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- PDB-7yqp: Xcc Nicotinamide Phosphoribosyltransferase -

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Basic information

Entry
Database: PDB / ID: 7yqp
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 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.088 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)53,2141
Polymers53,2141
Non-polymers00
Water1,27971
1
A: Pre-B cell enhancing factor related protein

A: Pre-B cell enhancing factor related protein


Theoretical massNumber of molelcules
Total (without water)106,4272
Polymers106,4272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_545-x,-y-1,z1
Buried area5850 Å2
ΔGint-24 kcal/mol
Surface area31700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.898, 115.898, 160.113
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-543-

HOH

21A-556-

HOH

31A-568-

HOH

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Components

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


Mass: 53213.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Strain: 8004 / Gene: XC_0719 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0H2X5R2
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 71 / 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: 2.92 Å3/Da / Density % sol: 57.83 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: ammonium tartrate, N,N-Bis(3-D-gluconamidopropyl) cholamide, N,N-Dimethyldecylamine-N-oxide

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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: Jan 12, 2020
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979183 Å / Relative weight: 1
ReflectionResolution: 2.08→100.62 Å / Num. obs: 25813 / % possible obs: 100 % / Redundancy: 14.05 % / CC1/2: 1 / Net I/σ(I): 21.8
Reflection shellResolution: 2.08→9.3 Å / Num. unique obs: 2831 / CC1/2: 0.9

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Processing

Software
NameVersionClassification
PHENIX1.15_3459refinement
PDB_EXTRACT3.27data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7YQO

7yqo


Resolution: 2.088→54.49 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2526 1998 7.74 %
Rwork0.2185 23815 -
obs0.2211 25813 67.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 145.63 Å2 / Biso mean: 56.8716 Å2 / Biso min: 25.74 Å2
Refinement stepCycle: final / Resolution: 2.088→54.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3259 0 0 71 3330
Biso mean---50.84 -
Num. residues----420
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.0882-2.14040.3571220.300926411
2.1404-2.19830.308450.240153022
2.1983-2.2630.3457520.27962325
2.263-2.3360.2882970.2638114946
2.336-2.41950.28941210.2439145558
2.4195-2.51640.31281400.243166267
2.5164-2.63090.28981700.26203382
2.6309-2.76960.28681090.2503128651
2.7696-2.94310.25562090.23862493100
2.9431-3.17040.27872110.2322528100
3.1704-3.48940.22362140.22732529100
3.4894-3.99410.28191590.1981191375
3.9941-5.03160.22992190.18352611100
5.0316-54.490.23452300.2235273999
Refinement TLS params.Method: refined / Origin x: 41.2073 Å / Origin y: -45.5019 Å / Origin z: 3.8366 Å
111213212223313233
T0.116 Å2-0.0083 Å20.0199 Å2-0.5726 Å2-0.003 Å2--0.295 Å2
L1.1181 °2-0.1143 °20.1119 °2-0.329 °2-0.1992 °2--0.5704 °2
S-0.0626 Å °-0.0045 Å °0.1833 Å °-0.0049 Å °0.0272 Å °0.0084 Å °-0.0238 Å °-0.0214 Å °-0.0112 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 468
2X-RAY DIFFRACTION1allS1 - 71

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