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- PDB-4q16: Structure of NAD+ Synthetase from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 4q16
TitleStructure of NAD+ Synthetase from Deinococcus radiodurans
ComponentsNH(3)-dependent NAD(+) synthetase
KeywordsLIGASE / NADS / NAD synthetase
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 speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsLee, J.Y. / Park, Y.W.
CitationJournal: To be Published
Title: Structural Analysis of the NH3-dependent NAD+ Synthetase from Deinococcus radiodurans
Authors: Lee, J.Y. / Park, Y.W. / Yeo, H.K.
History
DepositionApr 3, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 15, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
C: NH(3)-dependent NAD(+) synthetase
D: NH(3)-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)125,22012
Polymers124,4514
Non-polymers7698
Water6,521362
1
A: NH(3)-dependent NAD(+) synthetase
B: NH(3)-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6106
Polymers62,2262
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5740 Å2
ΔGint-84 kcal/mol
Surface area22130 Å2
MethodPISA
2
C: NH(3)-dependent NAD(+) synthetase
D: NH(3)-dependent NAD(+) synthetase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,6106
Polymers62,2262
Non-polymers3844
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5710 Å2
ΔGint-85 kcal/mol
Surface area21710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.230, 114.150, 121.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 31112.852 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Strain: R1 / Gene: nadE, DR_A0201 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RYV5, NAD+ synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 362 / 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: 3.16 Å3/Da / Density % sol: 61.05 %
Crystal growMethod: vapor diffusion, sitting drop / pH: 6
Details: 20% Poly ethylene glycol (PEG) 4000, 0.2M lithium sulfate, 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Jun 19, 2013
RadiationMonochromator: YALE MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 49185 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8.7 % / Biso Wilson estimate: 37.09 Å2 / Rmerge(I) obs: 0.096 / Net I/σ(I): 14.6

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Processing

Software
NameVersionClassificationNB
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.14data extraction
HKL-2000data collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→29.381 Å / FOM work R set: 0.7707 / SU ML: 0.4 / σ(F): 2 / σ(I): 2 / Phase error: 29.52 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2928 2460 5.07 %RANDOM
Rwork0.2391 ---
all0.2418 46018 --
obs0.2418 48478 98.73 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 96.44 Å2 / Biso mean: 41.74 Å2 / Biso min: 14.51 Å2
Refinement stepCycle: LAST / Resolution: 2.6→29.381 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7867 0 40 362 8269
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0028043
X-RAY DIFFRACTIONf_angle_d0.53910947
X-RAY DIFFRACTIONf_chiral_restr0.0341236
X-RAY DIFFRACTIONf_plane_restr0.0031457
X-RAY DIFFRACTIONf_dihedral_angle_d11.3622821
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.6-2.650.37421380.29782494263297
2.65-2.7040.36531250.28912467259297
2.704-2.76280.31541230.29322513263697
2.7628-2.8270.41711380.29772496263498
2.827-2.89770.32561260.28942496262298
2.8977-2.97590.38671450.29422537268298
2.9759-3.06340.34771370.28022511264899
3.0634-3.16220.3451370.28232550268799
3.1622-3.27510.3511430.27282516265999
3.2751-3.4060.32771430.25862551269499
3.406-3.56080.2851240.24182570269499
3.5608-3.74810.26491380.23422550268899
3.7481-3.98240.27571410.2232571271299
3.9824-4.28910.24721300.19792589271999
4.2891-4.71910.23081470.19512593274099
4.7191-5.39830.29961420.218826172759100
5.3983-6.78740.29011250.23562645277099
6.7874-29.38250.2161580.195427522910100

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