HEADER HYDROLASE 21-JAN-14 4OJT TITLE HELICOBACTER PYLORI MTAN COMPLEXED WITH S-RIBOSYLHOMOCYSTEINE AND TITLE 2 ADENINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MTA/SAH NUCLEOSIDASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 2-230; COMPND 5 SYNONYM: 5'-METHYLTHIOADENOSINE NUCLEOSIDASE, S-ADENOSYLHOMOCYSTEINE COMPND 6 NUCLEOSIDASE; COMPND 7 EC: 3.2.2.9; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 85963; SOURCE 4 STRAIN: J99 / ATCC 700824; SOURCE 5 GENE: JHP_0082, MTN, MTNN, PFS; 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_PLASMID: PET32 KEYWDS HOMODIMER, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR V.MISHRA,D.R.RONNING REVDAT 2 29-JUL-20 4OJT 1 COMPND REMARK SEQADV HETNAM REVDAT 2 2 1 SITE ATOM REVDAT 1 26-MAR-14 4OJT 0 JRNL AUTH V.MISHRA,D.R.RONNING JRNL TITL CRYSTAL STRUCTURES OF THE HELICOBACTER PYLORI MTAN ENZYME JRNL TITL 2 REVEAL SPECIFIC INTERACTIONS BETWEEN S-ADENOSYLHOMOCYSTEINE JRNL TITL 3 AND THE 5'-ALKYLTHIO BINDING SUBSITE. JRNL REF BIOCHEMISTRY V. 51 9763 2012 JRNL REFN ISSN 0006-2960 JRNL PMID 23148563 JRNL DOI 10.1021/BI301221K REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.7.2_869) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.80 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.4 REMARK 3 NUMBER OF REFLECTIONS : 40628 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 1979 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 34.8076 - 3.6202 0.98 2903 151 0.1623 0.1720 REMARK 3 2 3.6202 - 2.8739 1.00 2845 148 0.1832 0.1985 REMARK 3 3 2.8739 - 2.5107 1.00 2806 148 0.1835 0.2330 REMARK 3 4 2.5107 - 2.2812 0.99 2802 145 0.1878 0.2080 REMARK 3 5 2.2812 - 2.1177 0.99 2785 138 0.1816 0.1991 REMARK 3 6 2.1177 - 1.9929 0.99 2757 141 0.1807 0.2145 REMARK 3 7 1.9929 - 1.8931 0.98 2746 142 0.1884 0.2189 REMARK 3 8 1.8931 - 1.8107 0.99 2758 142 0.1858 0.2217 REMARK 3 9 1.8107 - 1.7410 0.98 2751 140 0.1928 0.2136 REMARK 3 10 1.7410 - 1.6809 0.98 2720 137 0.1861 0.2193 REMARK 3 11 1.6809 - 1.6284 0.98 2727 140 0.1986 0.2170 REMARK 3 12 1.6284 - 1.5818 0.98 2723 134 0.2119 0.2519 REMARK 3 13 1.5818 - 1.5402 0.98 2700 139 0.2266 0.2625 REMARK 3 14 1.5402 - 1.5000 0.95 2626 134 0.2448 0.2677 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.98 REMARK 3 K_SOL : 0.38 REMARK 3 B_SOL : 43.35 REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.970 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.05370 REMARK 3 B22 (A**2) : 3.05370 REMARK 3 B33 (A**2) : -6.10730 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1821 REMARK 3 ANGLE : 0.993 2452 REMARK 3 CHIRALITY : 0.069 286 REMARK 3 PLANARITY : 0.004 310 REMARK 3 DIHEDRAL : 12.929 654 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 4OJT COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JAN-14. REMARK 100 THE DEPOSITION ID IS D_1000084582. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : DIAMOND REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 40628 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 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 (%) : 98.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : 0.06200 REMARK 200 FOR THE DATA SET : 46.3890 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.5 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: EPMR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 51.94 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.56 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.05 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.1 M HEPES, 30 % (V/V) PEG-MME 550, PH 7.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.97067 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 22.48533 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 22.48533 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 44.97067 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: 4200 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 KCAL/MOL 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 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 89.94133 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 405 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 OE1 GLN A 2 NZ LYS A 72 2.19 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 LYS A 51 162.76 80.25 REMARK 500 ASN A 89 -16.17 86.35 REMARK 500 SER A 117 -150.94 -137.61 REMARK 500 HIS A 155 46.09 -151.04 REMARK 500 GLU A 175 -19.96 -140.67 REMARK 500 ASP A 201 -165.83 -112.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3NM4 RELATED DB: PDB REMARK 900 RELATED ID: 3NM5 RELATED DB: PDB REMARK 900 RELATED ID: 3NM6 RELATED DB: PDB DBREF 4OJT A 2 230 UNP Q9ZMY2 MTNN_HELPJ 2 230 SEQADV 4OJT MET A 0 UNP Q9ZMY2 EXPRESSION TAG SEQADV 4OJT GLY A 1 UNP Q9ZMY2 EXPRESSION TAG SEQRES 1 A 231 MET GLY GLN LYS ILE GLY ILE LEU GLY ALA MET ARG GLU SEQRES 2 A 231 GLU ILE THR PRO ILE LEU GLU LEU PHE GLY VAL ASP PHE SEQRES 3 A 231 GLU GLU ILE PRO LEU GLY GLY ASN VAL PHE HIS LYS GLY SEQRES 4 A 231 VAL TYR HIS ASN LYS GLU ILE ILE VAL ALA TYR SER LYS SEQRES 5 A 231 ILE GLY LYS VAL HIS SER THR LEU THR THR THR SER MET SEQRES 6 A 231 ILE LEU ALA PHE GLY VAL GLN LYS VAL LEU PHE SER GLY SEQRES 7 A 231 VAL ALA GLY SER LEU VAL LYS ASP LEU LYS ILE ASN ASP SEQRES 8 A 231 LEU LEU VAL ALA THR GLN LEU VAL GLN HIS ASP VAL ASP SEQRES 9 A 231 LEU SER ALA PHE ASP HIS PRO LEU GLY PHE ILE PRO GLU SEQRES 10 A 231 SER ALA ILE PHE ILE GLU THR SER GLY SER LEU ASN ALA SEQRES 11 A 231 LEU ALA LYS LYS ILE ALA ASN GLU GLN HIS ILE ALA LEU SEQRES 12 A 231 LYS GLU GLY VAL ILE ALA SER GLY ASP GLN PHE VAL HIS SEQRES 13 A 231 SER LYS GLU ARG LYS GLU PHE LEU VAL SER GLU PHE LYS SEQRES 14 A 231 ALA SER ALA VAL GLU MET GLU GLY ALA SER VAL ALA PHE SEQRES 15 A 231 VAL CYS GLN LYS PHE GLY VAL PRO CYS CYS VAL LEU ARG SEQRES 16 A 231 SER ILE SER ASP ASN ALA ASP GLU LYS ALA GLY MET SER SEQRES 17 A 231 PHE ASP GLU PHE LEU GLU LYS SER ALA HIS THR SER ALA SEQRES 18 A 231 LYS PHE LEU LYS SER MET VAL ASP GLU LEU HET 2WP A 301 17 HET ADE A 302 10 HETNAM 2WP S-RIBOSYLHOMOCYSTEINE HETNAM ADE ADENINE FORMUL 2 2WP C9 H17 N O6 S FORMUL 3 ADE C5 H5 N5 FORMUL 4 HOH *220(H2 O) HELIX 1 1 MET A 10 GLY A 22 1 13 HELIX 2 2 GLY A 53 GLY A 69 1 17 HELIX 3 3 LEU A 104 ASP A 108 5 5 HELIX 4 4 SER A 124 GLN A 138 1 15 HELIX 5 5 SER A 156 LYS A 168 1 13 HELIX 6 6 GLU A 175 GLY A 187 1 13 HELIX 7 7 LYS A 203 ASP A 228 1 26 SHEET 1 A 9 GLU A 26 LEU A 30 0 SHEET 2 A 9 ASN A 33 TYR A 40 -1 O PHE A 35 N ILE A 28 SHEET 3 A 9 LYS A 43 TYR A 49 -1 O VAL A 47 N HIS A 36 SHEET 4 A 9 LYS A 3 GLY A 8 1 N ILE A 6 O ILE A 46 SHEET 5 A 9 LYS A 72 SER A 81 1 O LYS A 72 N GLY A 5 SHEET 6 A 9 ALA A 171 GLU A 173 -1 O VAL A 172 N GLY A 80 SHEET 7 A 9 LYS A 143 SER A 149 1 N ALA A 148 O ALA A 171 SHEET 8 A 9 LEU A 91 GLN A 99 1 N VAL A 98 O SER A 149 SHEET 9 A 9 ILE A 121 GLU A 122 -1 O ILE A 121 N LEU A 97 SHEET 1 B 8 GLU A 26 LEU A 30 0 SHEET 2 B 8 ASN A 33 TYR A 40 -1 O PHE A 35 N ILE A 28 SHEET 3 B 8 LYS A 43 TYR A 49 -1 O VAL A 47 N HIS A 36 SHEET 4 B 8 LYS A 3 GLY A 8 1 N ILE A 6 O ILE A 46 SHEET 5 B 8 LYS A 72 SER A 81 1 O LYS A 72 N GLY A 5 SHEET 6 B 8 CYS A 190 ASP A 198 1 O ASP A 198 N SER A 81 SHEET 7 B 8 LEU A 91 GLN A 99 -1 N LEU A 92 O ARG A 194 SHEET 8 B 8 ILE A 121 GLU A 122 -1 O ILE A 121 N LEU A 97 CRYST1 81.241 81.241 67.456 90.00 90.00 120.00 P 32 2 1 6 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 0.012309 0.007107 0.000000 0.00000 SCALE2 0.000000 0.014213 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014824 0.00000 MASTER 263 0 2 7 17 0 0 6 0 0 0 18 END