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- PDB-1yir: Crystal Structure of a Nicotinate Phosphoribosyltransferase -

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Basic information

Entry
Database: PDB / ID: 1yir
TitleCrystal Structure of a Nicotinate Phosphoribosyltransferase
ComponentsNicotinate phosphoribosyltransferase 2
KeywordsTRANSFERASE / Structural genomics / Protein structure initiative / Hypothetical protein / NYSGXRC / T1804 / PSI / 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 / 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 2
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 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
DepositionJan 12, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_ref_seq_dif.details ..._audit_author.identifier_ORCID / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 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 2
B: Nicotinate phosphoribosyltransferase 2
C: Nicotinate phosphoribosyltransferase 2
D: Nicotinate phosphoribosyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)189,01216
Polymers187,8594
Non-polymers1,15312
Water12,899716
1
A: Nicotinate phosphoribosyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2534
Polymers46,9651
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nicotinate phosphoribosyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2534
Polymers46,9651
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Nicotinate phosphoribosyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2534
Polymers46,9651
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Nicotinate phosphoribosyltransferase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,2534
Polymers46,9651
Non-polymers2883
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)222.599, 113.355, 93.231
Angle α, β, γ (deg.)90.00, 104.07, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Nicotinate phosphoribosyltransferase 2 / NAPRTase 2


Mass: 46964.844 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Gene: pncB2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HW26, EC: 2.4.2.11
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 716 / 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: 3 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Ammonium Sulphate, PEG3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 273K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979, 0.97938, 0.95
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 18, 2004 / Details: mirrors
RadiationMonochromator: graphite / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979381
30.951
ReflectionResolution: 2.1→50 Å / Num. all: 129962 / Num. obs: 129962 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Biso Wilson estimate: 16.1 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.2
Reflection shellResolution: 2→2.18 Å / % possible all: 97.9

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→48.03 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 219957.01 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The atoms listed in remark 470 are missing due to lack of electron density.
RfactorNum. reflection% reflectionSelection details
Rfree0.247 12336 10 %RANDOM
Rwork0.213 ---
obs0.213 123291 94.2 %-
all-123291 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.0647 Å2 / ksol: 0.355384 e/Å3
Displacement parametersBiso mean: 27.1 Å2
Baniso -1Baniso -2Baniso -3
1--3.83 Å20 Å2-2.87 Å2
2--0.28 Å20 Å2
3---3.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.1→48.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12660 0 60 716 13436
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.912
X-RAY DIFFRACTIONc_scbond_it2.072
X-RAY DIFFRACTIONc_scangle_it2.962.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.007 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.297 1898 10 %
Rwork0.26 17111 -
obs-12764 87.5 %
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
X-RAY DIFFRACTION3ION.PARAM&_1_TOPOLOGY_INFILE_3

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