HEADER HYDROLASE 24-JUN-03 1PU7 TITLE CRYSTAL STRUCTURE OF H.PYLORI 3-METHYLADENINE DNA GLYCOSYLASE (MAGIII) TITLE 2 BOUND TO 3,9-DIMETHYLADENINE 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 6 15-NOV-23 1PU7 1 REMARK REVDAT 5 16-AUG-23 1PU7 1 REMARK SEQADV LINK REVDAT 4 13-JUL-11 1PU7 1 VERSN REVDAT 3 24-FEB-09 1PU7 1 VERSN REVDAT 2 21-OCT-03 1PU7 1 REMARK REVDAT 1 07-OCT-03 1PU7 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. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.5 REMARK 3 NUMBER OF REFLECTIONS : 33940 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) : 0.185 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1837 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) : 1.93 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.98 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1733 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3830 REMARK 3 BIN FREE R VALUE SET COUNT : 91 REMARK 3 BIN FREE R VALUE : 0.3900 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3461 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 32 REMARK 3 SOLVENT ATOMS : 362 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 21.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 12.48 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.81000 REMARK 3 B33 (A**2) : -0.97000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.30000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.168 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.151 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.636 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.927 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3578 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4824 ; 1.546 ; 1.974 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 428 ; 5.369 ; 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): 533 ; 0.099 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2658 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1829 ; 0.212 ; 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): 308 ; 0.138 ; 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): 79 ; 0.298 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 27 ; 0.133 ; 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): 2141 ; 0.737 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3418 ; 1.285 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1437 ; 2.196 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1406 ; 3.258 ; 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 : 7 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): 118.5609 19.0239 56.3694 REMARK 3 T TENSOR REMARK 3 T11: 0.1307 T22: 0.1737 REMARK 3 T33: 0.1310 T12: 0.0366 REMARK 3 T13: -0.0168 T23: -0.0072 REMARK 3 L TENSOR REMARK 3 L11: 1.6508 L22: 0.9220 REMARK 3 L33: 2.4192 L12: -0.1184 REMARK 3 L13: -0.2229 L23: 0.0377 REMARK 3 S TENSOR REMARK 3 S11: -0.0719 S12: -0.1369 S13: -0.0254 REMARK 3 S21: 0.0920 S22: 0.0485 S23: -0.0858 REMARK 3 S31: 0.0764 S32: 0.1806 S33: 0.0234 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 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 ORIGIN FOR THE GROUP (A): 109.6007 12.7822 34.7603 REMARK 3 T TENSOR REMARK 3 T11: 0.1301 T22: 0.1755 REMARK 3 T33: 0.1166 T12: -0.0026 REMARK 3 T13: 0.0120 T23: -0.0030 REMARK 3 L TENSOR REMARK 3 L11: 1.0299 L22: 1.7631 REMARK 3 L33: 1.4630 L12: 0.1039 REMARK 3 L13: 0.1786 L23: 0.5750 REMARK 3 S TENSOR REMARK 3 S11: 0.0039 S12: 0.0749 S13: -0.0285 REMARK 3 S21: -0.0500 S22: 0.0446 S23: -0.0700 REMARK 3 S31: 0.0136 S32: 0.0791 S33: -0.0485 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): 131.5428 41.1310 14.6352 REMARK 3 T TENSOR REMARK 3 T11: 0.1141 T22: 0.1872 REMARK 3 T33: 0.1334 T12: 0.0130 REMARK 3 T13: -0.0222 T23: -0.0097 REMARK 3 L TENSOR REMARK 3 L11: 1.8099 L22: 1.4995 REMARK 3 L33: 2.1616 L12: 0.0514 REMARK 3 L13: -0.0120 L23: -0.1418 REMARK 3 S TENSOR REMARK 3 S11: -0.0262 S12: -0.1520 S13: -0.0738 REMARK 3 S21: 0.1697 S22: 0.0797 S23: -0.1235 REMARK 3 S31: 0.0136 S32: 0.2532 S33: -0.0536 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 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 ORIGIN FOR THE GROUP (A): 120.4021 35.9920 -5.9139 REMARK 3 T TENSOR REMARK 3 T11: 0.1273 T22: 0.1765 REMARK 3 T33: 0.1373 T12: -0.0063 REMARK 3 T13: 0.0071 T23: -0.0047 REMARK 3 L TENSOR REMARK 3 L11: 0.8493 L22: 1.2452 REMARK 3 L33: 1.2754 L12: 0.0625 REMARK 3 L13: 0.0279 L23: 0.3513 REMARK 3 S TENSOR REMARK 3 S11: 0.0007 S12: 0.0067 S13: -0.0228 REMARK 3 S21: -0.0723 S22: 0.0365 S23: -0.0529 REMARK 3 S31: -0.0385 S32: 0.0588 S33: -0.0373 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 219 A 219 REMARK 3 ORIGIN FOR THE GROUP (A): 118.3511 9.3462 46.4965 REMARK 3 T TENSOR REMARK 3 T11: 0.1726 T22: 0.1682 REMARK 3 T33: 0.1694 T12: -0.0023 REMARK 3 T13: -0.0034 T23: -0.0080 REMARK 3 L TENSOR REMARK 3 L11:-106.3933 L22: -27.6151 REMARK 3 L33: -57.5695 L12: 62.9153 REMARK 3 L13: 21.4882 L23: 39.7698 REMARK 3 S TENSOR REMARK 3 S11: -0.0846 S12: -0.0960 S13: 0.1154 REMARK 3 S21: -0.9676 S22: -0.9871 S23: 0.0720 REMARK 3 S31: -0.7491 S32: 0.7146 S33: 1.0717 REMARK 3 REMARK 3 TLS GROUP : 6 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 220 B 220 REMARK 3 ORIGIN FOR THE GROUP (A): 130.4997 32.1031 4.2275 REMARK 3 T TENSOR REMARK 3 T11: 0.1734 T22: 0.1707 REMARK 3 T33: 0.1729 T12: -0.0027 REMARK 3 T13: -0.0031 T23: -0.0049 REMARK 3 L TENSOR REMARK 3 L11: -62.8036 L22: 3.4581 REMARK 3 L33: -44.8285 L12: 74.2296 REMARK 3 L13: 35.0608 L23: 23.8404 REMARK 3 S TENSOR REMARK 3 S11: -0.0804 S12: 0.1437 S13: -0.0213 REMARK 3 S21: -1.4505 S22: 0.4126 S23: 0.1670 REMARK 3 S31: -0.5931 S32: 0.8529 S33: -0.3322 REMARK 3 REMARK 3 TLS GROUP : 7 REMARK 3 NUMBER OF COMPONENTS GROUP : 2 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 303 A 662 REMARK 3 RESIDUE RANGE : B 301 B 659 REMARK 3 ORIGIN FOR THE GROUP (A): 116.8221 26.5569 21.7510 REMARK 3 T TENSOR REMARK 3 T11: 0.0216 T22: 0.0217 REMARK 3 T33: 0.0367 T12: -0.0158 REMARK 3 T13: -0.0033 T23: -0.0167 REMARK 3 L TENSOR REMARK 3 L11: 0.0596 L22: 0.0524 REMARK 3 L33: 0.4214 L12: -0.0019 REMARK 3 L13: -0.0451 L23: -0.0685 REMARK 3 S TENSOR REMARK 3 S11: -0.0016 S12: 0.0059 S13: -0.0034 REMARK 3 S21: 0.0045 S22: 0.0054 S23: -0.0119 REMARK 3 S31: 0.0167 S32: 0.0455 S33: -0.0038 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 1PU7 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_1000019569. 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 : ELLIOTT GX-13 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 : 35778 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.930 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 (%) : 95.2 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05000 REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.93 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29900 REMARK 200 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 VAL A 1 REMARK 465 LYS A 217 REMARK 465 LEU A 218 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 LYS A 18 CG CD CE NZ REMARK 470 LYS A 44 CD CE NZ REMARK 470 LYS A 50 CD CE NZ REMARK 470 LYS A 158 CE NZ REMARK 470 LYS A 159 CD CE REMARK 470 GLU A 165 CG CD OE1 OE2 REMARK 470 GLU A 190 CG CD OE1 OE2 REMARK 470 LYS A 213 CG CD CE NZ REMARK 470 VAL B 1 N CA CB CG1 CG2 REMARK 470 LYS B 18 CG CD CE NZ REMARK 470 LYS B 44 CG CD CE NZ REMARK 470 GLU B 76 CG CD OE1 OE2 REMARK 470 LYS B 106 NZ REMARK 470 LYS B 127 CD CE NZ REMARK 470 LYS B 151 NZ REMARK 470 LYS B 159 CD CE NZ REMARK 470 GLU B 190 CG CD OE1 OE2 REMARK 470 ASN B 191 CG OD1 ND2 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 159 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 64 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP A 150 CB - CG - OD2 ANGL. DEV. = 7.7 DEGREES REMARK 500 ASP A 168 CB - CG - OD2 ANGL. DEV. = 6.1 DEGREES REMARK 500 ASP B 64 CB - CG - OD2 ANGL. DEV. = 6.3 DEGREES REMARK 500 ASP B 150 CB - CG - OD2 ANGL. DEV. = 5.8 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 -59.53 66.96 REMARK 500 GLU A 62 -151.23 -125.32 REMARK 500 GLN A 109 -35.81 63.45 REMARK 500 ASP A 150 -177.88 -177.69 REMARK 500 GLU A 190 28.09 84.16 REMARK 500 ASP B 15 55.00 38.49 REMARK 500 TRP B 24 -57.78 71.49 REMARK 500 GLU B 62 -155.99 -125.98 REMARK 500 GLN B 109 -35.39 71.70 REMARK 500 ASP B 150 -179.73 -177.17 REMARK 500 TYR B 189 -66.33 -103.57 REMARK 500 GLU B 190 -96.12 -179.24 REMARK 500 ASN B 191 36.69 -140.56 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU B 190 ASN B 191 149.24 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 39A A 219 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 39A 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: 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 ENTRY REMARK 999 1PU6 AND IN THE DATABASE REFERENCE ARE DUE TO THE REMARK 999 PARTICULAR H.PYLORI STRAIN. DATABASE REFERENCE REFERS REMARK 999 TO H.PYLORI STRAIN J99; MAGIII WAS CLONED FROM H.PYLORI REMARK 999 STRAIN 13/5 (SEE REFERENCE 1) DBREF 1PU7 A 1 218 UNP O25323 O25323_HELPY 1 218 DBREF 1PU7 B 1 218 UNP O25323 O25323_HELPY 1 218 SEQADV 1PU7 VAL A 1 UNP O25323 MET 1 SEE REMARK 999 SEQADV 1PU7 GLY A 102 UNP O25323 LYS 102 SEE REMARK 999 SEQADV 1PU7 ARG A 120 UNP O25323 LYS 120 SEE REMARK 999 SEQADV 1PU7 ALA A 141 UNP O25323 VAL 141 SEE REMARK 999 SEQADV 1PU7 KCX A 205 UNP O25323 LYS 205 MODIFIED RESIDUE SEQADV 1PU7 VAL B 1 UNP O25323 MET 1 SEE REMARK 999 SEQADV 1PU7 GLY B 102 UNP O25323 LYS 102 SEE REMARK 999 SEQADV 1PU7 ARG B 120 UNP O25323 LYS 120 SEE REMARK 999 SEQADV 1PU7 ALA B 141 UNP O25323 VAL 141 SEE REMARK 999 SEQADV 1PU7 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 1PU7 KCX A 205 LYS LYSINE NZ-CARBOXYLIC ACID MODRES 1PU7 KCX B 205 LYS LYSINE NZ-CARBOXYLIC ACID HET KCX A 205 12 HET KCX B 205 12 HET 39A A 219 12 HET BME A 983 4 HET 39A B 220 12 HET BME B 983 4 HETNAM KCX LYSINE NZ-CARBOXYLIC ACID HETNAM 39A 6-AMINO-3,9-DIMETHYL-9H-PURIN-3-IUM HETNAM BME BETA-MERCAPTOETHANOL HETSYN 39A 3,9-DIMETHYLADENINE FORMUL 1 KCX 2(C7 H14 N2 O4) FORMUL 3 39A 2(C7 H10 N5 1+) FORMUL 4 BME 2(C2 H6 O S) FORMUL 7 HOH *362(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 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 2.01 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 SG CYS B 83 S2 BME B 983 1555 1555 2.00 LINK C GLY B 204 N KCX B 205 1555 1555 1.33 LINK C KCX B 205 N ILE B 206 1555 1555 1.32 SITE 1 AC1 7 TRP A 24 TRP A 25 PRO A 26 PHE A 45 SITE 2 AC1 7 LYS A 211 HOH A 326 HOH A 457 SITE 1 AC2 8 TRP B 24 TRP B 25 PRO B 26 THR B 40 SITE 2 AC2 8 PHE B 45 GLU B 208 LYS B 211 HOH B 468 SITE 1 AC3 2 ASN A 54 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