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- PDB-9ke8: Crystal Structure of HdNadV and its complex with NMN -

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Basic information

Entry
Database: PDB / ID: 9ke8
TitleCrystal Structure of HdNadV and its complex with NMN
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / Nadv-NMN 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
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological species[Haemophilus] ducreyi (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsLin, T. / Zhengjuan, W.
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 4, 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)112,0644
Polymers111,3942
Non-polymers6702
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-43 kcal/mol
Surface area32640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.520, 158.520, 130.400
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-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H16N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 4.25 Å3/Da / Density % sol: 71.03 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M trisodium citrate [pH 5.6] and 2.0 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 12, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.86→38.08 Å / Num. obs: 155560 / % possible obs: 99.94 % / Redundancy: 29.76 % / Biso Wilson estimate: 49.28 Å2 / CC1/2: 0.999 / Net I/σ(I): 1.34
Reflection shellResolution: 1.86→1.927 Å / Rmerge(I) obs: 1.34 / Num. unique obs: 155510

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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: 1.86→38.08 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 7957 5.12 %0
Rwork0.209 ---
obs0.2103 155510 99.96 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.86→38.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7590 0 44 198 7832
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0117812
X-RAY DIFFRACTIONf_angle_d1.60310595
X-RAY DIFFRACTIONf_dihedral_angle_d27.0751033
X-RAY DIFFRACTIONf_chiral_restr0.151190
X-RAY DIFFRACTIONf_plane_restr0.0111353
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.86-1.880.3992960.36524895X-RAY DIFFRACTION100
1.88-1.90.35912710.33414880X-RAY DIFFRACTION100
1.9-1.930.34182770.33994892X-RAY DIFFRACTION100
1.93-1.950.35862660.32134917X-RAY DIFFRACTION100
1.95-1.980.34392630.31084891X-RAY DIFFRACTION100
1.98-20.32992250.29674933X-RAY DIFFRACTION100
2-2.030.31682640.2964954X-RAY DIFFRACTION100
2.03-2.060.33522740.28464860X-RAY DIFFRACTION100
2.06-2.090.29642810.27524888X-RAY DIFFRACTION100
2.09-2.130.30792310.26234917X-RAY DIFFRACTION100
2.13-2.170.26862680.25264936X-RAY DIFFRACTION100
2.17-2.210.25912850.24294903X-RAY DIFFRACTION100
2.21-2.250.28822520.2434874X-RAY DIFFRACTION100
2.25-2.290.2412420.24014959X-RAY DIFFRACTION100
2.29-2.340.26292540.23684892X-RAY DIFFRACTION100
2.34-2.40.27072450.22794970X-RAY DIFFRACTION100
2.4-2.460.26292530.22744887X-RAY DIFFRACTION100
2.46-2.520.26042750.21314909X-RAY DIFFRACTION100
2.52-2.60.24952200.2134991X-RAY DIFFRACTION100
2.6-2.680.24222770.21844877X-RAY DIFFRACTION100
2.68-2.780.24922930.21194926X-RAY DIFFRACTION100
2.78-2.890.24162180.21284953X-RAY DIFFRACTION100
2.89-3.020.23552670.21334899X-RAY DIFFRACTION100
3.02-3.180.23673010.20964890X-RAY DIFFRACTION100
3.18-3.380.23193110.19894893X-RAY DIFFRACTION100
3.38-3.640.23192810.19144901X-RAY DIFFRACTION100
3.64-4.010.17322620.16924936X-RAY DIFFRACTION100
4.01-4.580.15932770.15054950X-RAY DIFFRACTION100
4.59-5.770.19972840.16984939X-RAY DIFFRACTION100
5.77-38.080.21712440.18465041X-RAY DIFFRACTION100

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