PDB Short entry for 1WXF HEADER LIGASE 23-JAN-05 1WXF TITLE E.COLI NAD SYNTHETASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NH(3)-DEPENDENT NAD(+) SYNTHETASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NAD SYNTHETASE, NITROGEN-REGULATORY PROTEIN; COMPND 5 EC: 6.3.1.5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PRSETHE KEYWDS NADE, NAD, E.COLI, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR R.JAUCH,A.HUMM,R.HUBER,M.C.WAHL REVDAT 5 13-MAR-24 1WXF 1 REMARK REVDAT 4 13-JUL-11 1WXF 1 VERSN REVDAT 3 24-FEB-09 1WXF 1 VERSN REVDAT 2 19-APR-05 1WXF 1 JRNL REVDAT 1 15-FEB-05 1WXF 0 JRNL AUTH R.JAUCH,A.HUMM,R.HUBER,M.C.WAHL JRNL TITL STRUCTURES OF ESCHERICHIA COLI NAD SYNTHETASE WITH JRNL TITL 2 SUBSTRATES AND PRODUCTS REVEAL MECHANISTIC REARRANGEMENTS JRNL REF J.BIOL.CHEM. V. 280 15131 2005 JRNL REFN ISSN 0021-9258 JRNL PMID 15699042 JRNL DOI 10.1074/JBC.M413195200 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 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) : 30.00 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 : 16080 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) : 0.183 REMARK 3 FREE R VALUE : 0.217 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 820 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 : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2006 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 165 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) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.005 REMARK 3 BOND ANGLES (DEGREES) : 1.080 REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : NULL 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 1WXF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 25-JAN-05. REMARK 100 THE DEPOSITION ID IS D_1000024115. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 295 REMARK 200 PH : 5.2 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 : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 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 : 16080 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%) : 97.7 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 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG400, MAGNESIUM CHLORIDE, SODIUM REMARK 280 -ACETATE, LITHIUM-META-TANTALATE, PH 5.2, VAPOR DIFFUSION, REMARK 280 TEMPERATURE 295K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 25.44033 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 50.88067 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 50.88067 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 25.44033 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 4810 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22290 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -39.0 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 50.88067 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 88 REMARK 465 ALA A 89 REMARK 465 ASP A 90 REMARK 465 LYS A 208 REMARK 465 ALA A 209 REMARK 465 PRO A 210 REMARK 465 THR A 211 REMARK 465 ALA A 212 REMARK 465 ASP A 213 REMARK 465 LEU A 214 REMARK 465 GLU A 215 REMARK 465 ASP A 216 REMARK 465 ASP A 217 REMARK 465 ARG A 218 REMARK 465 PRO A 219 REMARK 465 SER A 220 REMARK 465 LEU A 221 REMARK 465 PRO A 222 REMARK 465 ASP A 223 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 ARG A 186 -25.90 119.88 REMARK 500 TYR A 206 15.50 -144.87 REMARK 500 VAL A 225 -90.10 -22.58 REMARK 500 ASP A 271 -9.09 -140.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1WXE RELATED DB: PDB REMARK 900 E.COLI NAD SYNTHETASE, AMP REMARK 900 RELATED ID: 1WXG RELATED DB: PDB REMARK 900 E.COLI NAD SYNTHETASE, DND REMARK 900 RELATED ID: 1WXH RELATED DB: PDB REMARK 900 E.COLI NAD SYNTHETASE, NAD REMARK 900 RELATED ID: 1WXI RELATED DB: PDB REMARK 900 E.COLI NAD SYNTHETASE, AMP.PP DBREF 1WXF A 1 275 UNP P18843 NADE_ECOLI 1 275 SEQRES 1 A 275 MET THR LEU GLN GLN GLN ILE ILE LYS ALA LEU GLY ALA SEQRES 2 A 275 LYS PRO GLN ILE ASN ALA GLU GLU GLU ILE ARG ARG SER SEQRES 3 A 275 VAL ASP PHE LEU LYS SER TYR LEU GLN THR TYR PRO PHE SEQRES 4 A 275 ILE LYS SER LEU VAL LEU GLY ILE SER GLY GLY GLN ASP SEQRES 5 A 275 SER THR LEU ALA GLY LYS LEU CYS GLN MET ALA ILE ASN SEQRES 6 A 275 GLU LEU ARG LEU GLU THR GLY ASN GLU SER LEU GLN PHE SEQRES 7 A 275 ILE ALA VAL ARG LEU PRO TYR GLY VAL GLN ALA ASP GLU SEQRES 8 A 275 GLN ASP CYS GLN ASP ALA ILE ALA PHE ILE GLN PRO ASP SEQRES 9 A 275 ARG VAL LEU THR VAL ASN ILE LYS GLY ALA VAL LEU ALA SEQRES 10 A 275 SER GLU GLN ALA LEU ARG GLU ALA GLY ILE GLU LEU SER SEQRES 11 A 275 ASP PHE VAL ARG GLY ASN GLU LYS ALA ARG GLU ARG MET SEQRES 12 A 275 LYS ALA GLN TYR SER ILE ALA GLY MET THR SER GLY VAL SEQRES 13 A 275 VAL VAL GLY THR ASP HIS ALA ALA GLU ALA ILE THR GLY SEQRES 14 A 275 PHE PHE THR LYS TYR GLY ASP GLY GLY THR ASP ILE ASN SEQRES 15 A 275 PRO LEU TYR ARG LEU ASN LYS ARG GLN GLY LYS GLN LEU SEQRES 16 A 275 LEU ALA ALA LEU ALA CYS PRO GLU HIS LEU TYR LYS LYS SEQRES 17 A 275 ALA PRO THR ALA ASP LEU GLU ASP ASP ARG PRO SER LEU SEQRES 18 A 275 PRO ASP GLU VAL ALA LEU GLY VAL THR TYR ASP ASN ILE SEQRES 19 A 275 ASP ASP TYR LEU GLU GLY LYS ASN VAL PRO GLN GLN VAL SEQRES 20 A 275 ALA ARG THR ILE GLU ASN TRP TYR LEU LYS THR GLU HIS SEQRES 21 A 275 LYS ARG ARG PRO PRO ILE THR VAL PHE ASP ASP PHE TRP SEQRES 22 A 275 LYS LYS FORMUL 2 HOH *165(H2 O) HELIX 1 1 THR A 2 GLY A 12 1 11 HELIX 2 2 ASN A 18 TYR A 37 1 20 HELIX 3 3 GLY A 50 GLY A 72 1 23 HELIX 4 4 GLU A 91 GLN A 102 1 12 HELIX 5 5 ILE A 111 ALA A 125 1 15 HELIX 6 6 SER A 130 THR A 153 1 24 HELIX 7 7 HIS A 162 ILE A 167 1 6 HELIX 8 8 ASN A 188 LEU A 199 1 12 HELIX 9 9 PRO A 202 TYR A 206 5 5 HELIX 10 10 THR A 230 GLU A 239 1 10 HELIX 11 11 PRO A 244 THR A 258 1 15 HELIX 12 12 GLU A 259 ARG A 263 5 5 SHEET 1 A 4 ARG A 105 THR A 108 0 SHEET 2 A 4 GLN A 77 ARG A 82 1 N ARG A 82 O LEU A 107 SHEET 3 A 4 SER A 42 ILE A 47 1 N ILE A 47 O VAL A 81 SHEET 4 A 4 VAL A 156 VAL A 157 1 O VAL A 156 N VAL A 44 CRYST1 91.887 91.887 76.321 90.00 90.00 120.00 P 31 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 0.010883 0.006283 0.000000 0.00000 SCALE2 0.000000 0.012567 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013103 0.00000