HEADER HYDROLASE 24-JUN-03 1PU6 TITLE CRYSTAL STRUCTURE OF H.PYLORI 3-METHYLADENINE DNA TITLE 2 GLYCOSYLASE (MAGIII) COMPND MOL_ID: 1; COMPND 2 MOLECULE: 3-METHYLADENINE DNA GLYCOSYLASE; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 210; SOURCE 4 STRAIN: 13-5; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PGEX-6P-1 KEYWDS HELIX-HAIRPIN-HELIX, 3-METHYLADENINE, BASE EXCISION REPAIR, KEYWDS 2 GLYCOSYLASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.F.EICHMAN,E.J.O'ROURKE,J.P.RADICELLA,T.ELLENBERGER REVDAT 2 24-FEB-09 1PU6 1 VERSN REVDAT 1 07-OCT-03 1PU6 0 JRNL AUTH B.F.EICHMAN,E.J.O'ROURKE,J.P.RADICELLA, JRNL AUTH 2 T.ELLENBERGER JRNL TITL CRYSTAL STRUCTURES OF 3-METHYLADENINE DNA JRNL TITL 2 GLYCOSYLASE MAGIII AND THE RECOGNITION OF JRNL TITL 3 ALKYLATED BASES JRNL REF EMBO J. V. 22 4898 2003 JRNL REFN ISSN 0261-4189 JRNL PMID 14517230 JRNL DOI 10.1093/EMBOJ/CDG505 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.J.O'ROURKE,C.CHEVALIER,S.BOITEUX,A.LABIGNE, REMARK 1 AUTH 2 L.IELPI,J.P.RADICELLA REMARK 1 TITL A NOVEL 3-METHYLADENINE DNA GLYCOSYLASE FROM REMARK 1 TITL 2 HELICOBACTER PYLORI DEFINES A NEW CLASS WITHIN THE REMARK 1 TITL 3 ENDONUCLEASE III FAMILY OF BASE EXCISION REPAIR REMARK 1 TITL 4 GLYCOSYLASES REMARK 1 REF J.BIOL.CHEM. V. 275 20077 2000 REMARK 1 REFN ISSN 0021-9258 REMARK 1 DOI 10.1074/JBC.M001071200 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.41 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 57518 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) : 0.153 REMARK 3 R VALUE (WORKING SET) : 0.151 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.200 REMARK 3 FREE R VALUE TEST SET COUNT : 3124 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) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.68 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2809 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1430 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.1940 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3474 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 1 REMARK 3 SOLVENT ATOMS : 254 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.20000 REMARK 3 B22 (A**2) : 0.26000 REMARK 3 B33 (A**2) : -0.64000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.32000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.100 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.079 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.046 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.326 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3557 ; 0.021 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4799 ; 1.602 ; 1.968 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 432 ; 4.932 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 537 ; 0.160 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2622 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1515 ; 0.213 ; 0.200 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): 132 ; 0.129 ; 0.200 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): 48 ; 0.163 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 12 ; 0.140 ; 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): 2155 ; 1.943 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3439 ; 3.065 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1402 ; 4.799 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1360 ; 6.847 ; 4.500 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 : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: ANISOU PARAMETERS WERE DERIVED FROM REMARK 3 REFINED TLS PARAMETERS (5 TLS GROUPS) AND HELD FIXED DURING REMARK 3 REFINEMENT REMARK 4 REMARK 4 1PU6 COMPLIES WITH FORMAT V. 3.15, 01-DEC-08 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 03-JUL-03. REMARK 100 THE RCSB ID CODE IS RCSB019568. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-JAN-02; 19-JUL-02 REMARK 200 TEMPERATURE (KELVIN) : 110; 110 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : CHESS; NSLS REMARK 200 BEAMLINE : A1; X12C REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9450; 1.0000, 0.9686, 1.0083 REMARK 200 MONOCHROMATOR : NULL; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 210; CUSTOM-MADE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60643 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 8.100 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.09900 REMARK 200 FOR THE DATA SET : 21.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.71 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.33700 REMARK 200 FOR SHELL : 4.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL; MAD REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MAD REMARK 200 SOFTWARE USED: MLPHARE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.52 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, HEPES, MPD, PH 7.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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 73.30250 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.19950 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 73.30250 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.19950 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 VAL A 1 REMARK 465 VAL B 1 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 LYS A 18 CG CD CE NZ REMARK 470 LYS A 30 CE NZ REMARK 470 LYS A 44 CD CE NZ REMARK 470 LYS A 50 CD CE NZ REMARK 470 LYS A 71 NZ REMARK 470 GLU A 76 CD OE1 OE2 REMARK 470 GLU A 82 CG CD OE1 OE2 REMARK 470 LYS A 151 CD CE NZ REMARK 470 LYS A 159 CD CE NZ REMARK 470 GLU A 163 CD OE1 OE2 REMARK 470 GLU A 215 CD OE1 OE2 REMARK 470 LYS A 217 CG CD CE NZ REMARK 470 LEU A 218 C O CB CG CD1 CD2 REMARK 470 GLU B 32 CD REMARK 470 LYS B 44 CG CD CE NZ REMARK 470 LYS B 50 CD CE NZ REMARK 470 GLU B 62 CG CD OE1 OE2 REMARK 470 GLU B 76 OE1 OE2 REMARK 470 LYS B 106 NZ REMARK 470 GLU B 163 CD OE1 OE2 REMARK 470 GLU B 165 CG CD OE1 OE2 REMARK 470 LEU B 214 CG CD1 CD2 REMARK 470 GLU B 215 CD OE1 OE2 REMARK 470 LYS B 217 CD CE NZ 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 ASP A 150 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 LEU A 170 CB - CG - CD2 ANGL. DEV. = 13.9 DEGREES REMARK 500 ASP B 64 CB - CG - OD2 ANGL. DEV. = 5.8 DEGREES REMARK 500 LEU B 170 CB - CG - CD2 ANGL. DEV. = 10.8 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 TRP A 24 -55.66 70.24 REMARK 500 GLU A 62 -148.70 -132.48 REMARK 500 GLN A 109 -36.43 76.94 REMARK 500 ASP A 150 -179.57 -171.84 REMARK 500 TRP B 24 -54.71 68.26 REMARK 500 GLU B 62 -154.07 -127.14 REMARK 500 GLN B 109 -32.10 77.50 REMARK 500 ASP B 150 -178.07 -170.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 519 DISTANCE = 5.41 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 301 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 302 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 303 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MPD B 304 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PU7 RELATED DB: PDB REMARK 900 3,9-DIMETHYLADENINE BOUND TO MAGIII REMARK 900 RELATED ID: 1PU8 RELATED DB: PDB REMARK 900 1,N6-ETHENOADENINE BOUND TO MAGIII REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE DIFFERENCES BETWEEN THE SEQUENCES IN THE PDB REMARK 999 ENTRY 1PU6 AND IN THE DATABASE REFERENCE ARE DUE REMARK 999 TO THE PARTICULAR H.PYLORI STRAIN. DATABASE REMARK 999 REFERENCE REFERS TO H.PYLORI STRAIN J99; MAGIII REMARK 999 WAS CLONED FROM H.PYLORI STRAIN 13/5 REMARK 999 (SEE REFERENCE 1) DBREF 1PU6 A 1 218 UNP O25323 O25323_HELPY 1 218 DBREF 1PU6 B 1 218 UNP O25323 O25323_HELPY 1 218 SEQADV 1PU6 VAL A 1 UNP O25323 MET 1 SEE REMARK 999 SEQADV 1PU6 GLY A 102 UNP O25323 LYS 102 SEE REMARK 999 SEQADV 1PU6 ARG A 120 UNP O25323 LYS 120 SEE REMARK 999 SEQADV 1PU6 ALA A 141 UNP O25323 VAL 141 SEE REMARK 999 SEQADV 1PU6 KCX A 205 UNP O25323 LYS 205 MODIFIED RESIDUE SEQADV 1PU6 VAL B 1 UNP O25323 MET 1 SEE REMARK 999 SEQADV 1PU6 GLY B 102 UNP O25323 LYS 102 SEE REMARK 999 SEQADV 1PU6 ARG B 120 UNP O25323 LYS 120 SEE REMARK 999 SEQADV 1PU6 ALA B 141 UNP O25323 VAL 141 SEE REMARK 999 SEQADV 1PU6 KCX B 205 UNP O25323 LYS 205 MODIFIED RESIDUE SEQRES 1 A 218 VAL LEU ASP SER PHE GLU ILE LEU LYS ALA LEU LYS SER SEQRES 2 A 218 LEU ASP LEU LEU LYS ASN ALA PRO ALA TRP TRP TRP PRO SEQRES 3 A 218 ASN ALA LEU LYS PHE GLU ALA LEU LEU GLY ALA VAL LEU SEQRES 4 A 218 THR GLN ASN THR LYS PHE GLU ALA VAL LEU LYS SER LEU SEQRES 5 A 218 GLU ASN LEU LYS ASN ALA PHE ILE LEU GLU ASN ASP ASP SEQRES 6 A 218 GLU ILE ASN LEU LYS LYS ILE ALA TYR ILE GLU PHE SER SEQRES 7 A 218 LYS LEU ALA GLU CYS VAL ARG PRO SER GLY PHE TYR ASN SEQRES 8 A 218 GLN LYS ALA LYS ARG LEU ILE ASP LEU SER GLY ASN ILE SEQRES 9 A 218 LEU LYS ASP PHE GLN SER PHE GLU ASN PHE LYS GLN GLU SEQRES 10 A 218 VAL THR ARG GLU TRP LEU LEU ASP GLN LYS GLY ILE GLY SEQRES 11 A 218 LYS GLU SER ALA ASP ALA ILE LEU CYS TYR ALA CYS ALA SEQRES 12 A 218 LYS GLU VAL MET VAL VAL ASP LYS TYR SER TYR LEU PHE SEQRES 13 A 218 LEU LYS LYS LEU GLY ILE GLU ILE GLU ASP TYR ASP GLU SEQRES 14 A 218 LEU GLN HIS PHE PHE GLU LYS GLY VAL GLN GLU ASN LEU SEQRES 15 A 218 ASN SER ALA LEU ALA LEU TYR GLU ASN THR ILE SER LEU SEQRES 16 A 218 ALA GLN LEU TYR ALA ARG PHE HIS GLY KCX ILE VAL GLU SEQRES 17 A 218 PHE SER LYS GLN LYS LEU GLU LEU LYS LEU SEQRES 1 B 218 VAL LEU ASP SER PHE GLU ILE LEU LYS ALA LEU LYS SER SEQRES 2 B 218 LEU ASP LEU LEU LYS ASN ALA PRO ALA TRP TRP TRP PRO SEQRES 3 B 218 ASN ALA LEU LYS PHE GLU ALA LEU LEU GLY ALA VAL LEU SEQRES 4 B 218 THR GLN ASN THR LYS PHE GLU ALA VAL LEU LYS SER LEU SEQRES 5 B 218 GLU ASN LEU LYS ASN ALA PHE ILE LEU GLU ASN ASP ASP SEQRES 6 B 218 GLU ILE ASN LEU LYS LYS ILE ALA TYR ILE GLU PHE SER SEQRES 7 B 218 LYS LEU ALA GLU CYS VAL ARG PRO SER GLY PHE TYR ASN SEQRES 8 B 218 GLN LYS ALA LYS ARG LEU ILE ASP LEU SER GLY ASN ILE SEQRES 9 B 218 LEU LYS ASP PHE GLN SER PHE GLU ASN PHE LYS GLN GLU SEQRES 10 B 218 VAL THR ARG GLU TRP LEU LEU ASP GLN LYS GLY ILE GLY SEQRES 11 B 218 LYS GLU SER ALA ASP ALA ILE LEU CYS TYR ALA CYS ALA SEQRES 12 B 218 LYS GLU VAL MET VAL VAL ASP LYS TYR SER TYR LEU PHE SEQRES 13 B 218 LEU LYS LYS LEU GLY ILE GLU ILE GLU ASP TYR ASP GLU SEQRES 14 B 218 LEU GLN HIS PHE PHE GLU LYS GLY VAL GLN GLU ASN LEU SEQRES 15 B 218 ASN SER ALA LEU ALA LEU TYR GLU ASN THR ILE SER LEU SEQRES 16 B 218 ALA GLN LEU TYR ALA ARG PHE HIS GLY KCX ILE VAL GLU SEQRES 17 B 218 PHE SER LYS GLN LYS LEU GLU LEU LYS LEU MODRES 1PU6 KCX A 205 LYS LYSINE NZ-CARBOXYLIC ACID MODRES 1PU6 KCX B 205 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 205 12 HET KCX B 205 12 HET CL A 301 1 HET BME A 302 4 HET MPD B 303 8 HET MPD B 304 8 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM CL CHLORIDE ION HETNAM BME BETA-MERCAPTOETHANOL HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL FORMUL 1 KCX 2(C7 H14 N2 O4) FORMUL 3 CL CL 1- FORMUL 4 BME C2 H6 O S FORMUL 5 MPD 2(C6 H14 O2) FORMUL 7 HOH *234(H2 O) HELIX 1 1 ASP A 3 SER A 13 1 11 HELIX 2 2 LYS A 30 THR A 40 1 11 HELIX 3 3 LYS A 44 ALA A 58 1 15 HELIX 4 4 ASP A 64 ILE A 75 1 12 HELIX 5 5 GLU A 76 VAL A 84 1 9 HELIX 6 6 ARG A 85 GLY A 88 5 4 HELIX 7 7 PHE A 89 GLN A 109 1 21 HELIX 8 8 SER A 110 VAL A 118 1 9 HELIX 9 9 THR A 119 ASP A 125 1 7 HELIX 10 10 GLY A 130 ALA A 141 1 12 HELIX 11 11 ASP A 150 LEU A 160 1 11 HELIX 12 12 ASP A 166 GLU A 180 1 15 HELIX 13 13 ASN A 181 LEU A 188 1 8 HELIX 14 14 SER A 194 LEU A 216 1 23 HELIX 15 15 ASP B 3 SER B 13 1 11 HELIX 16 16 LYS B 30 THR B 40 1 11 HELIX 17 17 LYS B 44 ALA B 58 1 15 HELIX 18 18 ASP B 64 ILE B 75 1 12 HELIX 19 19 GLU B 76 VAL B 84 1 9 HELIX 20 20 ARG B 85 GLY B 88 5 4 HELIX 21 21 PHE B 89 GLN B 109 1 21 HELIX 22 22 SER B 110 VAL B 118 1 9 HELIX 23 23 THR B 119 ASP B 125 1 7 HELIX 24 24 GLY B 130 ALA B 141 1 12 HELIX 25 25 ASP B 150 LEU B 160 1 11 HELIX 26 26 ASP B 166 GLU B 180 1 15 HELIX 27 27 ASN B 181 LEU B 188 1 8 HELIX 28 28 SER B 194 LEU B 216 1 23 LINK C GLY A 204 N KCX A 205 1555 1555 1.34 LINK C KCX A 205 N ILE A 206 1555 1555 1.34 LINK C GLY B 204 N KCX B 205 1555 1555 1.34 LINK C KCX B 205 N ILE B 206 1555 1555 1.32 SITE 1 AC1 3 GLN A 41 ASN A 42 ARG A 96 SITE 1 AC2 6 TRP A 24 TRP A 25 THR A 40 PHE A 45 SITE 2 AC2 6 HOH A 373 HOH A 481 SITE 1 AC3 3 ALA A 187 GLU A 190 HOH B 468 SITE 1 AC4 4 SER A 184 ALA A 187 PHE B 209 GLN B 212 CRYST1 146.605 44.399 81.516 90.00 106.40 90.00 C 1 2 1 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 0.006821 0.000000 0.002008 0.00000 SCALE2 0.000000 0.022523 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012788 0.00000