HEADER HYDROLASE 12-MAY-13 4BMZ TITLE STRUCTURE OF FUTALOSINE HYDROLASE MUTANT OF HELICOBACTER PYLORI STRAIN TITLE 2 26695 COMPND MOL_ID: 1; COMPND 2 MOLECULE: MTA/SAH NUCLEOSIDASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 5-METHYLTHIOADENOSINE NUCLEOSIDASE, S-ADENOSYLHOMOCYSTEINE COMPND 5 NUCLEOSIDASE, FUTALOSINE HYDROLASE; COMPND 6 EC: 3.2.2.9; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 85962; SOURCE 4 STRAIN: 26695; SOURCE 5 ATCC: 700392; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_VECTOR: PET28A KEYWDS HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR R.Q.KIM,W.A.OFFEN,K.A.STUBBS,G.J.DAVIES REVDAT 4 20-DEC-23 4BMZ 1 REMARK SHEET REVDAT 3 22-JAN-14 4BMZ 1 JRNL REVDAT 2 15-JAN-14 4BMZ 1 JRNL REVDAT 1 11-SEP-13 4BMZ 0 JRNL AUTH R.Q.KIM,W.A.OFFEN,G.J.DAVIES,K.A.STUBBS JRNL TITL STRUCTURAL ENZYMOLOGY OF HELICOBACTER PYLORI JRNL TITL 2 METHYLTHIOADENOSINE NUCLEOSIDASE IN THE FUTALOSINE PATHWAY JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 177 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24419390 JRNL DOI 10.1107/S1399004713026655 REMARK 2 REMARK 2 RESOLUTION. 1.79 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.7.0032 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.79 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.55 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 38371 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2031 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) : 1.79 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2834 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3465 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 40 REMARK 3 SOLVENT ATOMS : 204 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.23000 REMARK 3 B22 (A**2) : -0.26000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.29000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.132 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.123 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.085 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.211 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3568 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4835 ; 1.843 ; 1.969 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 462 ; 5.799 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;35.915 ;25.435 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 591 ;13.509 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 6 ;15.670 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 580 ; 0.132 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2618 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 1854 ; 1.719 ; 2.045 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2314 ; 2.228 ; 3.055 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1714 ; 2.679 ; 2.330 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B -2 B 231 REMARK 3 ORIGIN FOR THE GROUP (A): -15.3150 1.2730 -15.4510 REMARK 3 T TENSOR REMARK 3 T11: 0.0508 T22: 0.1242 REMARK 3 T33: 0.0346 T12: 0.0379 REMARK 3 T13: 0.0188 T23: -0.0167 REMARK 3 L TENSOR REMARK 3 L11: 0.4294 L22: 0.3211 REMARK 3 L33: 0.2850 L12: -0.1681 REMARK 3 L13: -0.0729 L23: 0.1359 REMARK 3 S TENSOR REMARK 3 S11: 0.0144 S12: 0.0293 S13: -0.0064 REMARK 3 S21: 0.0775 S22: 0.0070 S23: 0.0308 REMARK 3 S31: 0.0837 S32: 0.1395 S33: -0.0214 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 2 A 231 REMARK 3 ORIGIN FOR THE GROUP (A): -38.2150 8.6330 -30.6450 REMARK 3 T TENSOR REMARK 3 T11: 0.0371 T22: 0.0726 REMARK 3 T33: 0.0888 T12: -0.0147 REMARK 3 T13: -0.0211 T23: -0.0151 REMARK 3 L TENSOR REMARK 3 L11: 0.3238 L22: 0.3277 REMARK 3 L33: 0.4840 L12: 0.1369 REMARK 3 L13: 0.1288 L23: -0.0450 REMARK 3 S TENSOR REMARK 3 S11: -0.0465 S12: 0.0579 S13: 0.0370 REMARK 3 S21: -0.0699 S22: 0.0369 S23: 0.1419 REMARK 3 S31: -0.0001 S32: 0.0762 S33: 0.0096 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS. REMARK 4 REMARK 4 4BMZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-MAY-13. REMARK 100 THE DEPOSITION ID IS D_1290056793. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9163 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40405 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.790 REMARK 200 RESOLUTION RANGE LOW (A) : 55.480 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 6.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.79 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.30 REMARK 200 R MERGE FOR SHELL (I) : 0.62000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 4BMX REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 39.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS PH 5.5, 25% PEG-3350, REMARK 280 0.2 M MGCL2.6H2O REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 20.80378 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 33.87300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 48.34831 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 20.80378 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 33.87300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 48.34831 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4640 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16630 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.9 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 MET A 1 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 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 38 CE NZ REMARK 470 ASN A 43 CG OD1 ND2 REMARK 470 LYS A 44 CE NZ REMARK 470 LYS A 85 CG CD CE NZ REMARK 470 LYS A 88 CD CE NZ REMARK 470 GLU A 126 CG CD OE1 OE2 REMARK 470 LYS A 133 CD CE NZ REMARK 470 GLU A 134 CG CD OE1 OE2 REMARK 470 ASN A 137 CG OD1 ND2 REMARK 470 GLU A 138 CD OE1 OE2 REMARK 470 VAL A 142 CG1 CG2 REMARK 470 LYS A 158 CD CE NZ REMARK 470 LYS A 169 CE NZ REMARK 470 GLU A 203 CG CD OE1 OE2 REMARK 470 GLU A 204 CG CD OE1 OE2 REMARK 470 LYS A 215 CD CE NZ REMARK 470 GLN A 218 CD OE1 NE2 REMARK 470 LYS A 222 CD CE NZ REMARK 470 GLU B 20 CG CD OE1 OE2 REMARK 470 LYS B 38 CD CE NZ REMARK 470 LYS B 85 CG CD CE NZ REMARK 470 LYS B 88 CD CE NZ REMARK 470 GLU B 134 CD OE1 OE2 REMARK 470 GLU B 138 CD OE1 OE2 REMARK 470 LYS B 169 CD CE NZ REMARK 470 GLU B 204 CD OE1 OE2 REMARK 470 GLU B 214 CD OE1 OE2 REMARK 470 LYS B 215 CD CE NZ REMARK 470 LYS B 222 CG CD CE NZ 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 ASN A 43 -12.10 76.40 REMARK 500 LYS A 52 168.45 88.86 REMARK 500 ASN A 90 -3.49 76.87 REMARK 500 SER A 118 -150.39 -136.23 REMARK 500 HIS A 156 31.37 -148.10 REMARK 500 ASP A 202 -164.45 -123.60 REMARK 500 LYS B 52 165.36 89.73 REMARK 500 ASN B 90 -16.79 74.06 REMARK 500 SER B 118 -153.81 -140.14 REMARK 500 HIS B 140 -16.27 70.02 REMARK 500 HIS B 156 47.51 -154.34 REMARK 500 GLU B 174 -169.74 -163.91 REMARK 500 ASP B 202 -161.24 -119.58 REMARK 500 ASP B 229 -6.68 -57.02 REMARK 500 REMARK 500 REMARK: NULL REMARK 700 REMARK 700 SHEET REMARK 700 THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN REMARK 700 ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, REMARK 700 TWO SHEETS ARE DEFINED. REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTA A 1232 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MTA B 1232 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4BMX RELATED DB: PDB REMARK 900 NATIVE STRUCTURE OF FUTALOSINE HYDROLASE OF HELICOBACTER PYLORI REMARK 900 STRAIN 26695 REMARK 900 RELATED ID: 4BMY RELATED DB: PDB REMARK 900 STRUCTURE OF FUTALOSINE HYDROLASE MUTANT OF HELICOBACTER PYLORI REMARK 900 STRAIN 26695 REMARK 900 RELATED ID: 4BN0 RELATED DB: PDB REMARK 900 STRUCTURE OF FUTALOSINE HYDROLASE MUTANT OF HELICOBACTER PYLORI REMARK 900 STRAIN 26695 DBREF 4BMZ A 1 231 UNP O24915 MTNN_HELPY 1 231 DBREF 4BMZ B 1 231 UNP O24915 MTNN_HELPY 1 231 SEQADV 4BMZ MET A -19 UNP O24915 EXPRESSION TAG SEQADV 4BMZ GLY A -18 UNP O24915 EXPRESSION TAG SEQADV 4BMZ SER A -17 UNP O24915 EXPRESSION TAG SEQADV 4BMZ SER A -16 UNP O24915 EXPRESSION TAG SEQADV 4BMZ HIS A -15 UNP O24915 EXPRESSION TAG SEQADV 4BMZ HIS A -14 UNP O24915 EXPRESSION TAG SEQADV 4BMZ HIS A -13 UNP O24915 EXPRESSION TAG SEQADV 4BMZ HIS A -12 UNP O24915 EXPRESSION TAG SEQADV 4BMZ HIS A -11 UNP O24915 EXPRESSION TAG SEQADV 4BMZ HIS A -10 UNP O24915 EXPRESSION TAG SEQADV 4BMZ SER A -9 UNP O24915 EXPRESSION TAG SEQADV 4BMZ SER A -8 UNP O24915 EXPRESSION TAG SEQADV 4BMZ GLY A -7 UNP O24915 EXPRESSION TAG SEQADV 4BMZ LEU A -6 UNP O24915 EXPRESSION TAG SEQADV 4BMZ VAL A -5 UNP O24915 EXPRESSION TAG SEQADV 4BMZ PRO A -4 UNP O24915 EXPRESSION TAG SEQADV 4BMZ ARG A -3 UNP O24915 EXPRESSION TAG SEQADV 4BMZ GLY A -2 UNP O24915 EXPRESSION TAG SEQADV 4BMZ SER A -1 UNP O24915 EXPRESSION TAG SEQADV 4BMZ HIS A 0 UNP O24915 EXPRESSION TAG SEQADV 4BMZ ASN A 199 UNP O24915 ASP 199 ENGINEERED MUTATION SEQADV 4BMZ MET B -19 UNP O24915 EXPRESSION TAG SEQADV 4BMZ GLY B -18 UNP O24915 EXPRESSION TAG SEQADV 4BMZ SER B -17 UNP O24915 EXPRESSION TAG SEQADV 4BMZ SER B -16 UNP O24915 EXPRESSION TAG SEQADV 4BMZ HIS B -15 UNP O24915 EXPRESSION TAG SEQADV 4BMZ HIS B -14 UNP O24915 EXPRESSION TAG SEQADV 4BMZ HIS B -13 UNP O24915 EXPRESSION TAG SEQADV 4BMZ HIS B -12 UNP O24915 EXPRESSION TAG SEQADV 4BMZ HIS B -11 UNP O24915 EXPRESSION TAG SEQADV 4BMZ HIS B -10 UNP O24915 EXPRESSION TAG SEQADV 4BMZ SER B -9 UNP O24915 EXPRESSION TAG SEQADV 4BMZ SER B -8 UNP O24915 EXPRESSION TAG SEQADV 4BMZ GLY B -7 UNP O24915 EXPRESSION TAG SEQADV 4BMZ LEU B -6 UNP O24915 EXPRESSION TAG SEQADV 4BMZ VAL B -5 UNP O24915 EXPRESSION TAG SEQADV 4BMZ PRO B -4 UNP O24915 EXPRESSION TAG SEQADV 4BMZ ARG B -3 UNP O24915 EXPRESSION TAG SEQADV 4BMZ GLY B -2 UNP O24915 EXPRESSION TAG SEQADV 4BMZ SER B -1 UNP O24915 EXPRESSION TAG SEQADV 4BMZ HIS B 0 UNP O24915 EXPRESSION TAG SEQADV 4BMZ ASN B 199 UNP O24915 ASP 199 ENGINEERED MUTATION SEQRES 1 A 251 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 251 LEU VAL PRO ARG GLY SER HIS MET VAL GLN LYS ILE GLY SEQRES 3 A 251 ILE LEU GLY ALA MET ARG GLU GLU ILE THR PRO ILE LEU SEQRES 4 A 251 GLU LEU PHE GLY VAL ASP PHE GLU GLU ILE PRO LEU GLY SEQRES 5 A 251 GLY ASN VAL PHE HIS LYS GLY VAL TYR HIS ASN LYS GLU SEQRES 6 A 251 ILE ILE VAL ALA TYR SER LYS ILE GLY LYS VAL HIS SER SEQRES 7 A 251 THR LEU THR THR THR SER MET ILE LEU ALA PHE GLY VAL SEQRES 8 A 251 GLN LYS VAL LEU PHE SER GLY VAL ALA GLY SER LEU VAL SEQRES 9 A 251 LYS ASP LEU LYS ILE ASN ASP LEU LEU VAL ALA ILE GLN SEQRES 10 A 251 LEU VAL GLN HIS ASP VAL ASP LEU SER ALA PHE ASP HIS SEQRES 11 A 251 PRO LEU GLY PHE ILE PRO GLU SER ALA ILE PHE ILE GLU SEQRES 12 A 251 THR SER GLU SER LEU ASN ALA LEU ALA LYS GLU VAL ALA SEQRES 13 A 251 ASN GLU GLN HIS ILE VAL LEU LYS GLU GLY VAL ILE ALA SEQRES 14 A 251 SER GLY ASP GLN PHE VAL HIS SER LYS GLU ARG LYS GLU SEQRES 15 A 251 PHE LEU VAL SER GLU PHE LYS ALA SER ALA VAL GLU MET SEQRES 16 A 251 GLU GLY ALA SER VAL ALA PHE VAL CYS GLN LYS PHE GLY SEQRES 17 A 251 VAL PRO CYS CYS VAL LEU ARG SER ILE SER ASN ASN ALA SEQRES 18 A 251 ASP GLU GLU ALA ASN MET SER PHE ASP ALA PHE LEU GLU SEQRES 19 A 251 LYS SER ALA GLN THR SER ALA LYS PHE LEU LYS SER MET SEQRES 20 A 251 VAL ASP GLU LEU SEQRES 1 B 251 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 251 LEU VAL PRO ARG GLY SER HIS MET VAL GLN LYS ILE GLY SEQRES 3 B 251 ILE LEU GLY ALA MET ARG GLU GLU ILE THR PRO ILE LEU SEQRES 4 B 251 GLU LEU PHE GLY VAL ASP PHE GLU GLU ILE PRO LEU GLY SEQRES 5 B 251 GLY ASN VAL PHE HIS LYS GLY VAL TYR HIS ASN LYS GLU SEQRES 6 B 251 ILE ILE VAL ALA TYR SER LYS ILE GLY LYS VAL HIS SER SEQRES 7 B 251 THR LEU THR THR THR SER MET ILE LEU ALA PHE GLY VAL SEQRES 8 B 251 GLN LYS VAL LEU PHE SER GLY VAL ALA GLY SER LEU VAL SEQRES 9 B 251 LYS ASP LEU LYS ILE ASN ASP LEU LEU VAL ALA ILE GLN SEQRES 10 B 251 LEU VAL GLN HIS ASP VAL ASP LEU SER ALA PHE ASP HIS SEQRES 11 B 251 PRO LEU GLY PHE ILE PRO GLU SER ALA ILE PHE ILE GLU SEQRES 12 B 251 THR SER GLU SER LEU ASN ALA LEU ALA LYS GLU VAL ALA SEQRES 13 B 251 ASN GLU GLN HIS ILE VAL LEU LYS GLU GLY VAL ILE ALA SEQRES 14 B 251 SER GLY ASP GLN PHE VAL HIS SER LYS GLU ARG LYS GLU SEQRES 15 B 251 PHE LEU VAL SER GLU PHE LYS ALA SER ALA VAL GLU MET SEQRES 16 B 251 GLU GLY ALA SER VAL ALA PHE VAL CYS GLN LYS PHE GLY SEQRES 17 B 251 VAL PRO CYS CYS VAL LEU ARG SER ILE SER ASN ASN ALA SEQRES 18 B 251 ASP GLU GLU ALA ASN MET SER PHE ASP ALA PHE LEU GLU SEQRES 19 B 251 LYS SER ALA GLN THR SER ALA LYS PHE LEU LYS SER MET SEQRES 20 B 251 VAL ASP GLU LEU HET MTA A1232 20 HET MTA B1232 20 HETNAM MTA 5'-DEOXY-5'-METHYLTHIOADENOSINE FORMUL 3 MTA 2(C11 H15 N5 O3 S) FORMUL 5 HOH *204(H2 O) HELIX 1 1 MET A 11 GLY A 23 1 13 HELIX 2 2 GLY A 54 ALA A 68 1 15 HELIX 3 3 LEU A 105 ASP A 109 5 5 HELIX 4 4 SER A 125 HIS A 140 1 16 HELIX 5 5 SER A 157 LYS A 169 1 13 HELIX 6 6 GLU A 176 GLY A 188 1 13 HELIX 7 7 GLU A 204 ASP A 229 1 26 HELIX 8 8 MET B 11 GLY B 23 1 13 HELIX 9 9 GLY B 54 GLY B 70 1 17 HELIX 10 10 LEU B 105 ASP B 109 5 5 HELIX 11 11 SER B 125 GLN B 139 1 15 HELIX 12 12 SER B 157 LYS B 169 1 13 HELIX 13 13 GLU B 176 PHE B 187 1 12 HELIX 14 14 GLU B 204 ASP B 229 1 26 SHEET 1 AA 7 GLU A 27 LEU A 31 0 SHEET 2 AA 7 ASN A 34 TYR A 41 -1 O ASN A 34 N LEU A 31 SHEET 3 AA 7 LYS A 44 TYR A 50 -1 O LYS A 44 N TYR A 41 SHEET 4 AA 7 LYS A 4 GLY A 9 1 O ILE A 5 N ILE A 47 SHEET 5 AA 7 LYS A 73 SER A 82 1 O LYS A 73 N GLY A 6 SHEET 6 AA 7 CYS A 191 ASN A 199 1 O CYS A 192 N PHE A 76 SHEET 7 AA 7 LEU A 92 GLN A 100 -1 O LEU A 93 N ARG A 195 SHEET 1 AB 2 GLU A 27 LEU A 31 0 SHEET 2 AB 2 LYS A 73 SER A 82 1 O LYS A 73 N GLY A 6 SHEET 1 BA 7 GLU B 27 LEU B 31 0 SHEET 2 BA 7 ASN B 34 TYR B 41 -1 O ASN B 34 N LEU B 31 SHEET 3 BA 7 LYS B 44 TYR B 50 -1 O LYS B 44 N TYR B 41 SHEET 4 BA 7 LYS B 4 GLY B 9 1 O ILE B 5 N ILE B 47 SHEET 5 BA 7 LYS B 73 SER B 82 1 O LYS B 73 N GLY B 6 SHEET 6 BA 7 CYS B 191 ASN B 199 1 O CYS B 192 N PHE B 76 SHEET 7 BA 7 LEU B 92 GLN B 100 -1 O LEU B 93 N ARG B 195 SHEET 1 BB 2 GLU B 27 LEU B 31 0 SHEET 2 BB 2 LYS B 73 SER B 82 1 O LYS B 73 N GLY B 6 SITE 1 AC1 17 ALA A 10 ILE A 53 VAL A 79 ALA A 80 SITE 2 AC1 17 GLY A 81 GLN A 153 PHE A 154 VAL A 155 SITE 3 AC1 17 VAL A 173 GLU A 174 MET A 175 GLU A 176 SITE 4 AC1 17 ASN A 199 ALA A 201 PHE A 209 HOH A2003 SITE 5 AC1 17 LEU B 105 SITE 1 AC2 17 LEU A 105 PHE A 108 HIS B 0 ALA B 10 SITE 2 AC2 17 VAL B 79 ALA B 80 GLY B 81 GLN B 153 SITE 3 AC2 17 PHE B 154 VAL B 155 GLU B 174 MET B 175 SITE 4 AC2 17 GLU B 176 ARG B 195 ASN B 199 PHE B 209 SITE 5 AC2 17 HOH B2007 CRYST1 67.445 67.746 100.089 90.00 104.96 90.00 I 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 0.014827 0.000000 0.003962 0.00000 SCALE2 0.000000 0.014761 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010342 0.00000