PDB Short entry for 1WTE HEADER HYDROLASE/DNA 22-NOV-04 1WTE TITLE CRYSTAL STRUCTURE OF TYPE II RESTRCITION ENDONUCLEASE, ECOO109I TITLE 2 COMPLEXED WITH COGNATE DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: 5'-D(*AP*CP*CP*GP*GP*GP*CP*CP*CP*TP*GP*CP*C)-3'; COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: 5'-D(*GP*GP*CP*AP*GP*GP*GP*CP*CP*CP*GP*GP*T)-3'; COMPND 7 CHAIN: Y; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: ECOO109IR; COMPND 11 CHAIN: A, B; COMPND 12 SYNONYM: TYPE II RESTRICTION ENDONUCLEASE; COMPND 13 EC: 3.1.21.4; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 MOL_ID: 2; SOURCE 4 SYNTHETIC: YES; SOURCE 5 MOL_ID: 3; SOURCE 6 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 7 ORGANISM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: HB101 KEYWDS RESTRICTION ENDONUCLEASE, DNA COMPLEX, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION NUMMDL 2 AUTHOR H.HASHIMOTO,T.SHIMIZU,T.IMASAKI,M.KATO,N.SHICHIJO,K.KITA,M.SATO REVDAT 4 13-MAR-24 1WTE 1 REMARK LINK REVDAT 3 24-FEB-09 1WTE 1 VERSN REVDAT 2 24-JAN-06 1WTE 1 JRNL REVDAT 1 14-DEC-04 1WTE 0 JRNL AUTH H.HASHIMOTO,T.SHIMIZU,T.IMASAKI,M.KATO,N.SHICHIJO,K.KITA, JRNL AUTH 2 M.SATO JRNL TITL CRYSTAL STRUCTURES OF TYPE II RESTRICTION ENDONUCLEASE JRNL TITL 2 ECOO109I AND ITS COMPLEX WITH COGNATE DNA JRNL REF J.BIOL.CHEM. V. 280 5605 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15590682 JRNL DOI 10.1074/JBC.M411684200 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.64 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.6 REMARK 3 NUMBER OF REFLECTIONS : 53090 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) : 0.173 REMARK 3 R VALUE (WORKING SET) : 0.171 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2841 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) : 1.91 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3624 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 91.95 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 213 REMARK 3 BIN FREE R VALUE : 0.3140 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4438 REMARK 3 NUCLEIC ACID ATOMS : 527 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 627 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.64 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.04000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : -0.02000 REMARK 3 B13 (A**2) : -0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.154 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.148 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.763 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5720 ; 0.018 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 4542 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7948 ; 1.794 ; 2.175 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10698 ; 1.004 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 542 ; 6.055 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 230 ;38.562 ;25.043 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 828 ;14.661 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;20.965 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 866 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5562 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 904 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1107 ; 0.271 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4469 ; 0.197 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2524 ; 0.194 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2484 ; 0.086 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 489 ; 0.198 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 12 ; 0.162 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 7 ; 0.151 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 28 ; 0.198 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.173 ; 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): 2700 ; 0.926 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1112 ; 0.285 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4356 ; 1.674 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3350 ; 2.495 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3592 ; 3.625 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 1WTE COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000023978. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.1 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 DATA SCALING SOFTWARE : CRYSTALCLEAR (MSC/RIGAKU) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 55952 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 67.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 89.4 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 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR 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 (%): 56.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 20000, SODIUM ACETATE, 6 REMARK 280 -AMINOCAPROIC ACID, PH 6.1, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 24.55150 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 101.62000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 35.93950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 101.62000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.55150 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 35.93950 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 APPLY THE FOLLOWING TO CHAINS: X, Y, A, B 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 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 1 DA X 1 O3' DA X 1 C3' -0.049 REMARK 500 1 GLU A 202 CG GLU A 202 CD 0.093 REMARK 500 1 GLU A 202 CD GLU A 202 OE1 0.078 REMARK 500 2 GLU A 202 CG GLU A 202 CD 0.093 REMARK 500 2 GLU A 202 CD GLU A 202 OE1 0.078 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 1 DC X 3 C3' - C2' - C1' ANGL. DEV. = -6.2 DEGREES REMARK 500 1 DG X 4 O4' - C1' - N9 ANGL. DEV. = 5.5 DEGREES REMARK 500 1 DG X 6 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG X 6 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DC X 7 O4' - C1' - N1 ANGL. DEV. = 2.8 DEGREES REMARK 500 1 DC X 8 O4' - C1' - N1 ANGL. DEV. = 7.8 DEGREES REMARK 500 1 DC X 9 O4' - C1' - N1 ANGL. DEV. = 3.0 DEGREES REMARK 500 1 DT X 10 O4' - C1' - N1 ANGL. DEV. = -5.0 DEGREES REMARK 500 1 DC X 12 O4' - C1' - N1 ANGL. DEV. = 8.3 DEGREES REMARK 500 1 DG Y 1 O4' - C1' - N9 ANGL. DEV. = 3.1 DEGREES REMARK 500 1 DG Y 5 O4' - C1' - N9 ANGL. DEV. = 2.7 DEGREES REMARK 500 1 DG Y 6 O4' - C4' - C3' ANGL. DEV. = -2.5 DEGREES REMARK 500 1 DG Y 6 O4' - C1' - N9 ANGL. DEV. = 3.5 DEGREES REMARK 500 1 DG Y 7 C4' - C3' - C2' ANGL. DEV. = -4.3 DEGREES REMARK 500 1 DG Y 7 O4' - C1' - N9 ANGL. DEV. = 4.8 DEGREES REMARK 500 1 DC Y 8 O4' - C1' - N1 ANGL. DEV. = 7.7 DEGREES REMARK 500 1 DC Y 10 O4' - C1' - N1 ANGL. DEV. = -7.2 DEGREES REMARK 500 1 DG Y 11 C1' - O4' - C4' ANGL. DEV. = -6.1 DEGREES REMARK 500 1 DG Y 12 O4' - C1' - N9 ANGL. DEV. = 5.2 DEGREES REMARK 500 1 ARG A 119 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 1 ARG A 119 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 1 ARG A 175 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 1 LEU A 177 CA - CB - CG ANGL. DEV. = 18.6 DEGREES REMARK 500 1 LEU A 177 CB - CG - CD2 ANGL. DEV. = 12.6 DEGREES REMARK 500 1 ARG A 178 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 1 ARG A 178 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 1 ARG B 21 CD - NE - CZ ANGL. DEV. = 8.5 DEGREES REMARK 500 1 ARG B 21 NE - CZ - NH1 ANGL. DEV. = 7.7 DEGREES REMARK 500 1 ARG B 21 NE - CZ - NH2 ANGL. DEV. = -7.5 DEGREES REMARK 500 1 ASP B 53 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 1 ARG B 119 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 1 ARG B 119 NE - CZ - NH2 ANGL. DEV. = -4.2 DEGREES REMARK 500 2 DG X 4 O4' - C1' - N9 ANGL. DEV. = 2.4 DEGREES REMARK 500 2 DG X 5 O4' - C1' - N9 ANGL. DEV. = 4.0 DEGREES REMARK 500 2 DG X 6 O4' - C1' - N9 ANGL. DEV. = 2.3 DEGREES REMARK 500 2 DC X 7 O4' - C1' - N1 ANGL. DEV. = 5.2 DEGREES REMARK 500 2 DC X 8 O4' - C1' - N1 ANGL. DEV. = 8.8 DEGREES REMARK 500 2 DT X 10 O4' - C1' - N1 ANGL. DEV. = -5.4 DEGREES REMARK 500 2 DG X 11 O4' - C1' - N9 ANGL. DEV. = -4.4 DEGREES REMARK 500 2 DC X 12 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 2 DG Y 2 O4' - C1' - N9 ANGL. DEV. = -5.2 DEGREES REMARK 500 2 DC Y 3 C3' - O3' - P ANGL. DEV. = 10.7 DEGREES REMARK 500 2 DG Y 6 O4' - C1' - N9 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 DG Y 7 O4' - C1' - N9 ANGL. DEV. = 3.8 DEGREES REMARK 500 2 DC Y 8 O4' - C1' - N1 ANGL. DEV. = 8.6 DEGREES REMARK 500 2 DC Y 9 O4' - C1' - N1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 DG Y 12 C1' - O4' - C4' ANGL. DEV. = -6.4 DEGREES REMARK 500 2 ARG A 119 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 2 ARG A 119 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 2 ARG A 175 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 60 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 1 PRO A 100 32.22 -97.56 REMARK 500 1 ASN A 208 46.47 -106.97 REMARK 500 1 GLN A 253 -18.66 -154.51 REMARK 500 1 ASN B 208 46.24 -104.16 REMARK 500 2 PRO A 100 32.22 -97.56 REMARK 500 2 ASN A 208 46.47 -106.97 REMARK 500 2 GLN A 253 -18.66 -154.51 REMARK 500 2 ASN B 208 46.24 -104.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A1001 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG X 6 OP1 REMARK 620 2 HOH X 27 O 78.9 REMARK 620 3 ASP A 110 OD2 105.4 169.4 REMARK 620 4 LEU A 125 O 157.9 79.7 96.6 REMARK 620 5 HOH A1018 O 93.4 86.6 83.5 90.9 REMARK 620 6 HOH A1022 O 87.8 96.8 93.1 89.1 176.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B1002 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DG Y 6 OP1 REMARK 620 2 HOH Y 29 O 73.3 REMARK 620 3 ASP B 110 OD2 104.2 172.9 REMARK 620 4 LEU B 125 O 152.8 82.0 101.7 REMARK 620 5 HOH B1004 O 98.1 86.9 86.9 91.5 REMARK 620 6 HOH B1066 O 85.1 95.9 90.4 86.5 176.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1001 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 1002 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WTD RELATED DB: PDB REMARK 900 TYPE II RESTRCITION ENDONUCLEASE, ECOO109I DBREF 1WTE A 1 272 UNP Q9RPJ3 Q9RPJ3_ECOLI 1 272 DBREF 1WTE B 1 272 UNP Q9RPJ3 Q9RPJ3_ECOLI 1 272 DBREF 1WTE X 1 13 PDB 1WTE 1WTE 1 13 DBREF 1WTE Y 1 13 PDB 1WTE 1WTE 1 13 SEQRES 1 X 13 DA DC DC DG DG DG DC DC DC DT DG DC DC SEQRES 1 Y 13 DG DG DC DA DG DG DG DC DC DC DG DG DT SEQRES 1 A 272 MET ASN LYS GLN GLU VAL ILE LEU LYS VAL GLN GLU CYS SEQRES 2 A 272 ALA ALA TRP TRP ILE LEU GLU ARG GLN SER LYS LEU THR SEQRES 3 A 272 LYS LEU MET SER GLU THR MET SER ILE ASN PRO PHE MET SEQRES 4 A 272 THR PRO PHE ILE PHE ASP TYR HIS SER LEU ASN ASP PHE SEQRES 5 A 272 ASP GLU LEU VAL GLU ALA ILE ILE ALA LYS HIS LEU MET SEQRES 6 A 272 THR GLY HIS ASP THR GLY PHE GLY LYS LEU ILE ASP GLU SEQRES 7 A 272 LYS ILE LEU PRO ARG VAL PHE GLY ALA TYR LYS LEU ASP SEQRES 8 A 272 LYS SER TYR ARG ALA ALA ASN GLU PRO PHE ILE HIS PRO SEQRES 9 A 272 CYS PHE ASP GLU ILE ASP HIS VAL ILE GLN ARG ASP ASP SEQRES 10 A 272 GLY ARG ILE GLU LEU LEU SER LEU LYS ALA GLY LYS TRP SEQRES 11 A 272 THR ILE GLN LEU THR MET ALA VAL GLN LEU ASN LYS ALA SEQRES 12 A 272 PHE HIS GLU ILE ILE ASN ASN TYR PRO GLY VAL ALA ASP SEQRES 13 A 272 ASN ILE VAL VAL GLY VAL PHE TYR GLY ASN SER HIS GLY SEQRES 14 A 272 LEU THR ASP LYS TYR ARG ILE LEU ARG GLY ILE ASN THR SEQRES 15 A 272 GLY ALA ASN HIS ASN VAL ILE ASP ILE ARG ASP LYS VAL SEQRES 16 A 272 HIS VAL TYR ALA GLY LYS GLU PHE TRP SER TRP LEU ASN SEQRES 17 A 272 ASN GLY GLU ALA GLU THR GLN HIS TRP VAL LEU GLU GLY SEQRES 18 A 272 ILE GLU ARG ALA VAL LYS GLU ALA ASP ILE LYS GLU LYS SEQRES 19 A 272 ASN LYS ASP LEU ILE GLU LYS PHE LYS GLU HIS VAL ALA SEQRES 20 A 272 LYS LYS TYR ASN GLU GLN VAL LEU ASN ALA ASP GLY THR SEQRES 21 A 272 ALA GLN TRP HIS LYS LEU LEU GLU MET ILE ASN GLU SEQRES 1 B 272 MET ASN LYS GLN GLU VAL ILE LEU LYS VAL GLN GLU CYS SEQRES 2 B 272 ALA ALA TRP TRP ILE LEU GLU ARG GLN SER LYS LEU THR SEQRES 3 B 272 LYS LEU MET SER GLU THR MET SER ILE ASN PRO PHE MET SEQRES 4 B 272 THR PRO PHE ILE PHE ASP TYR HIS SER LEU ASN ASP PHE SEQRES 5 B 272 ASP GLU LEU VAL GLU ALA ILE ILE ALA LYS HIS LEU MET SEQRES 6 B 272 THR GLY HIS ASP THR GLY PHE GLY LYS LEU ILE ASP GLU SEQRES 7 B 272 LYS ILE LEU PRO ARG VAL PHE GLY ALA TYR LYS LEU ASP SEQRES 8 B 272 LYS SER TYR ARG ALA ALA ASN GLU PRO PHE ILE HIS PRO SEQRES 9 B 272 CYS PHE ASP GLU ILE ASP HIS VAL ILE GLN ARG ASP ASP SEQRES 10 B 272 GLY ARG ILE GLU LEU LEU SER LEU LYS ALA GLY LYS TRP SEQRES 11 B 272 THR ILE GLN LEU THR MET ALA VAL GLN LEU ASN LYS ALA SEQRES 12 B 272 PHE HIS GLU ILE ILE ASN ASN TYR PRO GLY VAL ALA ASP SEQRES 13 B 272 ASN ILE VAL VAL GLY VAL PHE TYR GLY ASN SER HIS GLY SEQRES 14 B 272 LEU THR ASP LYS TYR ARG ILE LEU ARG GLY ILE ASN THR SEQRES 15 B 272 GLY ALA ASN HIS ASN VAL ILE ASP ILE ARG ASP LYS VAL SEQRES 16 B 272 HIS VAL TYR ALA GLY LYS GLU PHE TRP SER TRP LEU ASN SEQRES 17 B 272 ASN GLY GLU ALA GLU THR GLN HIS TRP VAL LEU GLU GLY SEQRES 18 B 272 ILE GLU ARG ALA VAL LYS GLU ALA ASP ILE LYS GLU LYS SEQRES 19 B 272 ASN LYS ASP LEU ILE GLU LYS PHE LYS GLU HIS VAL ALA SEQRES 20 B 272 LYS LYS TYR ASN GLU GLN VAL LEU ASN ALA ASP GLY THR SEQRES 21 B 272 ALA GLN TRP HIS LYS LEU LEU GLU MET ILE ASN GLU HET NA A1001 1 HET NA B1002 1 HETNAM NA SODIUM ION FORMUL 5 NA 2(NA 1+) FORMUL 7 HOH *627(H2 O) HELIX 1 1 ASN A 2 LYS A 27 1 26 HELIX 2 2 MET A 39 HIS A 47 1 9 HELIX 3 3 ASP A 51 LYS A 79 1 29 HELIX 4 4 LYS A 79 GLY A 86 1 8 HELIX 5 5 ASP A 91 ASN A 98 1 8 HELIX 6 6 HIS A 103 ILE A 109 5 7 HELIX 7 7 GLN A 133 TYR A 151 1 19 HELIX 8 8 PRO A 152 ALA A 155 5 4 HELIX 9 9 ASP A 172 LEU A 177 1 6 HELIX 10 10 GLY A 200 ASN A 208 1 9 HELIX 11 11 GLU A 213 ASP A 230 1 18 HELIX 12 12 GLU A 233 LYS A 249 1 17 HELIX 13 13 GLN A 262 GLU A 272 1 11 HELIX 14 14 ASN B 2 LYS B 27 1 26 HELIX 15 15 MET B 39 HIS B 47 1 9 HELIX 16 16 ASP B 51 LYS B 79 1 29 HELIX 17 17 LYS B 79 GLY B 86 1 8 HELIX 18 18 ASP B 91 ASN B 98 1 8 HELIX 19 19 HIS B 103 ILE B 109 5 7 HELIX 20 20 GLN B 133 TYR B 151 1 19 HELIX 21 21 PRO B 152 ALA B 155 5 4 HELIX 22 22 ASP B 172 LEU B 177 1 6 HELIX 23 23 GLY B 200 ASN B 208 1 9 HELIX 24 24 GLU B 213 ASP B 230 1 18 HELIX 25 25 LYS B 234 LYS B 248 1 15 HELIX 26 26 TYR B 250 LEU B 255 1 6 HELIX 27 27 GLN B 262 GLU B 272 1 11 SHEET 1 A 5 TYR A 88 LYS A 89 0 SHEET 2 A 5 HIS A 111 GLN A 114 -1 O VAL A 112 N TYR A 88 SHEET 3 A 5 ILE A 120 LYS A 126 -1 O GLU A 121 N ILE A 113 SHEET 4 A 5 ASN A 157 VAL A 162 1 O VAL A 159 N LEU A 122 SHEET 5 A 5 VAL A 195 ALA A 199 1 O HIS A 196 N VAL A 160 SHEET 1 B 5 TYR B 88 LYS B 89 0 SHEET 2 B 5 HIS B 111 GLN B 114 -1 O VAL B 112 N TYR B 88 SHEET 3 B 5 ILE B 120 LYS B 126 -1 O GLU B 121 N ILE B 113 SHEET 4 B 5 ASN B 157 VAL B 162 1 O VAL B 159 N LEU B 122 SHEET 5 B 5 VAL B 195 ALA B 199 1 O HIS B 196 N VAL B 160 LINK OP1 DG X 6 NA NA A1001 1555 1555 2.20 LINK O HOH X 27 NA NA A1001 1555 1555 2.35 LINK OP1 DG Y 6 NA NA B1002 1555 1555 2.22 LINK O HOH Y 29 NA NA B1002 1555 1555 2.47 LINK OD2 ASP A 110 NA NA A1001 1555 1555 2.27 LINK O LEU A 125 NA NA A1001 1555 1555 2.32 LINK NA NA A1001 O HOH A1018 1555 1555 2.40 LINK NA NA A1001 O HOH A1022 1555 1555 2.32 LINK OD2 ASP B 110 NA NA B1002 1555 1555 2.38 LINK O LEU B 125 NA NA B1002 1555 1555 2.30 LINK NA NA B1002 O HOH B1004 1555 1555 2.43 LINK NA NA B1002 O HOH B1066 1555 1555 2.18 CISPEP 1 GLU A 99 PRO A 100 1 -9.43 CISPEP 2 GLU B 99 PRO B 100 1 -0.11 CISPEP 3 GLU A 99 PRO A 100 2 -9.43 CISPEP 4 GLU B 99 PRO B 100 2 -0.11 SITE 1 AC1 6 ASP A 110 LEU A 125 HOH A1018 HOH A1022 SITE 2 AC1 6 DG X 6 HOH X 27 SITE 1 AC2 6 ASP B 110 LEU B 125 HOH B1004 HOH B1066 SITE 2 AC2 6 DG Y 6 HOH Y 29 CRYST1 49.103 71.879 203.240 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 0.020365 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013912 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004920 0.00000