C8 - N9 - C4 ANGL. DEV. = 2.7 DEGREES REMARK 500 DC C 40 O4' - C1' - N1 ANGL. DEV. = 4.8 DEGREES REMARK 500 DA C 41 O4' - C4' - C3' ANGL. DEV. = -2.4 DEGREES REMARK 500 DT C 43 N3 - C2 - O2 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT C 43 N3 - C4 - O4 ANGL. DEV. = -5.7 DEGREES REMARK 500 DT C 43 C5 - C4 - O4 ANGL. DEV. = 4.4 DEGREES REMARK 500 DT C 43 C4 - C5 - C7 ANGL. DEV. = 3.8 DEGREES REMARK 500 DT C 43 C3' - O3' - P ANGL. DEV. = -7.3 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 LYS A 109 56.72 -95.32 REMARK 500 ASP A 146 -4.59 63.63 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 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 214 REMARK 900 REMARK 900 RELATED ENTRIES 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: 3KEO RELATED DB: PDB REMARK 900 STRUCTURE AND FUNCTIONAL PROPERTIES OF THE STREPTOCOCCUS AGALACTIAE REMARK 900 TRANSCRIPTIONAL REPRESSOR REX 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 3KET A 1 212 UNP Q8E565 REX_STRA3 1 212 DBREF 3KET B 1 11 PDB 3KET 3KET 1 11 DBREF 3KET C 34 44 PDB 3KET 3KET 34 44 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 11 DA DA DT DT DG DT DG DA DA DA DT SEQRES 1 C 11 DA DT DT DT DC DA DC DA DA DT DT HET NAD A 213 44 HET MG A 214 1 HETNAM NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE HETNAM MG MAGNESIUM ION FORMUL 4 NAD C21 H27 N7 O14 P2 FORMUL 5 MG MG 2+ FORMUL 6 HOH *119(H2 O) HELIX 1 1 PRO A 8 ASP A 28 1 21 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 VAL A 68 LEU A 79 1 12 HELIX 5 5 GLY A 93 HIS A 101 1 9 HELIX 6 6 ARG A 103 ARG A 107 5 5 HELIX 7 7 THR A 139 LEU A 144 1 6 HELIX 8 8 PRO A 157 THR A 159 5 3 HELIX 9 9 GLU A 160 ALA A 171 1 12 HELIX 10 10 ASP A 196 GLN A 210 1 15 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 MET A 88 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 SITE 1 AC1 24 GLY A 91 CYS A 92 GLY A 93 ASN A 94 SITE 2 AC1 24 ILE A 95 ALA A 98 LEU A 99 TYR A 102 SITE 3 AC1 24 ASP A 117 LEU A 118 ILE A 137 THR A 155 SITE 4 AC1 24 VAL A 156 PRO A 157 SER A 158 VAL A 164 SITE 5 AC1 24 PHE A 179 SER A 180 THR A 198 HOH A 217 SITE 6 AC1 24 HOH A 220 HOH A 224 HOH A 226 HOH A 285 SITE 1 AC2 4 ARG A 20 TYR A 102 PRO A 181 THR A 198 CRYST1 48.720 107.030 153.950 90.00 90.00 90.00 I 2 2 2 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 0.020525 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009343 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006496 0.00000