HEADER DNA BINDING PROTEIN/DNA 08-SEP-09 3JRA TITLE CRYSTAL STRUCTURE OF FIS BOUND TO 27BP NON CONSENSUS SEQUENCE DNA F6 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA-BINDING PROTEIN FIS; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (27-MER); COMPND 7 CHAIN: C; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: DNA (27-MER); COMPND 11 CHAIN: D; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: FIS, B3261, JW3229; 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: PET11A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES; SOURCE 13 MOL_ID: 3; SOURCE 14 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, HTH DOMAIN, MINOR GROOVE COMPRESSION, DNA KEYWDS 2 BENDING, INDIRECT RECOGNITION, ACTIVATOR, DNA-BINDING, KEYWDS 3 TRANSCRIPTION, TRANSCRIPTION REGULATION, DNA BINDING PROTEIN-DNA KEYWDS 4 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.STELLA,D.CASCIO,R.C.JOHNSON REVDAT 4 21-FEB-24 3JRA 1 REMARK REVDAT 3 01-NOV-17 3JRA 1 REMARK REVDAT 2 13-JUL-11 3JRA 1 VERSN REVDAT 1 28-APR-10 3JRA 0 JRNL AUTH S.STELLA,D.CASCIO,R.C.JOHNSON JRNL TITL THE SHAPE OF THE DNA MINOR GROOVE DIRECTS BINDING BY THE JRNL TITL 2 DNA-BENDING PROTEIN FIS. JRNL REF GENES DEV. V. 24 814 2010 JRNL REFN ISSN 0890-9369 JRNL PMID 20395367 JRNL DOI 10.1101/GAD.1900610 REMARK 2 REMARK 2 RESOLUTION. 3.11 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) : 3.11 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 81.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 90.9 REMARK 3 NUMBER OF REFLECTIONS : 10999 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) : 0.240 REMARK 3 R VALUE (WORKING SET) : 0.238 REMARK 3 FREE R VALUE : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 527 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) : 3.11 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.19 REMARK 3 REFLECTION IN BIN (WORKING SET) : 142 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 17.60 REMARK 3 BIN R VALUE (WORKING SET) : 0.2980 REMARK 3 BIN FREE R VALUE SET COUNT : 9 REMARK 3 BIN FREE R VALUE : 0.4760 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1505 REMARK 3 NUCLEIC ACID ATOMS : 1101 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 8 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 48.16 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 9.911 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.453 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.384 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.922 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.889 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2752 ; 0.007 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1523 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3942 ; 1.331 ; 2.470 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3785 ; 1.030 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 187 ; 5.082 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 75 ;38.110 ;25.600 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 303 ;18.414 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;17.989 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): NULL ; NULL ; NULL REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2210 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 274 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 640 ; 0.209 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1771 ; 0.192 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1207 ; 0.207 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1175 ; 0.082 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 64 ; 0.137 ; 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): 18 ; 0.189 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 35 ; 0.172 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.137 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 4 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 8 A 98 REMARK 3 ORIGIN FOR THE GROUP (A): 12.8437 11.1893 8.8456 REMARK 3 T TENSOR REMARK 3 T11: -0.3989 T22: -0.1690 REMARK 3 T33: -0.3426 T12: -0.0198 REMARK 3 T13: -0.0022 T23: 0.0078 REMARK 3 L TENSOR REMARK 3 L11: 1.9047 L22: 6.2782 REMARK 3 L33: 3.8274 L12: -1.3523 REMARK 3 L13: 0.8569 L23: -0.7249 REMARK 3 S TENSOR REMARK 3 S11: -0.1649 S12: -0.0400 S13: -0.0745 REMARK 3 S21: 0.5457 S22: 0.1713 S23: -0.2072 REMARK 3 S31: 0.4875 S32: 0.2801 S33: -0.0063 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 98 REMARK 3 ORIGIN FOR THE GROUP (A): 9.7434 11.6706 2.1159 REMARK 3 T TENSOR REMARK 3 T11: -0.4578 T22: -0.1864 REMARK 3 T33: -0.3575 T12: 0.0623 REMARK 3 T13: -0.0219 T23: 0.0288 REMARK 3 L TENSOR REMARK 3 L11: 3.1166 L22: 5.5733 REMARK 3 L33: 3.2082 L12: 1.3736 REMARK 3 L13: -0.7219 L23: -0.2922 REMARK 3 S TENSOR REMARK 3 S11: -0.0450 S12: -0.2433 S13: -0.0275 REMARK 3 S21: 0.1191 S22: 0.0285 S23: 0.1909 REMARK 3 S31: 0.1481 S32: 0.0600 S33: 0.0164 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 1 C 27 REMARK 3 ORIGIN FOR THE GROUP (A): 11.5215 -9.6247 5.2404 REMARK 3 T TENSOR REMARK 3 T11: 0.2824 T22: -0.0913 REMARK 3 T33: -0.0827 T12: 0.0936 REMARK 3 T13: -0.0194 T23: 0.0378 REMARK 3 L TENSOR REMARK 3 L11: 1.5913 L22: 1.1586 REMARK 3 L33: 10.8906 L12: 0.1439 REMARK 3 L13: 2.8625 L23: 0.9704 REMARK 3 S TENSOR REMARK 3 S11: 0.5533 S12: 0.0454 S13: -0.7232 REMARK 3 S21: 0.2655 S22: 0.2603 S23: 0.0876 REMARK 3 S31: 2.0869 S32: 0.4582 S33: -0.8136 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 : D 1 D 27 REMARK 3 ORIGIN FOR THE GROUP (A): 10.6129 -9.6921 6.0444 REMARK 3 T TENSOR REMARK 3 T11: 0.3169 T22: -0.2194 REMARK 3 T33: -0.0368 T12: -0.0275 REMARK 3 T13: -0.0750 T23: -0.0022 REMARK 3 L TENSOR REMARK 3 L11: 1.9763 L22: 0.6135 REMARK 3 L33: 15.7395 L12: -0.0986 REMARK 3 L13: 3.9242 L23: -0.2085 REMARK 3 S TENSOR REMARK 3 S11: 0.4779 S12: -0.0924 S13: -0.7339 REMARK 3 S21: 0.1735 S22: 0.2873 S23: -0.0401 REMARK 3 S31: 1.8512 S32: -0.1477 S33: -0.7652 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 3JRA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 18-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055059. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-07 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 : ALS REMARK 200 BEAMLINE : 8.2.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 11963 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.100 REMARK 200 RESOLUTION RANGE LOW (A) : 90.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.8 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.13900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.21 REMARK 200 COMPLETENESS FOR SHELL (%) : 84.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.45300 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: 3IV5 REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 69.84 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M SODIUM CITRATE, 0.1 M TRIS-HCL REMARK 280 PH 8.5, 36% PEG 400, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277K 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 21.62000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 77.43500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 47.61000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 77.43500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 21.62000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 47.61000 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 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8770 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19040 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -62.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 PHE A 2 REMARK 465 GLU A 3 REMARK 465 GLN A 4 REMARK 465 ARG A 5 REMARK 465 VAL A 6 REMARK 465 ASN A 7 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 DA C 1 O4' - C1' - N9 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG C 7 O4' - C1' - N9 ANGL. DEV. = 4.2 DEGREES REMARK 500 DG C 8 O4' - C4' - C3' ANGL. DEV. = -5.2 DEGREES REMARK 500 DG C 8 C1' - O4' - C4' ANGL. DEV. = -6.3 DEGREES REMARK 500 DG C 8 O4' - C1' - N9 ANGL. DEV. = 5.4 DEGREES REMARK 500 DT C 9 O4' - C1' - N1 ANGL. DEV. = 4.6 DEGREES REMARK 500 DT C 13 O4' - C1' - N1 ANGL. DEV. = 4.5 DEGREES REMARK 500 DT C 14 C3' - O3' - P ANGL. DEV. = 7.8 DEGREES REMARK 500 DC C 20 O4' - C1' - N1 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT C 21 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA C 22 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 DA D 1 C3' - C2' - C1' ANGL. DEV. = -5.0 DEGREES REMARK 500 DA D 1 O4' - C1' - N9 ANGL. DEV. = 3.7 DEGREES REMARK 500 DT D 5 O4' - C1' - N1 ANGL. DEV. = 2.4 DEGREES REMARK 500 DA D 7 O4' - C1' - N9 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT D 9 O4' - C1' - N1 ANGL. DEV. = 3.6 DEGREES REMARK 500 DA D 12 C3' - C2' - C1' ANGL. DEV. = -5.1 DEGREES REMARK 500 DA D 19 O4' - C1' - N9 ANGL. DEV. = 2.0 DEGREES REMARK 500 DA D 19 C3' - O3' - P ANGL. DEV. = 8.6 DEGREES REMARK 500 DC D 21 O4' - C1' - N1 ANGL. DEV. = 3.4 DEGREES REMARK 500 DT D 25 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 DT D 25 C3' - O3' - P ANGL. DEV. = 7.4 DEGREES REMARK 500 DT D 26 O4' - C1' - N1 ANGL. DEV. = -4.4 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 ASN A 48 -77.82 -120.79 REMARK 500 ARG A 71 55.92 36.56 REMARK 500 GLN B 19 31.03 -99.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3IV5 RELATED DB: PDB REMARK 900 RELATED ID: 3JR9 RELATED DB: PDB REMARK 900 RELATED ID: 3JRB RELATED DB: PDB REMARK 900 RELATED ID: 3JRC RELATED DB: PDB REMARK 900 RELATED ID: 3JRD RELATED DB: PDB REMARK 900 RELATED ID: 3JRE RELATED DB: PDB REMARK 900 RELATED ID: 3JRF RELATED DB: PDB REMARK 900 RELATED ID: 3JRG RELATED DB: PDB REMARK 900 RELATED ID: 3JRH RELATED DB: PDB REMARK 900 RELATED ID: 3JRI RELATED DB: PDB DBREF 3JRA A 1 98 UNP P0A6R3 FIS_ECOLI 1 98 DBREF 3JRA B 1 98 UNP P0A6R3 FIS_ECOLI 1 98 DBREF 3JRA C 1 27 PDB 3JRA 3JRA 1 27 DBREF 3JRA D 1 27 PDB 3JRA 3JRA 1 27 SEQRES 1 A 98 MET PHE GLU GLN ARG VAL ASN SER ASP VAL LEU THR VAL SEQRES 2 A 98 SER THR VAL ASN SER GLN ASP GLN VAL THR GLN LYS PRO SEQRES 3 A 98 LEU ARG ASP SER VAL LYS GLN ALA LEU LYS ASN TYR PHE SEQRES 4 A 98 ALA GLN LEU ASN GLY GLN ASP VAL ASN ASP LEU TYR GLU SEQRES 5 A 98 LEU VAL LEU ALA GLU VAL GLU GLN PRO LEU LEU ASP MET SEQRES 6 A 98 VAL MET GLN TYR THR ARG GLY ASN GLN THR ARG ALA ALA SEQRES 7 A 98 LEU MET MET GLY ILE ASN ARG GLY THR LEU ARG LYS LYS SEQRES 8 A 98 LEU LYS LYS TYR GLY MET ASN SEQRES 1 B 98 MET PHE GLU GLN ARG VAL ASN SER ASP VAL LEU THR VAL SEQRES 2 B 98 SER THR VAL ASN SER GLN ASP GLN VAL THR GLN LYS PRO SEQRES 3 B 98 LEU ARG ASP SER VAL LYS GLN ALA LEU LYS ASN TYR PHE SEQRES 4 B 98 ALA GLN LEU ASN GLY GLN ASP VAL ASN ASP LEU TYR GLU SEQRES 5 B 98 LEU VAL LEU ALA GLU VAL GLU GLN PRO LEU LEU ASP MET SEQRES 6 B 98 VAL MET GLN TYR THR ARG GLY ASN GLN THR ARG ALA ALA SEQRES 7 B 98 LEU MET MET GLY ILE ASN ARG GLY THR LEU ARG LYS LYS SEQRES 8 B 98 LEU LYS LYS TYR GLY MET ASN SEQRES 1 C 27 DA DA DA DT DT DT DG DG DT DC DA DT DT SEQRES 2 C 27 DT DC DT DT DA DA DC DT DA DA DA DT DT SEQRES 3 C 27 DT SEQRES 1 D 27 DA DA DA DT DT DT DA DG DT DT DA DA DG SEQRES 2 D 27 DA DA DA DT DG DA DC DC DA DA DA DT DT SEQRES 3 D 27 DT FORMUL 5 HOH *8(H2 O) HELIX 1 1 LEU A 27 LEU A 42 1 16 HELIX 2 2 ASP A 49 THR A 70 1 22 HELIX 3 3 ASN A 73 GLY A 82 1 10 HELIX 4 4 ASN A 84 TYR A 95 1 12 HELIX 5 5 VAL B 6 VAL B 10 5 5 HELIX 6 6 LEU B 27 ASN B 43 1 17 HELIX 7 7 ASP B 49 THR B 70 1 22 HELIX 8 8 ASN B 73 GLY B 82 1 10 HELIX 9 9 ASN B 84 TYR B 95 1 12 SHEET 1 A 2 THR A 12 VAL A 16 0 SHEET 2 A 2 VAL A 22 PRO A 26 -1 O LYS A 25 N VAL A 13 SHEET 1 B 2 THR B 12 VAL B 16 0 SHEET 2 B 2 VAL B 22 PRO B 26 -1 O THR B 23 N THR B 15 CRYST1 43.240 95.220 154.870 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 0.023127 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010502 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006457 0.00000