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- PDB-3c2e: Crystal structure at 1.9A of the apo quinolinate phosphoribosyl t... -

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Basic information

Entry
Database: PDB / ID: 3c2e
TitleCrystal structure at 1.9A of the apo quinolinate phosphoribosyl transferase (BNA6) from Saccharomyces cerevisiae
ComponentsNicotinate-nucleotide pyrophosphorylase
KeywordsTRANSFERASE / QPRTase / PRTase / BNA6 / 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
Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.9 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 1.0Mar 25, 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 1.3Feb 21, 2024Group: Advisory / Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_unobs_or_zero_occ_atoms
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-nucleotide pyrophosphorylase


Theoretical massNumber of molelcules
Total (without water)32,2711
Polymers32,2711
Non-polymers00
Water4,360242
1
A: Nicotinate-nucleotide pyrophosphorylase
x 6


Theoretical massNumber of molelcules
Total (without water)193,6246
Polymers193,6246
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x,-x+y,-z-11
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation5_554x-y,-y,-z-11
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_554y,x,-z-11
Buried area28200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)154.913, 154.913, 68.946
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-312-

HOH

21A-361-

HOH

31A-398-

HOH

41A-429-

HOH

51A-480-

HOH

61A-518-

HOH

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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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 242 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 20% PEG 3350, 0.2 M ammonium formate; holo-quinolinate: 20% PEG 3000, 0.1 M citrate pH 5.5, 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: 0.979126 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationMonochromator: 0.979126 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979126 Å / Relative weight: 1
ReflectionRedundancy: 9 % / Av σ(I) over netI: 17.8 / Number: 213024 / Rmerge(I) obs: 0.064 / Χ2: 0.65 / D res high: 1.9 Å / D res low: 30 Å / Num. obs: 23727 / % possible obs: 94.9
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.093099.510.041.03610.2
3.254.0999.810.0530.30210.6
2.843.2510010.0510.8810.9
2.582.8410010.080.53810.7
2.392.5899.710.0920.7899.9
2.252.3998.810.1320.4448.9
2.142.2598.310.2320.3918.4
2.052.1495.410.2320.5427.3
1.972.0584.910.2010.8376.4
1.91.9772.510.310.7394.9
ReflectionResolution: 1.9→30 Å / Num. all: 25007 / Num. obs: 23727 / % possible obs: 94.9 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 9 % / Biso Wilson estimate: 44.4 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Χ2: 0.646 / Net I/σ(I): 17.8
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 2.98 / Num. unique all: 1810 / Rsym value: 0.31 / Χ2: 0.739 / % possible all: 72.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→28.1 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.927 / SU B: 5.254 / SU ML: 0.143 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 2 / ESU R: 0.208 / ESU R Free: 0.171 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1109 5.1 %RANDOM
Rwork0.234 ---
obs0.235 21799 91.87 %-
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: 44.407 Å2
Baniso -1Baniso -2Baniso -3
1--2.82 Å2-1.41 Å20 Å2
2---2.82 Å20 Å2
3---4.24 Å2
Refinement stepCycle: LAST / Resolution: 1.9→28.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2042 0 0 242 2284
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0222075
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9582807
X-RAY DIFFRACTIONr_dihedral_angle_1_deg1.3065264
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.55624.82887
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.83915357
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.57159
X-RAY DIFFRACTIONr_chiral_restr0.0970.2324
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021534
X-RAY DIFFRACTIONr_nbd_refined0.2840.21134
X-RAY DIFFRACTIONr_nbtor_refined0.3260.21464
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1760.2179
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2850.2108
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3540.228
X-RAY DIFFRACTIONr_mcbond_it8.8031.51349
X-RAY DIFFRACTIONr_mcangle_it10.49422112
X-RAY DIFFRACTIONr_scbond_it15.1713816
X-RAY DIFFRACTIONr_scangle_it18.7124.5695
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.546 45 -
Rwork0.457 933 -
all-978 -
obs--77.8 %

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