HEADER HYDROLASE 22-NOV-04 1WTD TITLE CRYSTAL STRUCTURE OF TYPE II RESTRCITION ENDONUCLEASE, ECOO109I DNA- TITLE 2 FREE FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: ECOO109IR; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TYPE II RESTRICTION ENDONUCLEASE; COMPND 5 EC: 3.1.21.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: HB101 KEYWDS RESTRICTION ENDONUCLEASE, DNA-FREE FROM, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR H.HASHIMOTO,T.SHIMIZU,T.IMASAKI,M.KATO,N.SHICHIJO,K.KITA,M.SATO REVDAT 5 13-MAR-24 1WTD 1 REMARK REVDAT 4 13-JUL-11 1WTD 1 VERSN REVDAT 3 24-FEB-09 1WTD 1 VERSN REVDAT 2 24-JAN-06 1WTD 1 JRNL REVDAT 1 14-DEC-04 1WTD 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 3 NUMBER OF REFLECTIONS : 25421 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) : 0.257 REMARK 3 R VALUE (WORKING SET) : 0.255 REMARK 3 FREE R VALUE : 0.297 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1343 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1883 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.3270 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.3920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4125 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 60 REMARK 3 SOLVENT ATOMS : 45 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 52.50 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.09000 REMARK 3 B22 (A**2) : 2.09000 REMARK 3 B33 (A**2) : -4.18000 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): 0.441 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.298 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL 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 : 0.896 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4268 ; 0.014 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3781 ; 0.000 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5776 ; 1.426 ; 1.938 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8736 ; 3.845 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 527 ; 5.785 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 197 ;40.519 ;25.127 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 684 ;17.626 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;20.469 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 636 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4759 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 847 ; 0.006 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1001 ; 0.211 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2086 ; 0.178 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 1966 ; 0.115 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 122 ; 0.178 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.277 ; 0.200 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): 2 ; 0.105 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 38 ; 0.180 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.158 ; 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): 2633 ; 0.702 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1086 ; 0.000 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4182 ; 1.272 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1635 ; 1.686 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1594 ; 2.643 ; 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: NULL REMARK 4 REMARK 4 1WTD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-NOV-04. REMARK 100 THE DEPOSITION ID IS D_1000023977. 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 : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000, 1.0082, 1.0089, 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 26765 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 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: MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD 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 (%): 54.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.70 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, POTASSIUM CHLORIDE, PH 8.0, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 4 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 -Y,X,Z REMARK 290 4555 Y,-X,Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -Y+1/2,X+1/2,Z+1/2 REMARK 290 8555 Y+1/2,-X+1/2,Z+1/2 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 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 87.77550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 87.77550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 22.30150 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 87.77550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 87.77550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 22.30150 REMARK 290 SMTRY1 7 0.000000 -1.000000 0.000000 87.77550 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 87.77550 REMARK 290 SMTRY3 7 0.000000 0.000000 1.000000 22.30150 REMARK 290 SMTRY1 8 0.000000 1.000000 0.000000 87.77550 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 87.77550 REMARK 290 SMTRY3 8 0.000000 0.000000 1.000000 22.30150 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8130 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 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 SER A 93 REMARK 465 TYR A 94 REMARK 465 ARG A 95 REMARK 465 ALA A 96 REMARK 465 ALA A 97 REMARK 465 ASN A 98 REMARK 465 GLU A 99 REMARK 465 PRO A 100 REMARK 465 ARG B 178 REMARK 465 GLY B 179 REMARK 465 ILE B 180 REMARK 465 ASN B 181 REMARK 465 THR B 182 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 GLU A 5 CG CD OE1 OE2 REMARK 470 LYS A 27 CG CD CE NZ REMARK 470 LYS A 74 CG CD CE NZ REMARK 470 LEU A 90 CG CD1 CD2 REMARK 470 ASP A 91 CG OD1 OD2 REMARK 470 LYS A 92 CG CD CE NZ REMARK 470 PHE A 101 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ILE A 102 CG1 CG2 CD1 REMARK 470 HIS A 103 CG ND1 CD2 CE1 NE2 REMARK 470 CYS A 105 SG REMARK 470 GLN A 114 CG CD OE1 NE2 REMARK 470 GLN A 133 CG CD OE1 NE2 REMARK 470 MET A 136 CG SD CE REMARK 470 GLN A 139 CG CD OE1 NE2 REMARK 470 LYS A 142 CG CD CE NZ REMARK 470 HIS A 145 CG ND1 CD2 CE1 NE2 REMARK 470 GLU A 146 CG CD OE1 OE2 REMARK 470 ILE A 148 CG1 CG2 CD1 REMARK 470 ASN A 149 CG OD1 ND2 REMARK 470 LEU A 170 CG CD1 CD2 REMARK 470 LYS A 173 CG CD CE NZ REMARK 470 ARG A 175 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 180 CG1 CG2 CD1 REMARK 470 ASN A 181 CG OD1 ND2 REMARK 470 ASN A 185 CG OD1 ND2 REMARK 470 ASN A 187 CG OD1 ND2 REMARK 470 ARG A 192 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 194 CG CD CE NZ REMARK 470 GLU A 233 CG CD OE1 OE2 REMARK 470 LYS A 248 CG CD CE NZ REMARK 470 LYS A 265 CG CD CE NZ REMARK 470 LYS B 9 CG CD CE NZ REMARK 470 LYS B 92 CG CD CE NZ REMARK 470 TYR B 94 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 ASN B 98 CG OD1 ND2 REMARK 470 GLU B 99 CG CD OE1 OE2 REMARK 470 LYS B 129 CG CD CE NZ REMARK 470 THR B 131 OG1 CG2 REMARK 470 LEU B 134 CG CD1 CD2 REMARK 470 MET B 136 CG SD CE REMARK 470 VAL B 138 CG1 CG2 REMARK 470 GLN B 139 CG CD OE1 NE2 REMARK 470 LYS B 142 CG CD CE NZ REMARK 470 LYS B 173 CG CD CE NZ REMARK 470 ARG B 175 CG CD NE CZ NH1 NH2 REMARK 470 ILE B 176 CG1 CG2 CD1 REMARK 470 LEU B 177 CG CD1 CD2 REMARK 470 ASN B 185 CG OD1 ND2 REMARK 470 HIS B 186 CG ND1 CD2 CE1 NE2 REMARK 470 ASN B 187 CG OD1 ND2 REMARK 470 VAL B 188 CG1 CG2 REMARK 470 ILE B 189 CG1 CG2 CD1 REMARK 470 ARG B 192 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 233 CG CD OE1 OE2 REMARK 470 LYS B 248 CG CD CE NZ REMARK 470 GLU B 252 CG CD OE1 OE2 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 MET A 1 CB - CA - C ANGL. DEV. = 13.0 DEGREES REMARK 500 MET A 1 N - CA - C ANGL. DEV. = -30.4 DEGREES REMARK 500 PRO B 100 C - N - CA ANGL. DEV. = 9.4 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 MET A 33 102.23 -41.29 REMARK 500 HIS A 103 -48.83 160.96 REMARK 500 PRO A 104 -118.05 -52.38 REMARK 500 CYS A 105 56.36 -101.74 REMARK 500 ASP A 117 -70.89 -73.95 REMARK 500 ALA A 127 -78.98 -104.32 REMARK 500 TRP A 130 63.91 74.91 REMARK 500 TYR A 151 68.73 25.44 REMARK 500 ALA A 155 61.40 -157.96 REMARK 500 LEU A 170 44.05 -76.89 REMARK 500 ILE A 180 48.67 -162.70 REMARK 500 THR A 182 -144.40 -83.47 REMARK 500 ASN A 187 66.06 -68.51 REMARK 500 ARG A 192 -37.05 -38.73 REMARK 500 GLU A 211 98.74 -54.08 REMARK 500 PHE B 85 -154.59 -101.99 REMARK 500 LEU B 90 64.05 -102.04 REMARK 500 PRO B 100 59.30 -6.90 REMARK 500 TRP B 130 75.69 52.24 REMARK 500 LEU B 134 -52.40 -25.52 REMARK 500 ILE B 176 -59.89 177.46 REMARK 500 ASN B 185 159.02 132.65 REMARK 500 HIS B 186 172.56 68.47 REMARK 500 VAL B 188 126.11 177.72 REMARK 500 ILE B 191 39.14 -140.74 REMARK 500 ASP B 230 71.65 53.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 307 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 310 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WTE RELATED DB: PDB REMARK 900 COMPLEXED WITH COGNATE DNA DBREF 1WTD A 1 272 UNP Q9RPJ3 Q9RPJ3_ECOLI 1 272 DBREF 1WTD B 1 272 UNP Q9RPJ3 Q9RPJ3_ECOLI 1 272 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 GOL A 304 6 HET GOL A 306 6 HET GOL A 309 6 HET GOL B 301 6 HET GOL B 302 6 HET GOL B 303 6 HET GOL B 305 6 HET GOL B 307 6 HET GOL B 308 6 HET GOL B 310 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 10(C3 H8 O3) FORMUL 13 HOH *45(H2 O) HELIX 1 1 ASN A 2 SER A 23 1 22 HELIX 2 2 THR A 26 GLU A 31 1 6 HELIX 3 3 MET A 39 HIS A 47 1 9 HELIX 4 4 ASP A 51 LYS A 79 1 29 HELIX 5 5 LYS A 79 GLY A 86 1 8 HELIX 6 6 GLN A 133 ASN A 150 1 18 HELIX 7 7 THR A 171 GLY A 179 1 9 HELIX 8 8 GLY A 200 ASN A 208 1 9 HELIX 9 9 GLU A 213 ASP A 230 1 18 HELIX 10 10 GLU A 233 LYS A 249 1 17 HELIX 11 11 TYR A 250 LEU A 255 1 6 HELIX 12 12 GLN A 262 GLU A 272 1 11 HELIX 13 13 ASN B 2 SER B 23 1 22 HELIX 14 14 THR B 26 GLU B 31 1 6 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 PHE B 85 1 7 HELIX 18 18 ASP B 91 ASN B 98 1 8 HELIX 19 19 HIS B 103 ASP B 107 5 5 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 LEU B 170 ARG B 175 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 ILE B 231 LEU B 255 1 25 HELIX 26 26 GLN B 262 ASN B 271 1 10 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 LEU A 123 N HIS A 111 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 LEU B 123 -1 O LEU B 123 N HIS B 111 SHEET 4 B 5 ASN B 157 VAL B 159 1 O VAL B 159 N LEU B 122 SHEET 5 B 5 VAL B 195 HIS B 196 1 O HIS B 196 N ILE B 158 SITE 1 AC1 3 GLU A 213 HIS A 216 GLU B 268 SITE 1 AC2 5 ALA A 15 SER B 23 THR B 26 MET B 29 SITE 2 AC2 5 HOH B 317 SITE 1 AC3 6 GLU A 223 ASP A 258 ALA B 261 GLN B 262 SITE 2 AC3 6 TRP B 263 HIS B 264 SITE 1 AC4 4 LYS A 9 GLU A 12 CYS A 13 ARG A 83 SITE 1 AC5 5 HIS A 47 GLU B 57 ILE B 60 ALA B 61 SITE 2 AC5 5 ILE B 239 SITE 1 AC6 5 SER A 23 THR A 26 GLU B 12 ALA B 15 SITE 2 AC6 5 LEU B 19 SITE 1 AC7 6 ASP A 69 HOH A 328 ILE B 35 ASN B 36 SITE 2 AC7 6 ILE B 59 LYS B 62 SITE 1 AC8 7 ALA A 61 LYS A 62 MET A 65 HIS B 47 SITE 2 AC8 7 ALA B 58 ALA B 61 LYS B 62 SITE 1 AC9 7 ASN A 36 ILE A 43 ILE A 59 LYS A 62 SITE 2 AC9 7 MET B 65 ASP B 69 HOH B 312 SITE 1 BC1 6 ARG B 21 LYS B 24 HIS B 63 LEU B 64 SITE 2 BC1 6 GLY B 67 HOH B 328 CRYST1 175.551 175.551 44.603 90.00 90.00 90.00 I 4 16 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 0.005696 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005696 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022420 0.00000