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- PDB-1xnh: Crystal Structure of NH3-dependent NAD+ synthetase from Helicobac... -

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Basic information

Entry
Database: PDB / ID: 1xnh
TitleCrystal Structure of NH3-dependent NAD+ synthetase from Helicobacter pylori
ComponentsNH(3)-dependent NAD(+) synthetase
KeywordsLIGASE / NH3-dependent NAD+ synthetase / Helicobacter pylori / amidotransferase
Function / homology
Function and homology information


NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD biosynthetic process / ATP binding / metal ion binding / cytoplasm
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
NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesHelicobacter pylori (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsKang, G.B. / Kim, Y.S. / Im, Y.J. / Rho, S.H. / Lee, J.H. / Eom, S.H.
CitationJournal: Proteins / Year: 2005
Title: Crystal structure of NH3-dependent NAD+ synthetase from Helicobacter pylori
Authors: Kang, G.B. / Kim, Y.S. / Im, Y.J. / Rho, S.H. / Lee, J.H. / Eom, S.H.
History
DepositionOct 5, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 5, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)30,3761
Polymers30,3761
Non-polymers00
Water66737
1
A: NH(3)-dependent NAD(+) synthetase

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


Theoretical massNumber of molelcules
Total (without water)60,7522
Polymers60,7522
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area4000 Å2
ΔGint-35 kcal/mol
Surface area22860 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)93.830, 48.320, 64.200
Angle α, β, γ (deg.)90.00, 109.97, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein NH(3)-dependent NAD(+) synthetase


Mass: 30376.047 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Helicobacter pylori (bacteria) / Plasmid: pET21a / Production host: Escherichia coli (E. coli) / References: UniProt: O25096, NAD+ synthase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.2 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6
Details: sodium acetate, PEG 1500, magnesium chloride, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
12941
22941
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONPhoton Factory BL-18B10.9794, 0.9793, 0.9716
SYNCHROTRONPhoton Factory BL-18B20.9202
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 12, 2001
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1GRAPHITEMADMx-ray1
2SINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97941
20.97931
30.97161
40.92021
ReflectionResolution: 2.3→26.74 Å / Num. all: 12172 / Num. obs: 12154 / % possible obs: 14.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1
Reflection shellResolution: 2.3→2.4 Å / % possible all: 99.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→26.74 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.295 1257 RANDOM
Rwork0.255 --
all0.259 12172 -
obs0.259 12154 -
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.32 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.3→26.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1964 0 0 37 2001
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.1
X-RAY DIFFRACTIONc_improper_angle_d0.87
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
2.3-2.40.33315410.30.30213450.0271503149999.7
2.4-2.530.2931459.70.27613480.0241494149399.9
2.53-2.690.33917011.20.28313490.0261521151999.9
2.69-2.90.3181489.80.26913580.0261508150699.9
2.9-3.190.30915510.20.26213610.0251517151699.9
3.19-3.650.28517511.50.25313520.0221528152799.9
3.65-4.590.277152100.22313660.0221519151899.9
4.59-26.740.277158100.23514180.0221584157699.5

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