PDB Short entry for 1PU8 HEADER HYDROLASE 24-JUN-03 1PU8 TITLE CRYSTAL STRUCTURE OF H.PYLORI 3-METHYLADENINE DNA GLYCOSYLASE (MAGIII) TITLE 2 BOUND TO 1,N6-ETHENOADENINE 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 5 15-NOV-23 1PU8 1 REMARK REVDAT 4 16-AUG-23 1PU8 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1PU8 1 VERSN REVDAT 2 24-FEB-09 1PU8 1 VERSN REVDAT 1 07-OCT-03 1PU8 0 JRNL AUTH B.F.EICHMAN,E.J.O'ROURKE,J.P.RADICELLA,T.ELLENBERGER JRNL TITL CRYSTAL STRUCTURES OF 3-METHYLADENINE DNA GLYCOSYLASE MAGIII JRNL TITL 2 AND THE RECOGNITION OF 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,L.IELPI, REMARK 1 AUTH 2 J.P.RADICELLA REMARK 1 TITL A NOVEL 3-METHYLADENINE DNA GLYCOSYLASE FROM HELICOBACTER REMARK 1 TITL 2 PYLORI DEFINES A NEW CLASS WITHIN THE ENDONUCLEASE III REMARK 1 TITL 3 FAMILY OF BASE EXCISION REPAIR 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. 2.13 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.19 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD WITH PHASES REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.13 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 26792 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) : 0.204 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.230 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1434 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) : 2.13 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.18 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1524 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.2640 REMARK 3 BIN FREE R VALUE SET COUNT : 77 REMARK 3 BIN FREE R VALUE : 0.2840 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3467 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 161 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 23.00 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.76 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.06000 REMARK 3 B22 (A**2) : 0.37000 REMARK 3 B33 (A**2) : -0.56000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.44000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.242 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.185 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.092 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.932 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3571 ; 0.013 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4814 ; 1.508 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 428 ; 5.211 ; 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): 532 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2652 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1826 ; 0.214 ; 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): 207 ; 0.121 ; 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): 61 ; 0.241 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.156 ; 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): 2140 ; 0.627 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3415 ; 1.162 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1431 ; 2.032 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1399 ; 3.052 ; 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 : 5 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 24 REMARK 3 RESIDUE RANGE : A 145 A 216 REMARK 3 ORIGIN FOR THE GROUP (A): 118.5179 18.9889 56.5131 REMARK 3 T TENSOR REMARK 3 T11: 0.0949 T22: 0.1116 REMARK 3 T33: 0.1099 T12: 0.0408 REMARK 3 T13: -0.0169 T23: -0.0066 REMARK 3 L TENSOR REMARK 3 L11: 2.6111 L22: 1.7178 REMARK 3 L33: 4.0394 L12: -0.1287 REMARK 3 L13: -0.0702 L23: 0.2670 REMARK 3 S TENSOR REMARK 3 S11: -0.0990 S12: -0.1559 S13: -0.1248 REMARK 3 S21: 0.0830 S22: 0.0621 S23: -0.0835 REMARK 3 S31: 0.1550 S32: 0.3385 S33: 0.0370 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 25 A 144 REMARK 3 RESIDUE RANGE : A 983 A 983 REMARK 3 RESIDUE RANGE : A 219 A 219 REMARK 3 ORIGIN FOR THE GROUP (A): 109.7365 12.6494 35.0295 REMARK 3 T TENSOR REMARK 3 T11: 0.1040 T22: 0.1188 REMARK 3 T33: 0.1034 T12: -0.0097 REMARK 3 T13: 0.0126 T23: 0.0034 REMARK 3 L TENSOR REMARK 3 L11: 1.5163 L22: 1.9506 REMARK 3 L33: 2.0552 L12: 0.1522 REMARK 3 L13: 0.4716 L23: 0.6978 REMARK 3 S TENSOR REMARK 3 S11: 0.0034 S12: 0.0943 S13: -0.0851 REMARK 3 S21: -0.0550 S22: 0.0556 S23: -0.0878 REMARK 3 S31: 0.0358 S32: 0.1153 S33: -0.0589 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 2 B 24 REMARK 3 RESIDUE RANGE : B 145 B 216 REMARK 3 ORIGIN FOR THE GROUP (A): 131.7845 41.2303 14.5073 REMARK 3 T TENSOR REMARK 3 T11: 0.0691 T22: 0.1706 REMARK 3 T33: 0.0955 T12: 0.0282 REMARK 3 T13: -0.0302 T23: -0.0125 REMARK 3 L TENSOR REMARK 3 L11: 2.4036 L22: 2.4202 REMARK 3 L33: 3.0448 L12: -0.4711 REMARK 3 L13: 0.1536 L23: 0.1347 REMARK 3 S TENSOR REMARK 3 S11: -0.0596 S12: -0.2075 S13: -0.0456 REMARK 3 S21: 0.2241 S22: 0.1013 S23: -0.1483 REMARK 3 S31: 0.0734 S32: 0.4200 S33: -0.0417 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 3 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 25 B 144 REMARK 3 RESIDUE RANGE : B 983 B 983 REMARK 3 RESIDUE RANGE : B 220 B 220 REMARK 3 ORIGIN FOR THE GROUP (A): 120.4862 35.8708 -5.8712 REMARK 3 T TENSOR REMARK 3 T11: 0.1008 T22: 0.1242 REMARK 3 T33: 0.1363 T12: -0.0048 REMARK 3 T13: 0.0055 T23: 0.0031 REMARK 3 L TENSOR REMARK 3 L11: 0.9975 L22: 1.5633 REMARK 3 L33: 1.6818 L12: 0.0598 REMARK 3 L13: 0.0599 L23: 0.5582 REMARK 3 S TENSOR REMARK 3 S11: 0.0096 S12: 0.0211 S13: -0.0234 REMARK 3 S21: -0.0721 S22: 0.0461 S23: -0.0914 REMARK 3 S31: 0.0164 S32: 0.0494 S33: -0.0557 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 301 A 459 REMARK 3 RESIDUE RANGE : B 303 B 461 REMARK 3 ORIGIN FOR THE GROUP (A): 115.7105 26.5796 18.9764 REMARK 3 T TENSOR REMARK 3 T11: 0.0399 T22: 0.0142 REMARK 3 T33: 0.0583 T12: -0.0120 REMARK 3 T13: -0.0050 T23: -0.0232 REMARK 3 L TENSOR REMARK 3 L11: 0.0689 L22: 0.0608 REMARK 3 L33: 0.4372 L12: 0.0126 REMARK 3 L13: -0.0781 L23: -0.1862 REMARK 3 S TENSOR REMARK 3 S11: -0.0160 S12: 0.0339 S13: -0.0234 REMARK 3 S21: 0.0065 S22: 0.0084 S23: -0.0209 REMARK 3 S31: 0.0579 S32: 0.0147 S33: 0.0076 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: NULL REMARK 4 REMARK 4 1PU8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-JUL-03. REMARK 100 THE DEPOSITION ID IS D_1000019570. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-SEP-02 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 7.0 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 : SIEMENS REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.542 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28226 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.130 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08400 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.13 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.36900 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.500 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 1PU6 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 LYS A 217 REMARK 465 LEU A 218 REMARK 465 VAL B 1 REMARK 465 LYS B 217 REMARK 465 LEU B 218 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 VAL A 1 N CA CB CG1 CG2 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 OE1 OE2 REMARK 470 LYS A 106 CE NZ REMARK 470 LYS A 151 CD CE NZ REMARK 470 LYS A 159 CD CE NZ REMARK 470 LYS B 44 CG CD CE NZ REMARK 470 GLU B 76 OE1 OE2 REMARK 470 LYS B 106 NZ REMARK 470 LYS B 127 CD CE NZ REMARK 470 LYS B 159 CD CE NZ REMARK 470 GLU B 165 CG CD OE1 OE2 REMARK 470 GLU B 190 CG CD OE1 OE2 REMARK 470 ASN B 191 CG OD1 ND2 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 64 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ASP A 166 CB - CG - OD2 ANGL. DEV. = 5.4 DEGREES REMARK 500 ASP A 168 CB - CG - OD2 ANGL. DEV. = 6.9 DEGREES REMARK 500 ASP B 125 CB - CG - OD2 ANGL. DEV. = 5.5 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 -60.50 71.05 REMARK 500 ALA A 28 151.26 -48.56 REMARK 500 GLU A 62 -145.69 -124.80 REMARK 500 GLN A 109 -32.55 67.15 REMARK 500 TYR A 189 -93.31 -100.42 REMARK 500 GLU A 190 -6.26 -154.29 REMARK 500 TRP B 24 -59.22 68.23 REMARK 500 GLU B 62 -151.08 -125.55 REMARK 500 GLN B 109 -33.32 71.63 REMARK 500 ASP B 150 -175.77 -176.93 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 EA1 A 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EA1 B 220 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME A 983 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE BME B 983 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1PU6 RELATED DB: PDB REMARK 900 UNLIGANDED MAGIII REMARK 900 RELATED ID: 1PU7 RELATED DB: PDB REMARK 900 3,9-DIMETHYLADENINE BOUND TO MAGIII REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE DIFFERENCES BETWEEN THE SEQUENCES IN THE 1PU6 PDB REMARK 999 AND IN THE DATABASE REFERENCE ARE DUE TO THE PARTICULAR REMARK 999 H.PYLORI STRAIN. DATABASE REFERENCE REFERS TO H.PYLORI REMARK 999 STRAIN J99; MAGIII WAS CLONED FROM H.PYLORI STRAIN 13/5 REMARK 999 (SEE REFERENCE 1) DBREF 1PU8 A 1 218 UNP O25323 O25323_HELPY 1 218 DBREF 1PU8 B 1 218 UNP O25323 O25323_HELPY 1 218 SEQADV 1PU8 VAL A 1 UNP O25323 MET 1 SEE REMARK 999 SEQADV 1PU8 GLY A 102 UNP O25323 LYS 102 SEE REMARK 999 SEQADV 1PU8 ARG A 120 UNP O25323 LYS 120 SEE REMARK 999 SEQADV 1PU8 ALA A 141 UNP O25323 VAL 141 SEE REMARK 999 SEQADV 1PU8 KCX A 205 UNP O25323 LYS 205 MODIFIED RESIDUE SEQADV 1PU8 VAL B 1 UNP O25323 MET 1 SEE REMARK 999 SEQADV 1PU8 GLY B 102 UNP O25323 LYS 102 SEE REMARK 999 SEQADV 1PU8 ARG B 120 UNP O25323 LYS 120 SEE REMARK 999 SEQADV 1PU8 ALA B 141 UNP O25323 VAL 141 SEE REMARK 999 SEQADV 1PU8 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 1PU8 KCX A 205 LYS LYSINE NZ-CARBOXYLIC ACID MODRES 1PU8 KCX B 205 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 205 12 HET KCX B 205 12 HET EA1 A 219 12 HET BME A 983 4 HET EA1 B 220 12 HET BME B 983 4 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM EA1 3H-IMIDAZO[2,1-I]PURINE HETNAM BME BETA-MERCAPTOETHANOL HETSYN EA1 1,N6-ETHENOADENINE FORMUL 1 KCX 2(C7 H14 N2 O4) FORMUL 3 EA1 2(C7 H5 N5) FORMUL 4 BME 2(C2 H6 O S) FORMUL 7 HOH *161(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 ASN A 181 1 16 HELIX 13 13 ASN A 181 ALA A 187 1 7 HELIX 14 14 SER A 194 LYS A 213 1 20 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 GLN B 212 1 19 LINK SG CYS A 83 S2 BME A 983 1555 1555 2.03 LINK C GLY A 204 N KCX A 205 1555 1555 1.33 LINK C KCX A 205 N ILE A 206 1555 1555 1.33 LINK SG CYS B 83 S2 BME B 983 1555 1555 2.03 LINK C GLY B 204 N KCX B 205 1555 1555 1.33 LINK C KCX B 205 N ILE B 206 1555 1555 1.33 SITE 1 AC1 7 TRP A 24 TRP A 25 PRO A 26 PHE A 45 SITE 2 AC1 7 GLU A 208 LYS A 211 HOH A 353 SITE 1 AC2 7 TRP B 24 TRP B 25 PRO B 26 THR B 40 SITE 2 AC2 7 PHE B 45 LYS B 211 HOH B 342 SITE 1 AC3 3 ASN A 54 ALA A 58 CYS A 83 SITE 1 AC4 4 GLU A 169 ASN B 54 ALA B 58 CYS B 83 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