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- PDB-2h3b: Crystal Structure of Mouse Nicotinamide Phosphoribosyltransferase... -

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Basic information

Entry
Database: PDB / ID: 2h3b
TitleCrystal Structure of Mouse Nicotinamide Phosphoribosyltransferase/Visfatin/Pre-B Cell Colony Enhancing Factor 1
ComponentsNicotinamide phosphoribosyltransferase
KeywordsTRANSFERASE / Apoenzyme / type II phsophoribosyltransferase
Function / homology
Function and homology information


regulation of lung blood pressure / Nicotinamide salvaging / nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthetic process / heterocyclic compound binding / positive regulation of nitric-oxide synthase biosynthetic process / negative regulation of cellular senescence / negative regulation of autophagy / cytokine activity ...regulation of lung blood pressure / Nicotinamide salvaging / nicotinamide phosphoribosyltransferase / nicotinamide phosphoribosyltransferase activity / NAD biosynthetic process / heterocyclic compound binding / positive regulation of nitric-oxide synthase biosynthetic process / negative regulation of cellular senescence / negative regulation of autophagy / cytokine activity / positive regulation of smooth muscle cell proliferation / microglial cell activation / circadian regulation of gene expression / circadian rhythm / cell junction / nuclear speck / nucleotide binding / positive regulation of transcription by RNA polymerase II / extracellular space / identical protein binding / cytoplasm / cytosol
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 class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Nicotinamide phosphoribosyltransferase
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.95 Å
AuthorsWang, T. / Zhang, X. / Bheda, P. / Revollo, J.R. / Imai, S.I. / Wolberger, C.
CitationJournal: Nat.Struct.Mol.Biol. / Year: 2006
Title: Structure of Nampt/PBEF/visfatin, a mammalian NAD(+) biosynthetic enzyme.
Authors: Wang, T. / Zhang, X. / Bheda, P. / Revollo, J.R. / Imai, S.I. / Wolberger, C.
History
DepositionMay 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 20, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _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)112,5074
Polymers112,3152
Non-polymers1922
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8910 Å2
ΔGint-73 kcal/mol
Surface area32500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.750, 107.490, 82.960
Angle α, β, γ (deg.)90.00, 97.47, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological assembly is the same as the dimer in the asymmetric unit.

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Components

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


Mass: 56157.473 Da / Num. of mol.: 2 / Mutation: L13M, L177M, L318M, and L432M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Nampt, Pbef1 / Plasmid: pET-28a(+)-Nampt / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta cells
References: UniProt: Q99KQ4, nicotinamide phosphoribosyltransferase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 291 K / pH: 8.2
Details: 5 mg/ml Se-Met LM1467 with 10 mM added nicotinamide, reservoir solution containing 0.1 M Tris pH 8.2, 0.2 M MgSO4, and 14% PEG8000, and acetone in a 1:0.6:0.4 ratio in a total initial drop ...Details: 5 mg/ml Se-Met LM1467 with 10 mM added nicotinamide, reservoir solution containing 0.1 M Tris pH 8.2, 0.2 M MgSO4, and 14% PEG8000, and acetone in a 1:0.6:0.4 ratio in a total initial drop volume of 2 microliter., VAPOR DIFFUSION, HANGING DROP, temperature 291K, pH 8.20

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9797,0.9796,1.0107
DetectorDetector: CCD / Date: Dec 3, 2005
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97961
31.01071
ReflectionResolution: 1.94→50 Å / Num. obs: 77921 / % possible obs: 99.6 % / Redundancy: 7.3 % / Biso Wilson estimate: 12.4 Å2 / Rsym value: 0.11 / Net I/σ(I): 17.9
Reflection shellResolution: 1.94→2.01 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 3.6 / Rsym value: 0.392 / % possible all: 96.3

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Processing

Software
NameVersionClassification
HKL-2000data reduction
SOLVEphasing
CNS1.1refinement
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.95→36.23 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1966856.87 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.215 3863 5 %RANDOM
Rwork0.191 ---
obs0.191 76595 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 38.698 Å2 / ksol: 0.3999622 e/Å3
Displacement parametersBiso mean: 18.8 Å2
Baniso -1Baniso -2Baniso -3
1-4.51 Å20 Å2-1.34 Å2
2---1.19 Å20 Å2
3----3.32 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.95→36.23 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7443 0 10 297 7750
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.24
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.221.5
X-RAY DIFFRACTIONc_mcangle_it1.812
X-RAY DIFFRACTIONc_scbond_it2.22
X-RAY DIFFRACTIONc_scangle_it3.252.5
LS refinement shellResolution: 1.95→2.07 Å / Rfactor Rfree error: 0.01 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 618 5 %
Rwork0.22 11839 -
obs--97.9 %

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