HEADER HYDROLASE/DNA 10-SEP-09 3JSP TITLE CLASSIC PROTEIN WITH A NEW TWIST: CRYSTAL STRUCTURE OF A LEXA TITLE 2 REPRESSOR DNA COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: LEXA REPRESSOR; COMPND 3 CHAIN: A, B; COMPND 4 EC: 3.4.21.88; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: DNA (5'- COMPND 9 D(*TP*AP*TP*AP*CP*TP*GP*TP*AP*TP*GP*CP*GP*CP*AP*TP*AP*CP*AP*GP*TP*A)- COMPND 10 3'); COMPND 11 CHAIN: C, D; COMPND 12 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI K-12; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: LEXA, EXRA, SPR, TSL, UMUA, B4043, JW4003; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3)PLYSS; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET21A; SOURCE 11 MOL_ID: 2; SOURCE 12 SYNTHETIC: YES KEYWDS PROTEIN-DNA COMPLEX, WINGED HELIX-TURN-HELIX, DOUBLE HELIX, KEYWDS 2 REPRESSOR, LEXA, SOS SYSTEM, AUTOCATALYTIC CLEAVAGE, DNA DAMAGE, DNA KEYWDS 3 REPAIR, DNA REPLICATION, DNA-BINDING, HYDROLASE, SOS RESPONSE, KEYWDS 4 TRANSCRIPTION, TRANSCRIPTION REGULATION, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.P.P.ZHANG,Y.Z.PIGLI,P.A.RICE REVDAT 5 21-FEB-24 3JSP 1 REMARK REVDAT 4 13-OCT-21 3JSP 1 SEQADV REVDAT 3 01-NOV-17 3JSP 1 REMARK REVDAT 2 21-MAR-12 3JSP 1 JRNL VERSN REVDAT 1 18-AUG-10 3JSP 0 JRNL AUTH A.P.ZHANG,Y.Z.PIGLI,P.A.RICE JRNL TITL STRUCTURE OF THE LEXA-DNA COMPLEX AND IMPLICATIONS FOR SOS JRNL TITL 2 BOX MEASUREMENT. JRNL REF NATURE V. 466 883 2010 JRNL REFN ISSN 0028-0836 JRNL PMID 20703307 JRNL DOI 10.1038/NATURE09200 REMARK 2 REMARK 2 RESOLUTION. 2.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0088 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) : 2.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.89 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 84.6 REMARK 3 NUMBER OF REFLECTIONS : 14241 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) : 0.267 REMARK 3 R VALUE (WORKING SET) : 0.266 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 721 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) : 2.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 546 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 48.39 REMARK 3 BIN R VALUE (WORKING SET) : 0.5240 REMARK 3 BIN FREE R VALUE SET COUNT : 41 REMARK 3 BIN FREE R VALUE : 0.5840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2973 REMARK 3 NUCLEIC ACID ATOMS : 896 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 11 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 78.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.12000 REMARK 3 B33 (A**2) : -0.11000 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): 1.198 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.480 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.534 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 69.429 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.926 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.925 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4020 ; 0.006 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5613 ; 1.149 ; 2.258 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 381 ; 4.781 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;34.572 ;23.841 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 551 ;15.299 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;16.660 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 645 ; 0.070 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2714 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 4 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 69 REMARK 3 RESIDUE RANGE : B 2 B 69 REMARK 3 RESIDUE RANGE : C 1 C 22 REMARK 3 RESIDUE RANGE : D 1 D 22 REMARK 3 ORIGIN FOR THE GROUP (A): 22.1170 9.3670 38.6840 REMARK 3 T TENSOR REMARK 3 T11: 0.0174 T22: 0.3612 REMARK 3 T33: 0.3005 T12: -0.0629 REMARK 3 T13: -0.0296 T23: -0.0235 REMARK 3 L TENSOR REMARK 3 L11: 0.7503 L22: 5.0672 REMARK 3 L33: 10.0531 L12: 0.5453 REMARK 3 L13: -0.4571 L23: -1.4015 REMARK 3 S TENSOR REMARK 3 S11: 0.0247 S12: 0.0232 S13: -0.0030 REMARK 3 S21: 0.0066 S22: -0.0279 S23: -0.0731 REMARK 3 S31: 0.2085 S32: -0.5934 S33: 0.0033 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 75 A 199 REMARK 3 RESIDUE RANGE : B 75 B 199 REMARK 3 ORIGIN FOR THE GROUP (A): 68.9990 19.5310 42.7950 REMARK 3 T TENSOR REMARK 3 T11: 0.7215 T22: 0.4397 REMARK 3 T33: 0.4546 T12: -0.2221 REMARK 3 T13: -0.1049 T23: -0.0665 REMARK 3 L TENSOR REMARK 3 L11: 1.5701 L22: 5.9997 REMARK 3 L33: 10.4083 L12: 0.4289 REMARK 3 L13: -1.1319 L23: -4.7372 REMARK 3 S TENSOR REMARK 3 S11: 0.0211 S12: 0.1561 S13: -0.1165 REMARK 3 S21: -0.3612 S22: 0.1429 S23: 0.4840 REMARK 3 S31: 1.2075 S32: -0.9227 S33: -0.1640 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 3JSP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055110. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : MIRROS 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 : 15637 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 5.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.7 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06900 REMARK 200 FOR THE DATA SET : 25.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLECULAR REPLACEMENT 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 (%): 60.90 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.15 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M BIS-TRIS PROPANE, 0.1M SODIUM REMARK 280 TARTRATE, 12% (W/V) PEG3350, PH 6.8, HANGING DROP, TEMPERATURE REMARK 280 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z 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 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 47.09650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 58.43450 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 47.09650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 58.43450 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: THE BIOLOGICAL UNIT IS A DIMERIC PROTEIN (CHAINS A & B) REMARK 300 BOUND TO A DNA DUPLEX (CHAINS C & D). 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: 8400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25740 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -47.0 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 GLU A 71 REMARK 465 GLU A 72 REMARK 465 GLU A 73 REMARK 465 GLU A 74 REMARK 465 ASP A 200 REMARK 465 TRP A 201 REMARK 465 LEU A 202 REMARK 465 MET B 1 REMARK 465 GLU B 72 REMARK 465 GLU B 73 REMARK 465 GLU B 74 REMARK 465 ALA B 83 REMARK 465 ALA B 84 REMARK 465 GLY B 85 REMARK 465 GLU B 86 REMARK 465 PRO B 87 REMARK 465 LEU B 88 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 GLN A 70 CG CD OE1 NE2 REMARK 470 GLN B 70 CG CD OE1 NE2 REMARK 470 GLU B 71 CG CD OE1 OE2 REMARK 470 LEU B 89 CG CD1 CD2 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 O LEU A 78 O ILE A 94 1.54 REMARK 500 OE1 GLU A 86 CE1 HIS A 93 1.83 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 DT C 1 O4' - C1' - N1 ANGL. DEV. = 3.9 DEGREES REMARK 500 DA C 2 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 DT C 3 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DA C 4 O4' - C1' - N9 ANGL. DEV. = 2.5 DEGREES REMARK 500 DA C 19 O4' - C1' - N9 ANGL. DEV. = 1.9 DEGREES REMARK 500 DT D 1 O4' - C1' - N1 ANGL. DEV. = 4.7 DEGREES REMARK 500 DT D 3 O4' - C1' - N1 ANGL. DEV. = 2.7 DEGREES REMARK 500 DA D 4 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 DT D 6 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DT D 8 C5' - C4' - O4' ANGL. DEV. = 7.1 DEGREES REMARK 500 DC D 12 O4' - C1' - N1 ANGL. DEV. = 2.1 DEGREES REMARK 500 DG D 13 C3' - O3' - P ANGL. DEV. = 7.2 DEGREES REMARK 500 DT D 16 O4' - C1' - N1 ANGL. DEV. = 2.0 DEGREES REMARK 500 DG D 20 O4' - C1' - N9 ANGL. DEV. = 2.2 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 PRO A 87 -119.59 -67.55 REMARK 500 LEU A 89 6.86 83.66 REMARK 500 GLN A 92 -14.49 82.15 REMARK 500 GLU A 95 -2.74 86.55 REMARK 500 ASP A 127 105.50 -48.01 REMARK 500 ASP A 151 14.20 59.20 REMARK 500 GLN A 161 65.10 -116.46 REMARK 500 ASN A 171 149.24 -171.09 REMARK 500 GLN A 183 18.93 -161.19 REMARK 500 ASN A 198 25.94 -150.48 REMARK 500 LEU B 69 -65.32 -125.58 REMARK 500 GLU B 95 -70.47 -124.76 REMARK 500 SER B 103 48.89 -82.11 REMARK 500 LYS B 159 85.75 -161.60 REMARK 500 ASN B 171 140.15 175.55 REMARK 500 GLN B 183 15.46 -143.01 REMARK 500 PHE B 186 111.27 -161.01 REMARK 500 ASP B 200 33.20 -99.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3JSO RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH A DIFFERENT DNA SUBSTRATE DBREF 3JSP A 1 202 UNP P0A7C2 LEXA_ECOLI 1 202 DBREF 3JSP B 1 202 UNP P0A7C2 LEXA_ECOLI 1 202 DBREF 3JSP C 1 22 PDB 3JSP 3JSP 1 22 DBREF 3JSP D 1 22 PDB 3JSP 3JSP 1 22 SEQADV 3JSP ALA A 156 UNP P0A7C2 LYS 156 ENGINEERED MUTATION SEQADV 3JSP ALA B 156 UNP P0A7C2 LYS 156 ENGINEERED MUTATION SEQRES 1 A 202 MET LYS ALA LEU THR ALA ARG GLN GLN GLU VAL PHE ASP SEQRES 2 A 202 LEU ILE ARG ASP HIS ILE SER GLN THR GLY MET PRO PRO SEQRES 3 A 202 THR ARG ALA GLU ILE ALA GLN ARG LEU GLY PHE ARG SER SEQRES 4 A 202 PRO ASN ALA ALA GLU GLU HIS LEU LYS ALA LEU ALA ARG SEQRES 5 A 202 LYS GLY VAL ILE GLU ILE VAL SER GLY ALA SER ARG GLY SEQRES 6 A 202 ILE ARG LEU LEU GLN GLU GLU GLU GLU GLY LEU PRO LEU SEQRES 7 A 202 VAL GLY ARG VAL ALA ALA GLY GLU PRO LEU LEU ALA GLN SEQRES 8 A 202 GLN HIS ILE GLU GLY HIS TYR GLN VAL ASP PRO SER LEU SEQRES 9 A 202 PHE LYS PRO ASN ALA ASP PHE LEU LEU ARG VAL SER GLY SEQRES 10 A 202 MET SER MET LYS ASP ILE GLY ILE MET ASP GLY ASP LEU SEQRES 11 A 202 LEU ALA VAL HIS LYS THR GLN ASP VAL ARG ASN GLY GLN SEQRES 12 A 202 VAL VAL VAL ALA ARG ILE ASP ASP GLU VAL THR VAL ALA SEQRES 13 A 202 ARG LEU LYS LYS GLN GLY ASN LYS VAL GLU LEU LEU PRO SEQRES 14 A 202 GLU ASN SER GLU PHE LYS PRO ILE VAL VAL ASP LEU ARG SEQRES 15 A 202 GLN GLN SER PHE THR ILE GLU GLY LEU ALA VAL GLY VAL SEQRES 16 A 202 ILE ARG ASN GLY ASP TRP LEU SEQRES 1 B 202 MET LYS ALA LEU THR ALA ARG GLN GLN GLU VAL PHE ASP SEQRES 2 B 202 LEU ILE ARG ASP HIS ILE SER GLN THR GLY MET PRO PRO SEQRES 3 B 202 THR ARG ALA GLU ILE ALA GLN ARG LEU GLY PHE ARG SER SEQRES 4 B 202 PRO ASN ALA ALA GLU GLU HIS LEU LYS ALA LEU ALA ARG SEQRES 5 B 202 LYS GLY VAL ILE GLU ILE VAL SER GLY ALA SER ARG GLY SEQRES 6 B 202 ILE ARG LEU LEU GLN GLU GLU GLU GLU GLY LEU PRO LEU SEQRES 7 B 202 VAL GLY ARG VAL ALA ALA GLY GLU PRO LEU LEU ALA GLN SEQRES 8 B 202 GLN HIS ILE GLU GLY HIS TYR GLN VAL ASP PRO SER LEU SEQRES 9 B 202 PHE LYS PRO ASN ALA ASP PHE LEU LEU ARG VAL SER GLY SEQRES 10 B 202 MET SER MET LYS ASP ILE GLY ILE MET ASP GLY ASP LEU SEQRES 11 B 202 LEU ALA VAL HIS LYS THR GLN ASP VAL ARG ASN GLY GLN SEQRES 12 B 202 VAL VAL VAL ALA ARG ILE ASP ASP GLU VAL THR VAL ALA SEQRES 13 B 202 ARG LEU LYS LYS GLN GLY ASN LYS VAL GLU LEU LEU PRO SEQRES 14 B 202 GLU ASN SER GLU PHE LYS PRO ILE VAL VAL ASP LEU ARG SEQRES 15 B 202 GLN GLN SER PHE THR ILE GLU GLY LEU ALA VAL GLY VAL SEQRES 16 B 202 ILE ARG ASN GLY ASP TRP LEU SEQRES 1 C 22 DT DA DT DA DC DT DG DT DA DT DG DC DG SEQRES 2 C 22 DC DA DT DA DC DA DG DT DA SEQRES 1 D 22 DT DA DT DA DC DT DG DT DA DT DG DC DG SEQRES 2 D 22 DC DA DT DA DC DA DG DT DA FORMUL 5 HOH *11(H2 O) HELIX 1 1 THR A 5 GLY A 23 1 19 HELIX 2 2 THR A 27 GLY A 36 1 10 HELIX 3 3 SER A 39 LYS A 53 1 15 HELIX 4 4 ASP A 101 PHE A 105 5 5 HELIX 5 5 MET A 120 GLY A 124 5 5 HELIX 6 6 THR B 5 GLY B 23 1 19 HELIX 7 7 THR B 27 GLY B 36 1 10 HELIX 8 8 SER B 39 LYS B 53 1 15 HELIX 9 9 MET B 120 GLY B 124 5 5 SHEET 1 A 2 ILE A 56 ILE A 58 0 SHEET 2 A 2 ILE A 66 LEU A 68 -1 O ARG A 67 N GLU A 57 SHEET 1 B 8 HIS A 97 TYR A 98 0 SHEET 2 B 8 LEU A 76 VAL A 79 -1 N LEU A 76 O TYR A 98 SHEET 3 B 8 PHE A 111 ARG A 114 1 O LEU A 112 N PRO A 77 SHEET 4 B 8 LEU A 130 HIS A 134 -1 O LEU A 131 N LEU A 113 SHEET 5 B 8 PHE A 186 ARG A 197 -1 O LEU A 191 N HIS A 134 SHEET 6 B 8 PHE B 186 ARG B 197 -1 O ARG B 197 N VAL A 195 SHEET 7 B 8 LEU B 130 HIS B 134 -1 N HIS B 134 O LEU B 191 SHEET 8 B 8 PHE B 111 ARG B 114 -1 N LEU B 113 O LEU B 131 SHEET 1 C10 ILE A 177 ASP A 180 0 SHEET 2 C10 LYS A 164 LEU A 168 -1 N LEU A 167 O ILE A 177 SHEET 3 C10 GLU A 152 GLN A 161 -1 N ARG A 157 O LEU A 168 SHEET 4 C10 VAL A 144 ILE A 149 -1 N ALA A 147 O THR A 154 SHEET 5 C10 PHE A 186 ARG A 197 -1 O GLU A 189 N VAL A 146 SHEET 6 C10 PHE B 186 ARG B 197 -1 O ARG B 197 N VAL A 195 SHEET 7 C10 VAL B 144 ILE B 149 -1 N VAL B 146 O GLU B 189 SHEET 8 C10 GLU B 152 GLN B 161 -1 O THR B 154 N ALA B 147 SHEET 9 C10 LYS B 164 LEU B 168 -1 O LEU B 168 N ARG B 157 SHEET 10 C10 ILE B 177 ASP B 180 -1 O VAL B 179 N VAL B 165 SHEET 1 D 2 ILE B 56 ILE B 58 0 SHEET 2 D 2 ILE B 66 LEU B 68 -1 O ARG B 67 N GLU B 57 SHEET 1 E 2 PRO B 77 LEU B 78 0 SHEET 2 E 2 GLY B 96 HIS B 97 -1 O GLY B 96 N LEU B 78 CISPEP 1 LEU A 88 LEU A 89 0 -13.54 CISPEP 2 LYS A 106 PRO A 107 0 1.33 CISPEP 3 GLN B 92 HIS B 93 0 -1.03 CISPEP 4 ILE B 94 GLU B 95 0 7.19 CISPEP 5 LYS B 106 PRO B 107 0 -4.48 CRYST1 94.193 116.869 66.477 90.00 90.00 90.00 P 21 21 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 0.010617 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008557 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015043 0.00000