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- PDB-1ifx: CRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS ... -

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Basic information

Entry
Database: PDB / ID: 1ifx
TitleCRYSTAL STRUCTURE OF NH3-DEPENDENT NAD+ SYNTHETASE FROM BACILLUS SUBTILIS COMPLEXED WITH TWO MOLECULES DEAMIDO-NAD
ComponentsNH(3)-DEPENDENT NAD(+) SYNTHETASE
KeywordsLIGASE / LYASE / AMIDOTRANSFERASE / NH3 DEPENDENT / ATP / PYROPHOSPHATASE
Function / homology
Function and homology information


NAD+ synthase / NAD+ synthase activity / NAD+ synthase (glutamine-hydrolyzing) activity / glutaminase activity / NAD+ biosynthetic process / sporulation resulting in formation of a cellular spore / 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
NICOTINIC ACID ADENINE DINUCLEOTIDE / NH(3)-dependent NAD(+) synthetase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 2.25 Å
AuthorsDevedjiev, Y. / Symersky, J. / Singh, R. / Brouillette, W. / Muccio, D. / Jedrzejas, M. / Brouillette, C. / DeLucas, L.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Stabilization of active-site loops in NH3-dependent NAD+ synthetase from Bacillus subtilis.
Authors: Devedjiev, Y. / Symersky, J. / Singh, R. / Jedrzejas, M. / Brouillette, C. / Brouillette, W. / Muccio, D. / Chattopadhyay, D. / DeLucas, L.
History
DepositionApr 13, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 6, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
B: NH(3)-DEPENDENT NAD(+) SYNTHETASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,9394
Polymers60,6082
Non-polymers1,3312
Water4,179232
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7410 Å2
ΔGint-53 kcal/mol
Surface area20660 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.060, 86.090, 61.080
Angle α, β, γ (deg.)90.00, 111.18, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe second part of the biological assembly is generated by the two fold axis

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Components

#1: Protein NH(3)-DEPENDENT NAD(+) SYNTHETASE / NAD(+) synthetase


Mass: 30303.994 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: NadE / Production host: Escherichia coli (E. coli)
References: UniProt: P08164, NAD+ synthase (glutamine-hydrolysing)
#2: Chemical ChemComp-DND / NICOTINIC ACID ADENINE DINUCLEOTIDE / DEAMIDO-NAD+


Mass: 665.418 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N6O15P2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 232 / 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: 2.15 Å3/Da / Density % sol: 42.67 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.2
Details: sodium acetate buffer, Magnesium chloride, PEG 400, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMsodium acetate1drop
250 mM1dropMgCl2
32.5 mMbeta-mercaptoethanol1drop
415 mg/mlprotein1drop
521-23 %(v/v)PEG4001reservoir
60.1 Msodium acetate1reservoir
750 mM1reservoirMgCl2
85 mMNaAD1reservoir

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 3, 1998 / Details: mirrors
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.25→25 Å / Num. all: 84706 / Num. obs: 24270 / % possible obs: 99.5 % / Observed criterion σ(I): 1 / Redundancy: 3.6 % / Biso Wilson estimate: 30.1 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.9
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.318 / Mean I/σ(I) obs: 3.2 / Num. unique all: 2401 / Rsym value: 31.8 / % possible all: 100
Reflection
*PLUS
Num. measured all: 162585
Reflection shell
*PLUS
% possible obs: 79.2 %

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Processing

Software
NameVersionClassification
X-PLOR3.851refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementStarting model: PDB ENTRY 1ee1

1ee1


Resolution: 2.25→8 Å / σ(F): 2 / Stereochemistry target values: Engh, Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.297 1126 -RANDOM
Rwork0.195 ---
all-24270 --
obs-23501 99.5 %-
Refinement stepCycle: LAST / Resolution: 2.25→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3854 0 88 232 4174
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.012
X-RAY DIFFRACTIONx_angle_deg2.19
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.177 / Total num. of bins used: 8 / % reflection obs: 99 %

Resolution (Å)Num. reflection RfreeNum. reflection obs
2.25-2.351412774
2.35-2.471372779
2.47-2.621422793
2.62-2.811392786
2.81-3.081392797
3.08-3.51472791
3.5-4.31362812
4.3-81452843
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 8 Å / σ(F): 2 / Rfactor obs: 0.216
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 4.3 Å / Lowest resolution: 8 Å / Rfactor Rfree: 0.297 / Rfactor Rwork: 0.177

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