HEADER LIGASE 05-OCT-04 1XNH TITLE CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM HELICOBACTER TITLE 2 PYLORI COMPND MOL_ID: 1; COMPND 2 MOLECULE: NH(3)-DEPENDENT NAD(+) SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 EC: 6.3.1.5; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 210; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PET21A KEYWDS NH3-DEPENDENT NAD+ SYNTHETASE, HELICOBACTER PYLORI, AMIDOTRANSFERASE, KEYWDS 2 LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR G.B.KANG,Y.S.KIM,Y.J.IM,S.H.RHO,J.H.LEE,S.H.EOM REVDAT 5 13-MAR-24 1XNH 1 SEQADV REVDAT 4 13-JUL-11 1XNH 1 VERSN REVDAT 3 24-FEB-09 1XNH 1 VERSN REVDAT 2 03-MAY-05 1XNH 1 JRNL AUTHOR REVDAT 1 05-APR-05 1XNH 0 JRNL AUTH G.B.KANG,Y.S.KIM,Y.J.IM,S.H.RHO,J.H.LEE,S.H.EOM JRNL TITL CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM JRNL TITL 2 HELICOBACTER PYLORI JRNL REF PROTEINS V. 58 985 2005 JRNL REFN ISSN 0887-3585 JRNL PMID 15645437 JRNL DOI 10.1002/PROT.20377 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.74 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 12154 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.255 REMARK 3 FREE R VALUE : 0.295 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1257 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 8 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.70 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 1345 REMARK 3 BIN R VALUE (WORKING SET) : 0.3020 REMARK 3 BIN FREE R VALUE : 0.3330 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 154 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.027 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1964 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 37 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) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.29 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.37 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.32 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.009 REMARK 3 BOND ANGLES (DEGREES) : 1.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 22.10 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.870 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1XNH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 06-OCT-04. REMARK 100 THE DEPOSITION ID IS D_1000030547. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-NOV-01; NULL REMARK 200 TEMPERATURE (KELVIN) : 294; 294 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y; Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY; PHOTON FACTORY REMARK 200 BEAMLINE : BL-18B; BL-18B REMARK 200 X-RAY GENERATOR MODEL : NULL; NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M; M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794, 0.9793, 0.9716; 0.9202 REMARK 200 MONOCHROMATOR : GRAPHITE; NULL REMARK 200 OPTICS : NULL; NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD; NULL REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4; NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12154 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 26.740 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 14.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 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: MAD; SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM ACETATE, PEG 1500, MAGNESIUM REMARK 280 CHLORIDE, PH 6.0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 294K 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 46.91500 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.16000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 46.91500 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 24.16000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22860 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -35.0 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 71.90390 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 60.33976 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 1 REMARK 465 GLN A 2 REMARK 465 LYS A 3 REMARK 465 ASP A 4 REMARK 465 ARG A 256 REMARK 465 PHE A 257 REMARK 465 ASN A 258 REMARK 465 PRO A 259 REMARK 465 GLU A 260 REMARK 465 LEU A 261 REMARK 465 GLU A 262 REMARK 465 HIS A 263 REMARK 465 HIS A 264 REMARK 465 HIS A 265 REMARK 465 HIS A 266 REMARK 465 HIS A 267 REMARK 465 HIS A 268 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 MET A 64 CG SD CE REMARK 470 GLU A 66 CG CD OE1 OE2 REMARK 470 LYS A 235 CG CD CE NZ REMARK 470 LYS A 255 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 LYS A 26 -1.04 -140.91 REMARK 500 LYS A 50 -114.12 53.89 REMARK 500 MET A 58 66.70 -112.66 REMARK 500 SER A 60 -165.38 -104.83 REMARK 500 ASP A 126 61.08 61.31 REMARK 500 SER A 183 111.79 -174.08 REMARK 500 ASP A 185 105.99 57.01 REMARK 500 LEU A 186 -14.00 -141.62 REMARK 500 PHE A 187 -141.65 -173.00 REMARK 500 GLU A 193 5.97 -67.72 REMARK 500 GLU A 211 50.68 -96.54 REMARK 500 ALA A 212 -30.96 -159.67 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1XNG RELATED DB: PDB REMARK 900 THE SAME PROTEIN COMPLEXED WITH NICOTINIC ACID ADENINE DINUCLEOTIDE DBREF 1XNH A 1 260 UNP O25096 NADE_HELPY 1 260 SEQADV 1XNH LEU A 261 UNP O25096 CLONING ARTIFACT SEQADV 1XNH GLU A 262 UNP O25096 CLONING ARTIFACT SEQADV 1XNH HIS A 263 UNP O25096 CLONING ARTIFACT SEQADV 1XNH HIS A 264 UNP O25096 CLONING ARTIFACT SEQADV 1XNH HIS A 265 UNP O25096 CLONING ARTIFACT SEQADV 1XNH HIS A 266 UNP O25096 CLONING ARTIFACT SEQADV 1XNH HIS A 267 UNP O25096 CLONING ARTIFACT SEQADV 1XNH HIS A 268 UNP O25096 CLONING ARTIFACT SEQRES 1 A 268 MET GLN LYS ASP TYR GLN LYS LEU ILE VAL TYR LEU CYS SEQRES 2 A 268 ASP PHE LEU GLU LYS GLU VAL GLN LYS ARG GLY PHE LYS SEQRES 3 A 268 LYS VAL VAL TYR GLY LEU SER GLY GLY LEU ASP SER ALA SEQRES 4 A 268 VAL VAL GLY VAL LEU CYS GLN LYS VAL PHE LYS GLU ASN SEQRES 5 A 268 ALA HIS ALA LEU LEU MET PRO SER SER VAL SER MET PRO SEQRES 6 A 268 GLU ASN LYS THR ASP ALA LEU ASN LEU CYS GLU LYS PHE SEQRES 7 A 268 SER ILE PRO TYR THR GLU TYR SER ILE ALA PRO TYR ASP SEQRES 8 A 268 ALA ILE PHE SER SER HIS PHE LYS ASP ALA SER LEU THR SEQRES 9 A 268 ARG LYS GLY ASN PHE CYS ALA ARG LEU ARG MET ALA PHE SEQRES 10 A 268 LEU TYR ASP TYR SER LEU LYS SER ASP SER LEU VAL ILE SEQRES 11 A 268 GLY THR SER ASN LYS SER GLU ARG MET LEU GLY TYR GLY SEQRES 12 A 268 THR LEU PHE GLY ASP LEU ALA CYS ALA ILE ASN PRO ILE SEQRES 13 A 268 GLY GLU LEU PHE LYS THR GLU VAL TYR GLU LEU ALA ARG SEQRES 14 A 268 ARG LEU ASN ILE PRO LYS LYS ILE LEU ASN LYS PRO PRO SEQRES 15 A 268 SER ALA ASP LEU PHE VAL GLY GLN SER ASP GLU LYS ASP SEQRES 16 A 268 LEU GLY TYR PRO TYR SER VAL ILE ASP PRO LEU LEU LYS SEQRES 17 A 268 ASP ILE GLU ALA LEU PHE GLN THR LYS PRO ILE ASP THR SEQRES 18 A 268 GLU THR LEU ALA GLN LEU GLY TYR ASP GLU ILE LEU VAL SEQRES 19 A 268 LYS ASN ILE THR SER ARG ILE GLN LYS ASN ALA PHE LYS SEQRES 20 A 268 LEU GLU LEU PRO ALA ILE ALA LYS ARG PHE ASN PRO GLU SEQRES 21 A 268 LEU GLU HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *37(H2 O) HELIX 1 1 TYR A 5 LYS A 22 1 18 HELIX 2 2 GLY A 35 LYS A 50 1 16 HELIX 3 3 MET A 64 SER A 79 1 16 HELIX 4 4 ILE A 87 PHE A 98 1 12 HELIX 5 5 SER A 102 ASP A 126 1 25 HELIX 6 6 ASN A 134 GLY A 141 1 8 HELIX 7 7 PHE A 160 LEU A 171 1 12 HELIX 8 8 PRO A 174 ASN A 179 1 6 HELIX 9 9 SER A 191 LEU A 196 1 6 HELIX 10 10 PRO A 199 PHE A 214 1 16 HELIX 11 11 ASP A 220 GLN A 226 1 7 HELIX 12 12 ASP A 230 ALA A 245 1 16 SHEET 1 A 4 TYR A 82 GLU A 84 0 SHEET 2 A 4 ALA A 53 LEU A 57 1 N ALA A 55 O THR A 83 SHEET 3 A 4 VAL A 28 GLY A 31 1 N VAL A 28 O HIS A 54 SHEET 4 A 4 LEU A 128 VAL A 129 1 O LEU A 128 N VAL A 29 CRYST1 93.830 48.320 64.200 90.00 109.97 90.00 C 1 2 1 4 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 0.010658 0.000000 0.003873 0.00000 SCALE2 0.000000 0.020695 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016573 0.00000