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- PDB-2im5: Crystal structure of Nicotinate phosphoribosyltransferase from Po... -

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Basic information

Entry
Database: PDB / ID: 2im5
TitleCrystal structure of Nicotinate phosphoribosyltransferase from Porphyromonas Gingivalis
ComponentsNicotinate phosphoribosyltransferase
KeywordsTRANSFERASE / Structural genomics / NYSGXRC / phosphoribosyltransferase / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


nicotinate phosphoribosyltransferase / nicotinate phosphoribosyltransferase activity / NAD+ biosynthetic process via the salvage pathway / glycosyltransferase activity / cytosol
Similarity search - Function
Nicotinate phosphoribosyltransferase / nicotinate phosphoribosyltransferase / nicotinate phosphoribosyltransferase / Nicotinate phosphoribosyltransferase, N-terminal domain / Nicotinate phosphoribosyltransferase (NAPRTase) N-terminal domain / Nicotinate phosphoribosyltransferase family / Nicotinate/nicotinamide phosphoribosyltransferase / Nicotinate phosphoribosyltransferase (NAPRTase) family / Nicotinate phosphoribosyltransferase-like, C-terminal / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Nicotinate phosphoribosyltransferase
Similarity search - Component
Biological speciesPorphyromonas gingivalis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsFedorov, A.A. / Fedorov, E.V. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Nicotinate phosphoribosyltransferase from Porphyromonas gingivalis
Authors: Fedorov, A.A. / Fedorov, E.V. / Sauder, J.M. / Burley, S.K. / Almo, S.C.
History
DepositionOct 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 24, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.4Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / citation_author
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID
Revision 1.5Feb 21, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nicotinate phosphoribosyltransferase
B: Nicotinate phosphoribosyltransferase
C: Nicotinate phosphoribosyltransferase
D: Nicotinate phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)182,1284
Polymers182,1284
Non-polymers00
Water6,539363
1
A: Nicotinate phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)45,5321
Polymers45,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nicotinate phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)45,5321
Polymers45,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nicotinate phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)45,5321
Polymers45,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nicotinate phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)45,5321
Polymers45,5321
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)88.873, 101.131, 191.051
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is the monomer

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Components

#1: Protein
Nicotinate phosphoribosyltransferase


Mass: 45531.992 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Porphyromonas gingivalis (bacteria) / Gene: pncB / Production host: Escherichia coli (E. coli) / References: UniProt: Q7MXV0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / 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: 2.36 Å3/Da / Density % sol: 47.8 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 18% PEG 3350, 0.2M tri-Ammonium citrate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.9789 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 30, 2006 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9789 Å / Relative weight: 1
ReflectionResolution: 2.2→25 Å / Num. all: 83311 / Num. obs: 83311 / % possible obs: 95.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.9 % / Rmerge(I) obs: 0.078 / Net I/σ(I): 14.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
ADSCQUANTUMdata collection
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→24.75 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 210710.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.241 4205 5 %RANDOM
Rwork0.22 ---
obs0.22 83311 95.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.2696 Å2 / ksol: 0.382523 e/Å3
Displacement parametersBiso mean: 26.1 Å2
Baniso -1Baniso -2Baniso -3
1--1.24 Å20 Å20 Å2
2--1.08 Å20 Å2
3---0.16 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.2→24.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12684 0 0 363 13047
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d20.9
X-RAY DIFFRACTIONc_improper_angle_d0.7
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it2.192
X-RAY DIFFRACTIONc_scangle_it3.32.5
LS refinement shellResolution: 2.2→2.28 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.287 389 5.2 %
Rwork0.254 7045 -
obs--85.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4
X-RAY DIFFRACTION5

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