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- PDB-1wxg: E.coli NAD Synthetase, DND -

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Basic information

Entry
Database: PDB / ID: 1wxg
TitleE.coli NAD Synthetase, DND
ComponentsNH(3)-dependent NAD(+) synthetase
KeywordsLIGASE / NADE / NAD / E.coli
Function / homology
Function and homology information


NAD salvage / 'de novo' NAD biosynthetic process from aspartate / NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / DNA damage response / magnesium ion binding / protein homodimerization activity / ATP binding / cytosol
Similarity search - Function
NH(3)-dependent NAD(+) synthetase / NAD(+) synthetase / NAD/GMP synthase / NAD synthase / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINIC ACID ADENINE DINUCLEOTIDE / NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsJauch, R. / Humm, A. / Huber, R. / Wahl, M.C.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structures of Escherichia coli NAD Synthetase with Substrates and Products Reveal Mechanistic Rearrangements
Authors: Jauch, R. / Humm, A. / Huber, R. / Wahl, M.C.
History
DepositionJan 23, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 2.0Mar 13, 2024Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _atom_site.occupancy / _database_2.pdbx_DOI ..._atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NH(3)-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3633
Polymers30,6731
Non-polymers6902
Water4,089227
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: NH(3)-dependent NAD(+) synthetase
hetero molecules

A: NH(3)-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,7256
Polymers61,3462
Non-polymers1,3794
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area7340 Å2
ΔGint-69 kcal/mol
Surface area21950 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)92.366, 67.792, 48.180
Angle α, β, γ (deg.)90.00, 104.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-584-

HOH

21A-614-

HOH

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Components

#1: Protein NH(3)-dependent NAD(+) synthetase / NAD Synthetase / Nitrogen-regulatory protein


Mass: 30672.777 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pRSETHE / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P18843, NAD+ synthase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+


Mass: 665.418 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N6O15P2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.2 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5.2
Details: PEG400, magnesium chloride, sodium-acetate, lithium-meta-tantalate, pH 5.2, VAPOR DIFFUSION, temperature 295K

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Data collection

DiffractionMean temperature: 295 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 22778 / Num. obs: 21526 / % possible obs: 94.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 1.9→1.95 Å / % possible all: 91.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→30 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.223 1249 RANDOM
Rwork0.199 --
obs0.199 21526 -
all-22778 -
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2006 0 45 227 2278
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.13

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