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- PDB-7yqq: Crystal Structure of Xcc NAMPT and its complex with NMN -

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Basic information

Entry
Database: PDB / ID: 7yqq
TitleCrystal Structure of Xcc NAMPT and its complex with NMN
ComponentsPre-B cell enhancing factor related protein
KeywordsTRANSFERASE / Xcc NAMPT in complexed state with NMN
Function / homology
Function and homology information


nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthetic process
Similarity search - Function
Nicotinamide phosphoribosyl transferase / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinamide phosphoribosyltransferase, N-terminal domain / Nicotinate/nicotinamide phosphoribosyltransferase / Nicotinate phosphoribosyltransferase (NAPRTase) family / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldolase-type TIM barrel
Similarity search - Domain/homology
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / PHOSPHATE ION / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsXu, G.L. / Ming, Z.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32160064 China
CitationJournal: To Be Published
Title: Structure of Xanthomonas campestris pv. campestris Nicotinamide Phosphoribosyltransferase: insights into bacterial NAD+ biosynthesis from the salvage pathway
Authors: Xu, G.L. / Ming, Z.H.
History
DepositionAug 8, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 14, 2024Provider: repository / Type: Initial release

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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
B: Pre-B cell enhancing factor related protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)106,8584
Polymers106,4272
Non-polymers4302
Water8,611478
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, Analytical Ultracentrifugation
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-39 kcal/mol
Surface area32410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.740, 115.740, 318.110
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11B-613-

HOH

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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 (bacteria)
Strain: 8004 / Gene: XC_0719 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0H2X5R2
#2: Chemical ChemComp-NMN / BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / NICOTINAMIDE MONONUCLEOTIDE


Mass: 335.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H16N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.89 Å3/Da / Density % sol: 57.43 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: ammonium tartrate, N,N-Bis(3-D-gluconamidopropyl) cholamide, N,N-Dimethyldecylamine-N-oxide, NMN

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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: 2.22→106.04 Å / Num. obs: 63152 / % possible obs: 99.9 % / Redundancy: 37.2 % / CC1/2: 0.999 / Net I/σ(I): 21.8
Reflection shellResolution: 2.22→2.28 Å / Num. unique obs: 4525 / CC1/2: 0.775

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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: 7YQO

7yqo


Resolution: 2.22→57.87 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 21.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2179 1861 3.15 %
Rwork0.1829 57131 -
obs0.184 58992 93.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 123.66 Å2 / Biso mean: 43.3291 Å2 / Biso min: 20.56 Å2
Refinement stepCycle: final / Resolution: 2.22→57.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7004 0 27 478 7509
Biso mean--67.85 45.66 -
Num. residues----901
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2201-2.28010.36481110.3439333173
2.2801-2.34720.28581240.2488400187
2.3472-2.42290.24311370.2058418091
2.4229-2.50950.2111370.2011423091
2.5095-2.610.23541380.1973427093
2.61-2.72880.27371430.1967434894
2.7288-2.87270.27161470.2008448396
2.8727-3.05260.22411470.1893452597
3.0526-3.28830.22321520.1788456698
3.2883-3.61920.20911480.1682465398
3.6192-4.14280.19921540.1604468199
4.1428-5.21890.16061570.14894796100
5.2189-57.870.21661660.1897506799
Refinement TLS params.Method: refined / Origin x: -17.292 Å / Origin y: -51.9618 Å / Origin z: -4.2112 Å
111213212223313233
T0.201 Å20.0058 Å2-0.0075 Å2-0.299 Å20.0373 Å2--0.4428 Å2
L0.7983 °20.1244 °2-0.1082 °2-0.0928 °20.0222 °2--0.4138 °2
S0.0044 Å °0.0767 Å °0.0573 Å °-0.0165 Å °0.0129 Å °-0.0003 Å °-0.0019 Å °-0.0283 Å °-0.0174 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA1 - 468
2X-RAY DIFFRACTION1allA501 - 601
3X-RAY DIFFRACTION1allB1 - 468
4X-RAY DIFFRACTION1allS1 - 478

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