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- PDB-2g96: Crystal Structure of Visfatin/Pre-B Cell Colony Enhancing Factor ... -

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Basic information

Entry
Database: PDB / ID: 2g96
TitleCrystal Structure of Visfatin/Pre-B Cell Colony Enhancing Factor 1/Nicotinamide Phosphoribosyltransferase In Complex with Niconamide Mononucleotide
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / Visfatin / PBEF / NAmPRTase / nmn / Rattus norvegicus
Function / homology
Function and homology information


response to D-galactose / : / regulation of lung blood pressure / nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD+ biosynthetic process / heterocyclic compound binding / negative regulation of cellular senescence / positive regulation of smooth muscle cell proliferation / negative regulation of autophagy ...response to D-galactose / : / regulation of lung blood pressure / nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD+ biosynthetic process / heterocyclic compound binding / negative regulation of cellular senescence / positive regulation of smooth muscle cell proliferation / negative regulation of autophagy / cytokine activity / cellular response to ionizing radiation / circadian regulation of gene expression / microglial cell activation / female pregnancy / circadian rhythm / cellular response to amyloid-beta / cellular response to hypoxia / positive regulation of ERK1 and ERK2 cascade / positive regulation of canonical NF-kappaB signal transduction / inflammatory response / nucleotide binding / positive regulation of gene expression / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / nucleus / cytoplasm
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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
BETA-NICOTINAMIDE RIBOSE MONOPHOSPHATE / Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
AuthorsEom, S.H. / Kim, M.-K.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Crystal Structure of Visfatin/Pre-B Cell Colony-enhancing Factor 1/Nicotinamide Phosphoribosyltransferase, Free and in Complex with the Anti-cancer Agent FK-866
Authors: Kim, M.-K. / Lee, J.H. / Kim, H. / Park, S.J. / Kim, S.H. / Kang, G.B. / Lee, Y.S. / Kim, J.B. / Kim, K.K. / Suh, S.W. / Eom, S.H.
History
DepositionMar 5, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 1, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)111,6964
Polymers111,0252
Non-polymers6702
Water2,378132
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9840 Å2
ΔGint-35 kcal/mol
Surface area31000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.893, 106.078, 117.305
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nicotinamide phosphoribosyltransferase / NAmPRTase / Nampt / Pre-B-cell colony-enhancing factor 1 homolog / PBEF / Visfatin


Mass: 55512.688 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Plasmid: pVFT / Production host: Escherichia coli (E. coli)
References: UniProt: Q80Z29, 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 132 / 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: 2.29 Å3/Da / Density % sol: 46.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 0.1M HEPES-NaOH (pH 7.5), 16% PEG3350, and 0.2M MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. all: 20714 / Num. obs: 20714 / % possible obs: 88.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.9→2.95 Å / % possible all: 89

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Processing

Software
NameClassification
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2G95

2g95


Resolution: 2.9→20 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.278 1884 RANDOM
Rwork0.229 --
all0.234 19114 -
obs0.234 19114 -
Refinement stepCycle: LAST / Resolution: 2.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7400 0 44 132 7576
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.008

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