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 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 MASTER 399 0 0 9 24 0 0 6 0 0 0 36 END