HEADER TRANSCRIPTION/DNA 12-APR-07 2YVH TITLE CRYSTAL STRUCTURE OF THE OPERATOR-BINDING FORM OF THE MULTI-DRUG TITLE 2 BINDING TRANSCRIPTIONAL REPRESSOR CGMR COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRANSCRIPTIONAL REGULATOR; COMPND 3 CHAIN: A, B, C, D; COMPND 4 SYNONYM: BACTERIAL REGULATORY PROTEIN, TETR FAMILY; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: 5'-D(*DTP*DAP*DAP*DCP*DTP*DGP*DTP*DAP*DCP*DCP*DGP*DAP*DCP*D COMPND 8 C)-3'; COMPND 9 CHAIN: E, G; COMPND 10 ENGINEERED: YES; COMPND 11 OTHER_DETAILS: CGL2612 OPERATOR DNA UPPER STRAND; COMPND 12 MOL_ID: 3; COMPND 13 MOLECULE: 5'-D(*DGP*DGP*DTP*DCP*DGP*DGP*DTP*DAP*DCP*DAP*DGP*DTP*DTP*D COMPND 14 A)-3'; COMPND 15 CHAIN: F, H; COMPND 16 ENGINEERED: YES; COMPND 17 OTHER_DETAILS: CGL2612 OPERATOR DNA LOWER STRAND SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CORYNEBACTERIUM GLUTAMICUM; SOURCE 3 ORGANISM_TAXID: 196627; SOURCE 4 STRAIN: ATCC13032; SOURCE 5 GENE: CGL2612; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET26B; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 OTHER_DETAILS: SEQUENCE FOUND IN THE C.GLUTAMICUM GENOME.; SOURCE 14 MOL_ID: 3; SOURCE 15 SYNTHETIC: YES; SOURCE 16 OTHER_DETAILS: SEQUENCE FOUND IN THE C.GLUTAMICUM GENOME. KEYWDS PROTEIN-DNA COMPLEX, HELIX-TURN-HELIX, TETR-FAMILY, TRANSCRIPTION-DNA KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR H.ITOU,Y.SHIRAKIHARA,I.TANAKA REVDAT 6 23-OCT-24 2YVH 1 LINK REVDAT 5 13-OCT-10 2YVH 1 JRNL REVDAT 4 18-AUG-10 2YVH 1 JRNL REVDAT 3 24-FEB-09 2YVH 1 VERSN REVDAT 2 01-JUL-08 2YVH 1 TITLE REMARK REVDAT 1 15-APR-08 2YVH 0 JRNL AUTH H.ITOU,N.WATANABE,M.YAO,Y.SHIRAKIHARA,I.TANAKA JRNL TITL CRYSTAL STRUCTURES OF THE MULTIDRUG BINDING REPRESSOR JRNL TITL 2 CORYNEBACTERIUMGLUTAMICUM CGMR IN COMPLEX WITH INDUCERS AND JRNL TITL 3 WITH AN OPERATOR JRNL REF J.MOL.BIOL. V. 403 174 2010 JRNL REFN ISSN 0022-2836 JRNL PMID 20691702 JRNL DOI 10.1016/J.JMB.2010.07.042 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 30388 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) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1595 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2072 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.36 REMARK 3 BIN R VALUE (WORKING SET) : 0.3200 REMARK 3 BIN FREE R VALUE SET COUNT : 124 REMARK 3 BIN FREE R VALUE : 0.3710 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5530 REMARK 3 NUCLEIC ACID ATOMS : 1136 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 3 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 46.70 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 53.42 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.53000 REMARK 3 B22 (A**2) : -1.41000 REMARK 3 B33 (A**2) : -1.05000 REMARK 3 B12 (A**2) : -0.32000 REMARK 3 B13 (A**2) : -3.16000 REMARK 3 B23 (A**2) : -0.80000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.757 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.310 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.225 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.039 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6926 ; 0.017 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9656 ; 2.165 ; 2.185 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 682 ; 6.498 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 272 ;39.883 ;24.118 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 982 ;23.504 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 40 ;17.337 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1108 ; 0.133 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4856 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3044 ; 0.253 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 4511 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 205 ; 0.203 ; 0.200 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): 48 ; 0.244 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.290 ; 0.200 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): 3533 ; 1.097 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5574 ; 1.809 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4235 ; 2.422 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4082 ; 3.626 ; 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A C REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 8 A 171 4 REMARK 3 1 C 8 C 171 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 1323 ; 0.29 ; 0.50 REMARK 3 MEDIUM THERMAL 1 A (A**2): 1323 ; 0.88 ; 2.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : B D REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 B 8 B 171 4 REMARK 3 1 D 8 D 171 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 B (A): 1323 ; 0.27 ; 0.50 REMARK 3 MEDIUM THERMAL 2 B (A**2): 1323 ; 0.87 ; 2.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 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 2YVH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-APR-07. REMARK 100 THE DEPOSITION ID IS D_1000027185. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-DEC-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97909 REMARK 200 MONOCHROMATOR : SI(111) REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32512 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 100.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.09100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.0 REMARK 200 DATA REDUNDANCY IN SHELL : 7.30 REMARK 200 R MERGE FOR SHELL (I) : 0.48000 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: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05M TRIS-HCL, 0.1M CACL2, 4% PEG REMARK 280 400, PH 8.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: OCTAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: OCTAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 15750 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 37430 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -106.5 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E, F, G, H 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 MSE A 1 REMARK 465 ARG A 2 REMARK 465 THR A 3 REMARK 465 SER A 175 REMARK 465 GLN A 176 REMARK 465 THR A 177 REMARK 465 MSE B 1 REMARK 465 ARG B 2 REMARK 465 SER B 175 REMARK 465 GLN B 176 REMARK 465 THR B 177 REMARK 465 MSE C 1 REMARK 465 ARG C 2 REMARK 465 THR C 3 REMARK 465 SER C 175 REMARK 465 GLN C 176 REMARK 465 THR C 177 REMARK 465 MSE D 1 REMARK 465 ARG D 2 REMARK 465 SER D 175 REMARK 465 GLN D 176 REMARK 465 THR D 177 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OG SER D 21 OE1 GLU D 23 1.94 REMARK 500 OG SER B 21 OE1 GLU B 23 2.05 REMARK 500 O LEU A 25 NH2 ARG A 48 2.13 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 GLU A 23 CG GLU A 23 CD 0.127 REMARK 500 DT E 3 C5' DT E 3 C4' 0.044 REMARK 500 DA E 10 O3' DA E 10 C3' -0.038 REMARK 500 DC E 11 O3' DC E 11 C3' -0.063 REMARK 500 DC E 12 O3' DC E 12 C3' -0.045 REMARK 500 DA G 10 O3' DA G 10 C3' -0.064 REMARK 500 DC G 11 O3' DC G 11 C3' -0.037 REMARK 500 DC G 12 O3' DC G 12 C3' -0.064 REMARK 500 DC G 12 C1' DC G 12 N1 0.083 REMARK 500 DG H 18 O3' DG H 18 C3' -0.037 REMARK 500 DG H 21 O3' DG H 21 C3' -0.047 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 11 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 LEU A 67 CA - CB - CG ANGL. DEV. = 23.3 DEGREES REMARK 500 LEU C 67 CA - CB - CG ANGL. DEV. = 16.5 DEGREES REMARK 500 LEU D 127 CA - CB - CG ANGL. DEV. = 15.5 DEGREES REMARK 500 DT E 3 C5' - C4' - O4' ANGL. DEV. = 8.4 DEGREES REMARK 500 DT E 3 O4' - C1' - N1 ANGL. DEV. = 5.0 DEGREES REMARK 500 DA E 5 O4' - C1' - N9 ANGL. DEV. = 3.6 DEGREES REMARK 500 DG E 8 C3' - O3' - P ANGL. DEV. = 8.4 DEGREES REMARK 500 DT E 9 O5' - C5' - C4' ANGL. DEV. = -7.0 DEGREES REMARK 500 DT E 9 C4 - C5 - C7 ANGL. DEV. = 5.7 DEGREES REMARK 500 DT E 9 C6 - C5 - C7 ANGL. DEV. = -4.0 DEGREES REMARK 500 DA E 10 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DC E 11 O5' - P - OP1 ANGL. DEV. = -5.4 DEGREES REMARK 500 DC E 11 O4' - C1' - C2' ANGL. DEV. = 4.3 DEGREES REMARK 500 DA E 14 C2 - N3 - C4 ANGL. DEV. = 3.4 DEGREES REMARK 500 DA E 14 C3' - O3' - P ANGL. DEV. = 8.8 DEGREES REMARK 500 DG F 17 C5' - C4' - O4' ANGL. DEV. = 7.4 DEGREES REMARK 500 DG F 17 O4' - C1' - N9 ANGL. DEV. = 14.1 DEGREES REMARK 500 DG F 17 N7 - C8 - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 DG F 17 C8 - N9 - C4 ANGL. DEV. = -3.6 DEGREES REMARK 500 DG F 17 N9 - C4 - C5 ANGL. DEV. = 2.7 DEGREES REMARK 500 DG F 18 O4' - C4' - C3' ANGL. DEV. = -3.8 DEGREES REMARK 500 DG F 18 C5' - C4' - O4' ANGL. DEV. = -19.0 DEGREES REMARK 500 DG F 18 O4' - C1' - N9 ANGL. DEV. = -4.6 DEGREES REMARK 500 DT F 19 O4' - C1' - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 DT F 19 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 DG F 21 O3' - P - OP2 ANGL. DEV. = 10.0 DEGREES REMARK 500 DG F 21 O5' - C5' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG F 21 O4' - C1' - N9 ANGL. DEV. = 8.4 DEGREES REMARK 500 DG F 22 O5' - P - OP2 ANGL. DEV. = -6.3 DEGREES REMARK 500 DG F 22 O5' - C5' - C4' ANGL. DEV. = -7.4 DEGREES REMARK 500 DG F 22 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 DG F 22 N1 - C6 - O6 ANGL. DEV. = -3.6 DEGREES REMARK 500 DT F 23 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT F 23 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DA F 24 O4' - C1' - N9 ANGL. DEV. = 2.9 DEGREES REMARK 500 DC F 25 C1' - O4' - C4' ANGL. DEV. = -6.6 DEGREES REMARK 500 DC F 25 O4' - C1' - N1 ANGL. DEV. = 9.8 DEGREES REMARK 500 DA F 26 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DG F 27 O4' - C1' - N9 ANGL. DEV. = 4.4 DEGREES REMARK 500 DG F 27 C3' - O3' - P ANGL. DEV. = 7.7 DEGREES REMARK 500 DT G 3 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT G 3 C3' - O3' - P ANGL. DEV. = 12.3 DEGREES REMARK 500 DA G 4 C3' - C2' - C1' ANGL. DEV. = -5.9 DEGREES REMARK 500 DA G 4 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA G 5 O4' - C1' - N9 ANGL. DEV. = 6.4 DEGREES REMARK 500 DC G 6 O4' - C4' - C3' ANGL. DEV. = -4.1 DEGREES REMARK 500 DA G 10 O4' - C1' - N9 ANGL. DEV. = 2.2 DEGREES REMARK 500 DA G 10 N1 - C2 - N3 ANGL. DEV. = -3.2 DEGREES REMARK 500 DA G 10 C3' - O3' - P ANGL. DEV. = 7.6 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 83 ANGLE DEVIATIONS. 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 TYR A 20 -106.56 -119.59 REMARK 500 GLU A 66 -7.21 -59.84 REMARK 500 ARG A 68 -53.20 -139.83 REMARK 500 ASP A 73 74.47 -174.23 REMARK 500 GLU A 75 -74.30 -38.07 REMARK 500 GLU A 90 -14.72 -141.85 REMARK 500 SER A 93 -138.97 -132.09 REMARK 500 GLN A 119 -20.26 143.69 REMARK 500 TRP A 120 -57.03 -127.63 REMARK 500 ASP A 155 94.54 -165.62 REMARK 500 LEU A 172 1.19 -59.26 REMARK 500 LYS B 5 7.31 -69.47 REMARK 500 TYR B 20 -105.34 -128.13 REMARK 500 SER B 21 -168.54 -173.08 REMARK 500 SER B 93 -148.15 -131.39 REMARK 500 THR B 115 -72.52 -56.80 REMARK 500 TRP B 120 -25.32 -143.16 REMARK 500 THR B 124 52.58 -68.21 REMARK 500 ASP B 130 96.52 -179.41 REMARK 500 ASP B 155 64.16 -179.44 REMARK 500 ILE B 173 -101.75 -65.05 REMARK 500 TYR C 20 -98.47 -116.84 REMARK 500 GLU C 32 -74.68 -50.02 REMARK 500 ASP C 69 6.01 -65.67 REMARK 500 GLU C 75 -86.29 -56.31 REMARK 500 ASN C 91 39.42 -141.98 REMARK 500 SER C 93 -144.39 -126.70 REMARK 500 ASN C 117 0.43 -54.87 REMARK 500 HIS C 118 93.71 -168.67 REMARK 500 GLN C 119 -42.05 146.88 REMARK 500 ASP C 126 13.62 91.97 REMARK 500 ASP C 155 106.61 179.16 REMARK 500 LEU C 172 -23.82 -30.83 REMARK 500 TYR D 20 -90.05 -121.96 REMARK 500 SER D 21 -179.60 173.66 REMARK 500 GLU D 90 -31.79 -149.35 REMARK 500 SER D 93 -151.00 -129.32 REMARK 500 PRO D 104 -17.15 -48.91 REMARK 500 ASP D 154 78.83 50.84 REMARK 500 ASP D 155 66.99 153.06 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2ZOY RELATED DB: PDB REMARK 900 THE SAME PROTEIN IN LIGAND-FREE STATE REMARK 900 RELATED ID: 2ZOZ RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH ETHIDIUM REMARK 900 RELATED ID: 2YVE RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH METHYLENE BLUE DBREF 2YVH A 1 177 UNP Q8NMG3 Q8NMG3_CORGL 1 177 DBREF 2YVH B 1 177 UNP Q8NMG3 Q8NMG3_CORGL 1 177 DBREF 2YVH C 1 177 UNP Q8NMG3 Q8NMG3_CORGL 1 177 DBREF 2YVH D 1 177 UNP Q8NMG3 Q8NMG3_CORGL 1 177 DBREF 2YVH E 3 16 PDB 2YVH 2YVH 3 16 DBREF 2YVH G 3 16 PDB 2YVH 2YVH 3 16 DBREF 2YVH F 17 30 PDB 2YVH 2YVH 17 30 DBREF 2YVH H 17 30 PDB 2YVH 2YVH 17 30 SEQRES 1 A 177 MSE ARG THR SER LYS LYS GLU MSE ILE LEU ARG THR ALA SEQRES 2 A 177 ILE ASP TYR ILE GLY GLU TYR SER LEU GLU THR LEU SER SEQRES 3 A 177 TYR ASP SER LEU ALA GLU ALA THR GLY LEU SER LYS SER SEQRES 4 A 177 GLY LEU ILE TYR HIS PHE PRO SER ARG HIS ALA LEU LEU SEQRES 5 A 177 LEU GLY MSE HIS GLU LEU LEU ALA ASP ASP TRP ASP LYS SEQRES 6 A 177 GLU LEU ARG ASP ILE THR ARG ASP PRO GLU ASP PRO LEU SEQRES 7 A 177 GLU ARG LEU ARG ALA VAL VAL VAL THR LEU ALA GLU ASN SEQRES 8 A 177 VAL SER ARG PRO GLU LEU LEU LEU LEU ILE ASP ALA PRO SEQRES 9 A 177 SER HIS PRO ASP PHE LEU ASN ALA TRP ARG THR VAL ASN SEQRES 10 A 177 HIS GLN TRP ILE PRO ASP THR ASP ASP LEU GLU ASN ASP SEQRES 11 A 177 ALA HIS LYS ARG ALA VAL TYR LEU VAL GLN LEU ALA ALA SEQRES 12 A 177 ASP GLY LEU PHE VAL HIS ASP TYR ILE HIS ASP ASP VAL SEQRES 13 A 177 LEU SER LYS SER LYS ARG GLN ALA MSE LEU GLU THR ILE SEQRES 14 A 177 LEU GLU LEU ILE PRO SER GLN THR SEQRES 1 B 177 MSE ARG THR SER LYS LYS GLU MSE ILE LEU ARG THR ALA SEQRES 2 B 177 ILE ASP TYR ILE GLY GLU TYR SER LEU GLU THR LEU SER SEQRES 3 B 177 TYR ASP SER LEU ALA GLU ALA THR GLY LEU SER LYS SER SEQRES 4 B 177 GLY LEU ILE TYR HIS PHE PRO SER ARG HIS ALA LEU LEU SEQRES 5 B 177 LEU GLY MSE HIS GLU LEU LEU ALA ASP ASP TRP ASP LYS SEQRES 6 B 177 GLU LEU ARG ASP ILE THR ARG ASP PRO GLU ASP PRO LEU SEQRES 7 B 177 GLU ARG LEU ARG ALA VAL VAL VAL THR LEU ALA GLU ASN SEQRES 8 B 177 VAL SER ARG PRO GLU LEU LEU LEU LEU ILE ASP ALA PRO SEQRES 9 B 177 SER HIS PRO ASP PHE LEU ASN ALA TRP ARG THR VAL ASN SEQRES 10 B 177 HIS GLN TRP ILE PRO ASP THR ASP ASP LEU GLU ASN ASP SEQRES 11 B 177 ALA HIS LYS ARG ALA VAL TYR LEU VAL GLN LEU ALA ALA SEQRES 12 B 177 ASP GLY LEU PHE VAL HIS ASP TYR ILE HIS ASP ASP VAL SEQRES 13 B 177 LEU SER LYS SER LYS ARG GLN ALA MSE LEU GLU THR ILE SEQRES 14 B 177 LEU GLU LEU ILE PRO SER GLN THR SEQRES 1 C 177 MSE ARG THR SER LYS LYS GLU MSE ILE LEU ARG THR ALA SEQRES 2 C 177 ILE ASP TYR ILE GLY GLU TYR SER LEU GLU THR LEU SER SEQRES 3 C 177 TYR ASP SER LEU ALA GLU ALA THR GLY LEU SER LYS SER SEQRES 4 C 177 GLY LEU ILE TYR HIS PHE PRO SER ARG HIS ALA LEU LEU SEQRES 5 C 177 LEU GLY MSE HIS GLU LEU LEU ALA ASP ASP TRP ASP LYS SEQRES 6 C 177 GLU LEU ARG ASP ILE THR ARG ASP PRO GLU ASP PRO LEU SEQRES 7 C 177 GLU ARG LEU ARG ALA VAL VAL VAL THR LEU ALA GLU ASN SEQRES 8 C 177 VAL SER ARG PRO GLU LEU LEU LEU LEU ILE ASP ALA PRO SEQRES 9 C 177 SER HIS PRO ASP PHE LEU ASN ALA TRP ARG THR VAL ASN SEQRES 10 C 177 HIS GLN TRP ILE PRO ASP THR ASP ASP LEU GLU ASN ASP SEQRES 11 C 177 ALA HIS LYS ARG ALA VAL TYR LEU VAL GLN LEU ALA ALA SEQRES 12 C 177 ASP GLY LEU PHE VAL HIS ASP TYR ILE HIS ASP ASP VAL SEQRES 13 C 177 LEU SER LYS SER LYS ARG GLN ALA MSE LEU GLU THR ILE SEQRES 14 C 177 LEU GLU LEU ILE PRO SER GLN THR SEQRES 1 D 177 MSE ARG THR SER LYS LYS GLU MSE ILE LEU ARG THR ALA SEQRES 2 D 177 ILE ASP TYR ILE GLY GLU TYR SER LEU GLU THR LEU SER SEQRES 3 D 177 TYR ASP SER LEU ALA GLU ALA THR GLY LEU SER LYS SER SEQRES 4 D 177 GLY LEU ILE TYR HIS PHE PRO SER ARG HIS ALA LEU LEU SEQRES 5 D 177 LEU GLY MSE HIS GLU LEU LEU ALA ASP ASP TRP ASP LYS SEQRES 6 D 177 GLU LEU ARG ASP ILE THR ARG ASP PRO GLU ASP PRO LEU SEQRES 7 D 177 GLU ARG LEU ARG ALA VAL VAL VAL THR LEU ALA GLU ASN SEQRES 8 D 177 VAL SER ARG PRO GLU LEU LEU LEU LEU ILE ASP ALA PRO SEQRES 9 D 177 SER HIS PRO ASP PHE LEU ASN ALA TRP ARG THR VAL ASN SEQRES 10 D 177 HIS GLN TRP ILE PRO ASP THR ASP ASP LEU GLU ASN ASP SEQRES 11 D 177 ALA HIS LYS ARG ALA VAL TYR LEU VAL GLN LEU ALA ALA SEQRES 12 D 177 ASP GLY LEU PHE VAL HIS ASP TYR ILE HIS ASP ASP VAL SEQRES 13 D 177 LEU SER LYS SER LYS ARG GLN ALA MSE LEU GLU THR ILE SEQRES 14 D 177 LEU GLU LEU ILE PRO SER GLN THR SEQRES 1 E 14 DT DA DA DC DT DG DT DA DC DC DG DA DC SEQRES 2 E 14 DC SEQRES 1 F 14 DG DG DT DC DG DG DT DA DC DA DG DT DT SEQRES 2 F 14 DA SEQRES 1 G 14 DT DA DA DC DT DG DT DA DC DC DG DA DC SEQRES 2 G 14 DC SEQRES 1 H 14 DG DG DT DC DG DG DT DA DC DA DG DT DT SEQRES 2 H 14 DA MODRES 2YVH MSE A 8 MET SELENOMETHIONINE MODRES 2YVH MSE A 55 MET SELENOMETHIONINE MODRES 2YVH MSE A 165 MET SELENOMETHIONINE MODRES 2YVH MSE B 8 MET SELENOMETHIONINE MODRES 2YVH MSE B 55 MET SELENOMETHIONINE MODRES 2YVH MSE B 165 MET SELENOMETHIONINE MODRES 2YVH MSE C 8 MET SELENOMETHIONINE MODRES 2YVH MSE C 55 MET SELENOMETHIONINE MODRES 2YVH MSE C 165 MET SELENOMETHIONINE MODRES 2YVH MSE D 8 MET SELENOMETHIONINE MODRES 2YVH MSE D 55 MET SELENOMETHIONINE MODRES 2YVH MSE D 165 MET SELENOMETHIONINE HET MSE A 8 8 HET MSE A 55 8 HET MSE A 165 8 HET MSE B 8 8 HET MSE B 55 8 HET MSE B 165 8 HET MSE C 8 8 HET MSE C 55 8 HET MSE C 165 8 HET MSE D 8 8 HET MSE D 55 8 HET MSE D 165 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 12(C5 H11 N O2 SE) FORMUL 9 HOH *3(H2 O) HELIX 1 1 SER A 4 TYR A 20 1 17 HELIX 2 2 SER A 26 GLY A 35 1 10 HELIX 3 3 SER A 37 PHE A 45 1 9 HELIX 4 4 SER A 47 GLU A 66 1 20 HELIX 5 5 ASP A 76 ASN A 91 1 16 HELIX 6 6 SER A 93 ALA A 103 1 11 HELIX 7 7 HIS A 106 TRP A 113 1 8 HELIX 8 8 TRP A 113 HIS A 118 1 6 HELIX 9 9 ASP A 130 HIS A 153 1 24 HELIX 10 10 SER A 158 LEU A 172 1 15 HELIX 11 11 LYS B 5 TYR B 20 1 16 HELIX 12 12 SER B 26 GLY B 35 1 10 HELIX 13 13 SER B 37 PHE B 45 1 9 HELIX 14 14 SER B 47 ASP B 69 1 23 HELIX 15 15 ASP B 76 ASN B 91 1 16 HELIX 16 16 SER B 93 ALA B 103 1 11 HELIX 17 17 HIS B 106 TRP B 113 1 8 HELIX 18 18 TRP B 113 GLN B 119 1 7 HELIX 19 19 ASP B 126 ASN B 129 5 4 HELIX 20 20 ASP B 130 HIS B 153 1 24 HELIX 21 21 SER B 158 LEU B 172 1 15 HELIX 22 22 SER C 4 TYR C 20 1 17 HELIX 23 23 SER C 21 LEU C 25 5 5 HELIX 24 24 SER C 26 GLY C 35 1 10 HELIX 25 25 SER C 37 PHE C 45 1 9 HELIX 26 26 SER C 47 LEU C 67 1 21 HELIX 27 27 ASP C 76 ASN C 91 1 16 HELIX 28 28 SER C 93 ALA C 103 1 11 HELIX 29 29 HIS C 106 HIS C 118 1 13 HELIX 30 30 ASP C 130 HIS C 153 1 24 HELIX 31 31 SER C 158 LEU C 172 1 15 HELIX 32 32 LYS D 5 TYR D 20 1 16 HELIX 33 33 SER D 26 GLY D 35 1 10 HELIX 34 34 SER D 37 PHE D 45 1 9 HELIX 35 35 SER D 47 THR D 71 1 25 HELIX 36 36 ASP D 76 ASN D 91 1 16 HELIX 37 37 SER D 93 ALA D 103 1 11 HELIX 38 38 HIS D 106 TRP D 113 1 8 HELIX 39 39 ARG D 114 GLN D 119 1 6 HELIX 40 40 ASP D 130 HIS D 153 1 24 HELIX 41 41 SER D 158 LEU D 172 1 15 LINK C GLU A 7 N MSE A 8 1555 1555 1.33 LINK C MSE A 8 N ILE A 9 1555 1555 1.34 LINK C GLY A 54 N MSE A 55 1555 1555 1.34 LINK C MSE A 55 N HIS A 56 1555 1555 1.33 LINK C ALA A 164 N MSE A 165 1555 1555 1.33 LINK C MSE A 165 N LEU A 166 1555 1555 1.34 LINK C GLU B 7 N MSE B 8 1555 1555 1.33 LINK C MSE B 8 N ILE B 9 1555 1555 1.34 LINK C GLY B 54 N MSE B 55 1555 1555 1.33 LINK C MSE B 55 N HIS B 56 1555 1555 1.34 LINK C ALA B 164 N MSE B 165 1555 1555 1.33 LINK C MSE B 165 N LEU B 166 1555 1555 1.34 LINK C GLU C 7 N MSE C 8 1555 1555 1.34 LINK C MSE C 8 N ILE C 9 1555 1555 1.34 LINK C GLY C 54 N MSE C 55 1555 1555 1.34 LINK C MSE C 55 N HIS C 56 1555 1555 1.32 LINK C ALA C 164 N MSE C 165 1555 1555 1.34 LINK C MSE C 165 N LEU C 166 1555 1555 1.33 LINK C GLU D 7 N MSE D 8 1555 1555 1.33 LINK C MSE D 8 N ILE D 9 1555 1555 1.33 LINK C GLY D 54 N MSE D 55 1555 1555 1.33 LINK C MSE D 55 N HIS D 56 1555 1555 1.34 LINK C ALA D 164 N MSE D 165 1555 1555 1.33 LINK C MSE D 165 N LEU D 166 1555 1555 1.34 CRYST1 39.011 80.095 87.056 108.98 102.25 96.14 P 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 0.025634 0.002760 0.007018 0.00000 SCALE2 0.000000 0.012557 0.004817 0.00000 SCALE3 0.000000 0.000000 0.012589 0.00000