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- PDB-7yqo: Xcc Nicotinamide Phosphoribosyltransferase -

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Basic information

Entry
Database: PDB / ID: 7yqo
TitleXcc Nicotinamide Phosphoribosyltransferase
ComponentsPre-B cell enhancing factor related protein
KeywordsTRANSFERASE / NAMPT in isolation
Function / homology
Function and homology information


nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD+ biosynthetic process
Similarity search - Function
Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinamide phosphoribosyl transferase / Nicotinate/nicotinamide phosphoribosyltransferase / Nicotinate phosphoribosyltransferase (NAPRTase) family / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldolase-type TIM barrel
Similarity search - Domain/homology
Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris str. 8004 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsXu, G.L. / Ming, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32160064 China
CitationJournal: Commun Biol / Year: 2024
Title: Structural insights into Xanthomonas campestris pv. campestris NAD + biosynthesis via the NAM salvage pathway.
Authors: Xu, G. / Ma, J. / Fang, Q. / Peng, Q. / Jiao, X. / Hu, W. / Zhao, Q. / Kong, Y. / Liu, F. / Shi, X. / Tang, D.J. / Tang, J.L. / Ming, Z.
History
DepositionAug 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 4, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 4, 2026Group: Refinement description / Structure summary
Category: pdbx_entry_details / pdbx_initial_refinement_model
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pre-B cell enhancing factor related protein
B: Pre-B cell enhancing factor related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,5203
Polymers106,4272
Non-polymers921
Water9,800544
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Analytical Ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8620 Å2
ΔGint-41 kcal/mol
Surface area31790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.610, 151.480, 70.810
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Pre-B cell enhancing factor related protein / Nicotinamide Phosphoribosyltransferase


Mass: 53213.746 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris str. 8004 (bacteria)
Strain: 8004 / Gene: XC_0719 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2X5R2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 544 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: Citric acid, BIS-TRIS propane, Polyethylene glycol 3350), GSH (L-Glutathione reduced), 0.01 M GSSG

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979183 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 6, 2019
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 1.79→91.61 Å / Num. obs: 93464 / % possible obs: 99.9 % / Redundancy: 13.085 % / CC1/2: 0.999 / Rmerge(I) obs: 0.109 / Net I/σ(I): 16.8
Reflection shellResolution: 1.79→8.01 Å / Num. unique obs: 6845 / CC1/2: 0.657

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Starting model: 6.0E+68 / Resolution: 1.79→70.81 Å / SU ML: 0.17 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 19.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1985 1978 2.14 %
Rwork0.1783 90379 -
obs0.1788 92357 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 102.58 Å2 / Biso mean: 32.736 Å2 / Biso min: 13.25 Å2
Refinement stepCycle: final / Resolution: 1.79→70.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7101 0 6 544 7651
Biso mean--36.37 38.47 -
Num. residues----912
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7901-1.83480.29981320.2664621796
1.8348-1.88440.27681390.2366621897
1.8844-1.93990.26031380.2163627897
1.9399-2.00250.23751380.2087632298
2.0025-2.07410.21681410.1917640199
2.0741-2.15710.21771400.1829640799
2.1571-2.25530.19981400.1773644599
2.2553-2.37420.20991420.1833645399
2.3742-2.5230.19561410.17926497100
2.523-2.71780.2181430.18336521100
2.7178-2.99130.21641430.186533100
2.9913-3.42410.17771440.16656578100
3.4241-4.3140.18261460.15116642100
4.314-70.810.17271510.1794686799

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