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- PDB-1ybe: Crystal Structure of a Nicotinate phosphoribosyltransferase -

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Basic information

Entry
Database: PDB / ID: 1ybe
TitleCrystal Structure of a Nicotinate phosphoribosyltransferase
ComponentsNicotinate phosphoribosyltransferase
KeywordsTRANSFERASE / Structural genomics / Protein structure initiative / NYSGXRC / T1764 / PSI / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


nicotinate phosphoribosyltransferase / nicotinate phosphoribosyltransferase activity / nicotinate-nucleotide diphosphorylase (carboxylating) activity / NAD biosynthetic process
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 speciesAgrobacterium tumefaciens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsSeetharaman, J. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of a Nicotinate phosphoribosyltransferase
Authors: Seetharaman, J. / Swaminathan, S.
History
DepositionDec 20, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 30, 2014Group: Data collection
Revision 1.4Feb 3, 2021Group: Database references / Structure summary / Category: audit_author / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details
Revision 1.5Feb 14, 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

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Assembly

Deposited unit
A: Nicotinate phosphoribosyltransferase
B: Nicotinate phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)103,2842
Polymers103,2842
Non-polymers00
Water5,837324
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)179.768, 69.428, 87.990
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Nicotinate phosphoribosyltransferase / / NAPRTase


Mass: 51641.801 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Agrobacterium tumefaciens (bacteria) / Gene: pncB / Production host: Escherichia coli (E. coli) / References: UniProt: Q8UIS9, EC: 2.4.2.11
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 324 / 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: 2.7 Å3/Da / Density % sol: 53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Bis-Tris, PEGMME5000, PEG400, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.9796, 0.9792, 0.95
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Jun 27, 2004 / Details: mirrors
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97961
20.97921
30.951
ReflectionResolution: 2.5→50 Å / Num. all: 39072 / Num. obs: 39072 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 27.6 % / Biso Wilson estimate: 33.5 Å2 / Rmerge(I) obs: 0.13 / Net I/σ(I): 10
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 27 % / Rmerge(I) obs: 0.58 / Mean I/σ(I) obs: 10 / Num. unique all: 4748 / % possible all: 96.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→45.36 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 228541.84 / 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
Rfree0.272 3895 10.2 %RANDOM
Rwork0.222 ---
obs0.222 38319 98.4 %-
all-39072 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.3246 Å2 / ksol: 0.327121 e/Å3
Displacement parametersBiso mean: 40.6 Å2
Baniso -1Baniso -2Baniso -3
1--3.89 Å20 Å20 Å2
2--8.1 Å20 Å2
3----4.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.5→45.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6586 0 0 324 6910
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_d
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.271.5
X-RAY DIFFRACTIONc_mcangle_it2.12
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.348 573 9.3 %
Rwork0.297 5565 -
obs--96.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAM&_1_TOPOLOGY_INFILE_1
X-RAY DIFFRACTION2WATER_REP.PARAM&_1_TOPOLOGY_INFILE_2

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