PDB Short entry for 1DIZ HEADER HYDROLASE/DNA 30-NOV-99 1DIZ TITLE CRYSTAL STRUCTURE OF E. COLI 3-METHYLADENINE DNA GLYCOSYLASE (ALKA) TITLE 2 COMPLEXED WITH DNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DNA (5'-D(*GP*AP*CP*AP*TP*GP*AP*(NRI)P*TP*GP*CP*CP*T)-3'); COMPND 3 CHAIN: C, E; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: DNA (5'-D(*GP*GP*CP*AP*AP*TP*CP*AP*TP*GP*TP*CP*A)-3'); COMPND 7 CHAIN: D, F; COMPND 8 ENGINEERED: YES; COMPND 9 MOL_ID: 3; COMPND 10 MOLECULE: 3-METHYLADENINE DNA GLYCOSYLASE II; COMPND 11 CHAIN: A, B; COMPND 12 SYNONYM: 3-METHYLADENINE-DNA GLYCOSYLASE II, INDUCIBLE, TAG II, ALKA; COMPND 13 EC: 3.2.2.21; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 SYNTHETIC: YES; SOURCE 3 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 4 ORGANISM_TAXID: 562; SOURCE 5 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN E. COLI; SOURCE 6 MOL_ID: 2; SOURCE 7 SYNTHETIC: YES; SOURCE 8 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 9 ORGANISM_TAXID: 562; SOURCE 10 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN E. COLI; SOURCE 11 MOL_ID: 3; SOURCE 12 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 13 ORGANISM_TAXID: 562; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS 3-METHYLADENINE DNA GLYCOSYLASE, ALKA, HELIX-HAIRPIN-HELIX, PROTEIN- KEYWDS 2 DNA COMPLEX, 1-AZARIBOSE, HYDROLASE-DNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.HOLLIS,Y.ICHIKAWA,T.E.ELLENBERGER REVDAT 5 07-FEB-24 1DIZ 1 REMARK LINK REVDAT 4 27-APR-16 1DIZ 1 CONECT LINK SOURCE VERSN REVDAT 3 24-FEB-09 1DIZ 1 VERSN REVDAT 2 20-JUN-00 1DIZ 1 LINK REVDAT 1 20-MAR-00 1DIZ 0 JRNL AUTH T.HOLLIS,Y.ICHIKAWA,T.ELLENBERGER JRNL TITL DNA BENDING AND A FLIP-OUT MECHANISM FOR BASE EXCISION BY JRNL TITL 2 THE HELIX-HAIRPIN-HELIX DNA GLYCOSYLASE, ESCHERICHIA COLI JRNL TITL 3 ALKA. JRNL REF EMBO J. V. 19 758 2000 JRNL REFN ISSN 0261-4189 JRNL PMID 10675345 JRNL DOI 10.1093/EMBOJ/19.4.758 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1074819.790 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 97.8 REMARK 3 NUMBER OF REFLECTIONS : 26809 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 SET) : 0.250 REMARK 3 FREE R VALUE : 0.290 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.300 REMARK 3 FREE R VALUE TEST SET COUNT : 2495 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.006 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.65 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.10 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 4126 REMARK 3 BIN R VALUE (WORKING SET) : 0.3230 REMARK 3 BIN FREE R VALUE : 0.4130 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.10 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 220 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.028 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4398 REMARK 3 NUCLEIC ACID ATOMS : 1036 REMARK 3 HETEROGEN ATOMS : 2 REMARK 3 SOLVENT ATOMS : 207 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 44.20 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.25000 REMARK 3 B22 (A**2) : 0.25000 REMARK 3 B33 (A**2) : -0.51000 REMARK 3 B12 (A**2) : -0.79000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM SIGMAA (A) : 0.33 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.50 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.43 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.600 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.010 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.44 REMARK 3 BSOL : 56.80 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : PROTEIN_REP.PA REMARK 3 PARAMETER FILE 2 : DNA-AZA.PARAM REMARK 3 PARAMETER FILE 3 : WATER_REP.PARA REMARK 3 PARAMETER FILE 4 : ION.PARAM REMARK 3 PARAMETER FILE 5 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : DNA-AZA.TOP REMARK 3 TOPOLOGY FILE 3 : WATER.TOP REMARK 3 TOPOLOGY FILE 4 : ION.TOP REMARK 3 TOPOLOGY FILE 5 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DIZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010118. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUN-99 REMARK 200 TEMPERATURE (KELVIN) : 138 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X25 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : BRANDEIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27877 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 8.000 REMARK 200 R MERGE (I) : 0.08500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 0.21000 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: NULL REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG 4000, 100MM HEPES, 100MM NACL, REMARK 280 50MM MGCL2, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 66.56667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 133.13333 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 133.13333 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 66.56667 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: E, F, A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, D, 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 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 ARG A 56 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 97 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 133 CG CD CE NZ REMARK 470 ARG B 56 CG CD NE CZ NH1 NH2 REMARK 470 ARG B 97 CG CD NE CZ NH1 NH2 REMARK 470 LYS B 133 CG CD CE NZ 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 ARG B 80 OD1 ASP B 83 2.13 REMARK 500 NH1 ARG A 80 OE1 GLU B 73 2.16 REMARK 500 REMARK 500 REMARK: NULL 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 NRI E 8 O3' DT E 9 P 0.172 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 9 O3' - P - O5' ANGL. DEV. = -17.9 DEGREES REMARK 500 DT C 9 O3' - P - OP2 ANGL. DEV. = 23.4 DEGREES REMARK 500 DA E 7 C3' - O3' - P ANGL. DEV. = 9.9 DEGREES REMARK 500 NRI E 8 C3' - O3' - P ANGL. DEV. = 7.3 DEGREES REMARK 500 DT E 9 O3' - P - O5' ANGL. DEV. = -17.4 DEGREES REMARK 500 DT E 9 O3' - P - OP2 ANGL. DEV. = 19.6 DEGREES REMARK 500 PRO A 150 C - N - CA ANGL. DEV. = 10.6 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 SER A 26 -7.33 80.29 REMARK 500 HIS A 57 51.77 39.08 REMARK 500 ALA A 94 -32.11 -134.55 REMARK 500 LEU A 125 -55.25 55.76 REMARK 500 ALA A 164 155.12 -46.18 REMARK 500 ALA A 171 5.80 -57.65 REMARK 500 LEU A 235 76.39 -113.39 REMARK 500 PHE A 245 65.24 -112.42 REMARK 500 GLU A 275 -71.45 -25.03 REMARK 500 ASP A 280 98.32 -66.86 REMARK 500 GLU A 281 118.03 -31.50 REMARK 500 VAL B 41 78.85 -113.42 REMARK 500 VAL B 70 42.10 -108.04 REMARK 500 ASP B 83 70.84 32.16 REMARK 500 LEU B 125 -63.80 56.17 REMARK 500 PHE B 149 67.56 -151.06 REMARK 500 PHE B 245 68.92 -107.23 REMARK 500 ALA B 251 0.12 -60.89 REMARK 500 GLU B 275 -72.18 -25.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 DA D 18 0.06 SIDE CHAIN REMARK 500 DA F 18 0.08 SIDE CHAIN 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 B 824 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC C 11 OP2 REMARK 620 2 GLN B 210 O 125.8 REMARK 620 3 PHE B 212 O 129.1 103.2 REMARK 620 4 ILE B 215 O 81.4 84.5 91.3 REMARK 620 5 HOH B 844 O 75.2 71.3 141.1 125.2 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 825 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 DC E 11 OP2 REMARK 620 2 GLN A 210 O 140.7 REMARK 620 3 PHE A 212 O 110.4 100.3 REMARK 620 4 ILE A 215 O 75.4 85.9 81.4 REMARK 620 5 HOH A 850 O 98.9 74.3 134.6 140.8 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA B 824 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 825 DBREF 1DIZ A 1 282 UNP P04395 3MG2_ECOLI 1 282 DBREF 1DIZ B 1 282 UNP P04395 3MG2_ECOLI 1 282 DBREF 1DIZ C 1 13 PDB 1DIZ 1DIZ 1 13 DBREF 1DIZ D 14 26 PDB 1DIZ 1DIZ 14 26 DBREF 1DIZ E 1 13 PDB 1DIZ 1DIZ 1 13 DBREF 1DIZ F 14 26 PDB 1DIZ 1DIZ 14 26 SEQRES 1 C 13 DG DA DC DA DT DG DA NRI DT DG DC DC DT SEQRES 1 D 13 DG DG DC DA DA DT DC DA DT DG DT DC DA SEQRES 1 E 13 DG DA DC DA DT DG DA NRI DT DG DC DC DT SEQRES 1 F 13 DG DG DC DA DA DT DC DA DT DG DT DC DA SEQRES 1 A 282 MET TYR THR LEU ASN TRP GLN PRO PRO TYR ASP TRP SER SEQRES 2 A 282 TRP MET LEU GLY PHE LEU ALA ALA ARG ALA VAL SER SER SEQRES 3 A 282 VAL GLU THR VAL ALA ASP SER TYR TYR ALA ARG SER LEU SEQRES 4 A 282 ALA VAL GLY GLU TYR ARG GLY VAL VAL THR ALA ILE PRO SEQRES 5 A 282 ASP ILE ALA ARG HIS THR LEU HIS ILE ASN LEU SER ALA SEQRES 6 A 282 GLY LEU GLU PRO VAL ALA ALA GLU CYS LEU ALA LYS MET SEQRES 7 A 282 SER ARG LEU PHE ASP LEU GLN CYS ASN PRO GLN ILE VAL SEQRES 8 A 282 ASN GLY ALA LEU GLY ARG LEU GLY ALA ALA ARG PRO GLY SEQRES 9 A 282 LEU ARG LEU PRO GLY CYS VAL ASP ALA PHE GLU GLN GLY SEQRES 10 A 282 VAL ARG ALA ILE LEU GLY GLN LEU VAL SER VAL ALA MET SEQRES 11 A 282 ALA ALA LYS LEU THR ALA ARG VAL ALA GLN LEU TYR GLY SEQRES 12 A 282 GLU ARG LEU ASP ASP PHE PRO GLU TYR ILE CYS PHE PRO SEQRES 13 A 282 THR PRO GLN ARG LEU ALA ALA ALA ASP PRO GLN ALA LEU SEQRES 14 A 282 LYS ALA LEU GLY MET PRO LEU LYS ARG ALA GLU ALA LEU SEQRES 15 A 282 ILE HIS LEU ALA ASN ALA ALA LEU GLU GLY THR LEU PRO SEQRES 16 A 282 MET THR ILE PRO GLY ASP VAL GLU GLN ALA MET LYS THR SEQRES 17 A 282 LEU GLN THR PHE PRO GLY ILE GLY ARG TRP THR ALA ASN SEQRES 18 A 282 TYR PHE ALA LEU ARG GLY TRP GLN ALA LYS ASP VAL PHE SEQRES 19 A 282 LEU PRO ASP ASP TYR LEU ILE LYS GLN ARG PHE PRO GLY SEQRES 20 A 282 MET THR PRO ALA GLN ILE ARG ARG TYR ALA GLU ARG TRP SEQRES 21 A 282 LYS PRO TRP ARG SER TYR ALA LEU LEU HIS ILE TRP TYR SEQRES 22 A 282 THR GLU GLY TRP GLN PRO ASP GLU ALA SEQRES 1 B 282 MET TYR THR LEU ASN TRP GLN PRO PRO TYR ASP TRP SER SEQRES 2 B 282 TRP MET LEU GLY PHE LEU ALA ALA ARG ALA VAL SER SER SEQRES 3 B 282 VAL GLU THR VAL ALA ASP SER TYR TYR ALA ARG SER LEU SEQRES 4 B 282 ALA VAL GLY GLU TYR ARG GLY VAL VAL THR ALA ILE PRO SEQRES 5 B 282 ASP ILE ALA ARG HIS THR LEU HIS ILE ASN LEU SER ALA SEQRES 6 B 282 GLY LEU GLU PRO VAL ALA ALA GLU CYS LEU ALA LYS MET SEQRES 7 B 282 SER ARG LEU PHE ASP LEU GLN CYS ASN PRO GLN ILE VAL SEQRES 8 B 282 ASN GLY ALA LEU GLY ARG LEU GLY ALA ALA ARG PRO GLY SEQRES 9 B 282 LEU ARG LEU PRO GLY CYS VAL ASP ALA PHE GLU GLN GLY SEQRES 10 B 282 VAL ARG ALA ILE LEU GLY GLN LEU VAL SER VAL ALA MET SEQRES 11 B 282 ALA ALA LYS LEU THR ALA ARG VAL ALA GLN LEU TYR GLY SEQRES 12 B 282 GLU ARG LEU ASP ASP PHE PRO GLU TYR ILE CYS PHE PRO SEQRES 13 B 282 THR PRO GLN ARG LEU ALA ALA ALA ASP PRO GLN ALA LEU SEQRES 14 B 282 LYS ALA LEU GLY MET PRO LEU LYS ARG ALA GLU ALA LEU SEQRES 15 B 282 ILE HIS LEU ALA ASN ALA ALA LEU GLU GLY THR LEU PRO SEQRES 16 B 282 MET THR ILE PRO GLY ASP VAL GLU GLN ALA MET LYS THR SEQRES 17 B 282 LEU GLN THR PHE PRO GLY ILE GLY ARG TRP THR ALA ASN SEQRES 18 B 282 TYR PHE ALA LEU ARG GLY TRP GLN ALA LYS ASP VAL PHE SEQRES 19 B 282 LEU PRO ASP ASP TYR LEU ILE LYS GLN ARG PHE PRO GLY SEQRES 20 B 282 MET THR PRO ALA GLN ILE ARG ARG TYR ALA GLU ARG TRP SEQRES 21 B 282 LYS PRO TRP ARG SER TYR ALA LEU LEU HIS ILE TRP TYR SEQRES 22 B 282 THR GLU GLY TRP GLN PRO ASP GLU ALA HET NRI C 8 11 HET NRI E 8 11 HET NA A 825 1 HET NA B 824 1 HETNAM NRI PHOSPHORIC ACID MONO-(4-HYDROXY-PYRROLIDIN-3-YLMETHYL) HETNAM 2 NRI ESTER HETNAM NA SODIUM ION FORMUL 1 NRI 2(C5 H12 N O5 P) FORMUL 7 NA 2(NA 1+) FORMUL 9 HOH *207(H2 O) HELIX 1 1 ASP A 11 ARG A 22 1 12 HELIX 2 2 ALA A 65 PRO A 69 5 5 HELIX 3 3 VAL A 70 PHE A 82 1 13 HELIX 4 4 ASN A 87 ASN A 92 1 6 HELIX 5 5 VAL A 91 GLY A 96 1 6 HELIX 6 6 GLY A 96 ALA A 101 1 6 HELIX 7 7 ASP A 112 LEU A 122 1 11 HELIX 8 8 SER A 127 GLY A 143 1 17 HELIX 9 9 THR A 157 ALA A 164 1 8 HELIX 10 10 ASP A 165 ALA A 171 1 7 HELIX 11 11 PRO A 175 GLY A 192 1 18 HELIX 12 12 ASP A 201 GLN A 210 1 10 HELIX 13 13 GLY A 216 TRP A 228 1 13 HELIX 14 14 ASP A 238 GLN A 243 1 6 HELIX 15 15 THR A 197 GLU A 258 1 62 HELIX 16 16 ARG A 259 LYS A 261 5 3 HELIX 17 17 TRP A 263 TYR A 273 1 11 HELIX 18 18 ASP B 11 ALA B 23 1 13 HELIX 19 19 ALA B 65 PRO B 69 5 5 HELIX 20 20 VAL B 70 PHE B 82 1 13 HELIX 21 21 ASN B 87 GLY B 96 1 10 HELIX 22 22 ARG B 97 GLY B 99 5 3 HELIX 23 23 ASP B 112 GLY B 123 1 12 HELIX 24 24 SER B 127 GLY B 143 1 17 HELIX 25 25 THR B 157 ALA B 163 1 7 HELIX 26 26 ASP B 165 ALA B 171 1 7 HELIX 27 27 PRO B 175 GLY B 192 1 18 HELIX 28 28 ASP B 201 GLN B 210 1 10 HELIX 29 29 GLY B 216 TRP B 228 1 13 HELIX 30 30 LEU B 240 PHE B 245 1 6 HELIX 31 31 THR B 249 GLU B 258 1 10 HELIX 32 32 ARG B 259 LYS B 261 5 3 HELIX 33 33 TRP B 263 TYR B 273 1 11 SHEET 1 A 5 TYR A 2 ASN A 5 0 SHEET 2 A 5 THR A 58 LEU A 63 -1 N LEU A 59 O LEU A 4 SHEET 3 A 5 TYR A 44 ASP A 53 -1 O THR A 49 N ASN A 62 SHEET 4 A 5 TYR A 35 VAL A 41 -1 O TYR A 35 N ALA A 50 SHEET 5 A 5 GLU A 28 VAL A 30 -1 N THR A 29 O ALA A 36 SHEET 1 B 5 TYR B 2 ASN B 5 0 SHEET 2 B 5 THR B 58 LEU B 63 -1 N LEU B 59 O LEU B 4 SHEET 3 B 5 TYR B 44 ASP B 53 -1 O THR B 49 N ASN B 62 SHEET 4 B 5 TYR B 35 VAL B 41 -1 O TYR B 35 N ALA B 50 SHEET 5 B 5 GLU B 28 VAL B 30 -1 N THR B 29 O ALA B 36 SHEET 1 C 2 ARG B 145 LEU B 146 0 SHEET 2 C 2 PHE B 149 ILE B 153 -1 N PHE B 149 O LEU B 146 LINK O3' DA C 7 P NRI C 8 1555 1555 1.57 LINK O3' NRI C 8 P DT C 9 1555 1555 1.68 LINK O3' DA E 7 P NRI E 8 1555 1555 1.55 LINK O3' NRI E 8 P DT E 9 1555 1555 1.78 LINK OP2 DC C 11 NA NA B 824 1555 1555 2.57 LINK OP2 DC E 11 NA NA A 825 1555 1555 2.53 LINK O GLN A 210 NA NA A 825 1555 1555 2.54 LINK O PHE A 212 NA NA A 825 1555 1555 2.84 LINK O ILE A 215 NA NA A 825 1555 1555 2.74 LINK NA NA A 825 O HOH A 850 1555 1555 2.57 LINK O GLN B 210 NA NA B 824 1555 1555 2.68 LINK O PHE B 212 NA NA B 824 1555 1555 2.62 LINK O ILE B 215 NA NA B 824 1555 1555 2.68 LINK NA NA B 824 O HOH B 844 1555 1555 2.84 CISPEP 1 PRO A 8 PRO A 9 0 0.11 CISPEP 2 LYS A 261 PRO A 262 0 -0.20 CISPEP 3 PRO B 8 PRO B 9 0 0.09 CISPEP 4 LYS B 261 PRO B 262 0 -0.42 SITE 1 AC1 5 GLN B 210 PHE B 212 ILE B 215 HOH B 844 SITE 2 AC1 5 DC C 11 SITE 1 AC2 5 GLN A 210 PHE A 212 ILE A 215 HOH A 850 SITE 2 AC2 5 DC E 11 CRYST1 82.400 82.400 199.700 90.00 90.00 120.00 P 31 2 1 12 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 0.012136 0.007007 0.000000 0.00000 SCALE2 0.000000 0.014013 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005008 0.00000