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- PDB-9keo: Crystal Structure of HdNadV and its complex with NAM -

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Basic information

Entry
Database: PDB / ID: 9keo
TitleCrystal Structure of HdNadV and its complex with NAM
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / HdNadV-NAM complex
Function / homology
Function and homology information


nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD+ biosynthetic process
Similarity search - Function
Nicotinamide phosphoribosyl transferase / Nicotinate/nicotinamide phosphoribosyltransferase / Nicotinate phosphoribosyltransferase (NAPRTase) family / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldolase-type TIM barrel
Similarity search - Domain/homology
NICOTINAMIDE / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological species[Haemophilus] ducreyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.62 Å
AuthorsLin, T. / ZhengJuan, W. / Jia, Y.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The Structural Basis of NMN Synthesis Catalyzed by NadV from Haemophilus ducreyi
Authors: Lin, T. / ZhengJuan, W. / Jia, Y.
History
DepositionNov 5, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 12, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicotinamide phosphoribosyltransferase
B: Nicotinamide phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,8826
Polymers111,3942
Non-polymers4894
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11020 Å2
ΔGint-24 kcal/mol
Surface area32840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)160.820, 160.820, 129.790
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Nicotinamide phosphoribosyltransferase


Mass: 55696.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) [Haemophilus] ducreyi (bacteria) / Gene: nadV, PNAD10009, RZ57_05785 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: G1U9V7, nicotinamide phosphoribosyltransferase
#2: Chemical
ChemComp-NCA / NICOTINAMIDE


Mass: 122.125 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H6N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 4.35 Å3/Da / Density % sol: 71.72 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 1.5 M ammonium sulfate and 0.1 M sodium acetate trihydrate [pH 4.6]) in the presence of 5 mM NAM

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 15, 2022
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.62→52.64 Å / Num. obs: 57240 / % possible obs: 99.9 % / Redundancy: 1.32 % / Biso Wilson estimate: 44.04 Å2 / CC1/2: 0.9 / Net I/σ(I): 1.34
Reflection shellResolution: 2.62→2.714 Å / Num. unique obs: 57275 / CC1/2: 0.9
Serial crystallography sample deliveryMethod: fixed target

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Processing

Software
NameVersionClassification
PHENIX(1.18.2_3874: ???)refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.62→52.64 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.51 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2277 2786 4.87 %
Rwork0.1917 --
obs0.1935 57240 99.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.62→52.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7584 0 36 132 7752
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.017797
X-RAY DIFFRACTIONf_angle_d1.47910565
X-RAY DIFFRACTIONf_dihedral_angle_d25.8851032
X-RAY DIFFRACTIONf_chiral_restr0.0691181
X-RAY DIFFRACTIONf_plane_restr0.011356
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.62-2.670.34691360.31532729X-RAY DIFFRACTION100
2.67-2.710.32581060.29792749X-RAY DIFFRACTION100
2.71-2.770.3271370.29192701X-RAY DIFFRACTION100
2.77-2.820.29221100.27682759X-RAY DIFFRACTION100
2.82-2.880.31911820.26752647X-RAY DIFFRACTION100
2.88-2.950.30651540.2482695X-RAY DIFFRACTION100
2.95-3.020.30421560.24042697X-RAY DIFFRACTION100
3.02-3.110.27771340.23122718X-RAY DIFFRACTION100
3.11-3.20.27821620.22432695X-RAY DIFFRACTION100
3.2-3.30.2421370.20952714X-RAY DIFFRACTION100
3.3-3.420.20341450.20542720X-RAY DIFFRACTION100
3.42-3.560.23151310.19252722X-RAY DIFFRACTION100
3.56-3.720.23411340.1732731X-RAY DIFFRACTION100
3.72-3.910.20781380.1642727X-RAY DIFFRACTION100
3.91-4.160.18141710.1492680X-RAY DIFFRACTION100
4.16-4.480.17621230.13922761X-RAY DIFFRACTION100
4.48-4.930.17271260.14472730X-RAY DIFFRACTION100
4.93-5.640.19081350.16922741X-RAY DIFFRACTION100
5.65-7.10.22191380.19732759X-RAY DIFFRACTION100
7.11-52.640.19451310.16972779X-RAY DIFFRACTION99

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