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- PDB-3c2f: Crystal structure of the quinolinate phosphoribosyl transferase (... -

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Basic information

Entry
Database: PDB / ID: 3c2f
TitleCrystal structure of the quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae complexed with PRPP
ComponentsNicotinate-nucleotide pyrophosphorylase
KeywordsTRANSFERASE / QPRTase / PRTase / BNA6 / PRPP / Cytoplasm / Glycosyltransferase / Nucleus / Pyridine nucleotide biosynthesis
Function / homology
Function and homology information


Nicotinate metabolism / quinolinate catabolic process / nicotinate-nucleotide diphosphorylase (carboxylating) / nicotinate-nucleotide diphosphorylase (carboxylating) activity / 'de novo' NAD biosynthetic process from tryptophan / NAD biosynthetic process / nucleus / cytoplasm
Similarity search - Function
Nicotinate-nucleotide pyrophosphorylase / Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldehyde Oxidoreductase; domain 3 ...Nicotinate-nucleotide pyrophosphorylase / Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Nicotinate phosphoribosyltransferase-like, C-terminal / Aldehyde Oxidoreductase; domain 3 / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-PRP / Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.35 Å
Authorsdi Luccio, E. / Wilson, D.K.
CitationJournal: Biochemistry / Year: 2008
Title: Comprehensive X-ray Structural Studies of the Quinolinate Phosphoribosyl Transferase (BNA6) from Saccharomyces cerevisiae.
Authors: di Luccio, E. / Wilson, D.K.
History
DepositionJan 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / database_PDB_caveat ...chem_comp / database_PDB_caveat / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Feb 21, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
Item: _chem_comp.pdbx_synonyms / _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-nucleotide pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,6612
Polymers32,2711
Non-polymers3901
Water1,44180
1
A: Nicotinate-nucleotide pyrophosphorylase
hetero molecules
x 6


Theoretical massNumber of molelcules
Total (without water)195,96512
Polymers193,6246
Non-polymers2,3406
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_556x-y,-y,-z+11
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation6_556-x,-x+y,-z+11
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area31870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.905, 154.905, 70.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-311-

HOH

DetailsThe biological assembly is a hexamer composed of a trimer of dimer in the asymmetric unit generated by the operations: -Y, X-Y, Z ; Y-X, -X, Z; Y, X, -Z ; X-Y, -Y, -Z ; -X, Y-X, -Z ; dimer is generated by : -X, Y-X, -Z

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Components

#1: Protein Nicotinate-nucleotide pyrophosphorylase / Quinolinate phosphoribosyltransferase / QAPRTase


Mass: 32270.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Gene: BNA6, QPT1 / Plasmid: pTYB12 / Production host: Escherichia coli (E. coli)
References: UniProt: P43619, nicotinate-nucleotide diphosphorylase (carboxylating)
#2: Sugar ChemComp-PRP / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribofuranose / ALPHA-PHOSPHORIBOSYLPYROPHOSPHORIC ACID / 1-O-pyrophosphono-5-O-phosphono-alpha-D-ribose / 1-O-pyrophosphono-5-O-phosphono-D-ribose / 1-O-pyrophosphono-5-O-phosphono-ribose


Type: D-saccharide / Mass: 390.070 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H13O14P3
IdentifierTypeProgram
a-D-Ribf1PO35PO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 80 / 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: 2.51 Å3/Da / Density % sol: 51.08 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2 M ammonium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.979397 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 12, 2005
RadiationMonochromator: 0.979397 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979397 Å / Relative weight: 1
ReflectionRedundancy: 4.8 % / Av σ(I) over netI: 14.9 / Number: 64403 / Rmerge(I) obs: 0.068 / Χ2: 1.07 / D res high: 2.35 Å / D res low: 30 Å / Num. obs: 13552 / % possible obs: 99.6
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
5.063099.810.0350.9314.6
4.025.0699.810.0481.0214.8
3.514.0299.910.0460.8554.9
3.193.5110010.0660.9854.9
2.963.1999.910.0981.0594.9
2.792.9610010.131.1254.9
2.652.7910010.1861.184.9
2.532.6510010.2311.1474.9
2.432.5399.510.2851.2084.6
2.352.439710.3021.2164.1
ReflectionResolution: 2.35→30 Å / Num. all: 13619 / Num. obs: 13552 / % possible obs: 99.6 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 4.8 % / Biso Wilson estimate: 45.432 Å2 / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 5.1
Reflection shellResolution: 2.35→2.43 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.302 / Mean I/σ(I) obs: 5.1 / Num. unique all: 1313 / Rsym value: 0.302 / % possible all: 97

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.35→29.27 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.92 / SU B: 6.841 / SU ML: 0.166 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.383 / ESU R Free: 0.248 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.246 518 4 %RANDOM
Rwork0.21 ---
obs0.212 12878 95.06 %-
all-12360 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 45.432 Å2
Baniso -1Baniso -2Baniso -3
1--3.29 Å2-1.65 Å20 Å2
2---3.29 Å20 Å2
3---4.94 Å2
Refinement stepCycle: LAST / Resolution: 2.35→29.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 22 80 2144
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0222097
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.972842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3925264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.58624.82887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.82815357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.452159
X-RAY DIFFRACTIONr_chiral_restr0.3020.2328
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021534
X-RAY DIFFRACTIONr_nbd_refined0.2820.21026
X-RAY DIFFRACTIONr_nbtor_refined0.330.21487
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2180.283
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2410.283
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.212
X-RAY DIFFRACTIONr_mcbond_it9.6111.51350
X-RAY DIFFRACTIONr_mcangle_it11.55622112
X-RAY DIFFRACTIONr_scbond_it16.8363838
X-RAY DIFFRACTIONr_scangle_it19.6164.5730
LS refinement shellResolution: 2.35→2.411 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.387 40 -
Rwork0.243 779 -
all-819 -
obs--85.67 %

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