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- PDB-3c2r: Crystal structure of the quinolinate phosphoribosyl transferase (... -

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Basic information

Entry
Database: PDB / ID: 3c2r
TitleCrystal structure of the quinolinate phosphoribosyl transferase (BNA6) from Sachharomyces cerevisiae complexed with the inhibitor phthalate
ComponentsNicotinate-nucleotide pyrophosphorylase
KeywordsTRANSFERASE / QPRTase / PRTase / BNA6 / quinolinate / phthalate / 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
PHTHALIC ACID / Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.4 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 25, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nicotinate-nucleotide pyrophosphorylase
B: Nicotinate-nucleotide pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,1364
Polymers64,8042
Non-polymers3322
Water1,820101
1
A: Nicotinate-nucleotide pyrophosphorylase
B: Nicotinate-nucleotide pyrophosphorylase
hetero molecules

A: Nicotinate-nucleotide pyrophosphorylase
B: Nicotinate-nucleotide pyrophosphorylase
hetero molecules

A: Nicotinate-nucleotide pyrophosphorylase
B: Nicotinate-nucleotide pyrophosphorylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,40812
Polymers194,4116
Non-polymers9976
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area31690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)155.524, 155.524, 121.072
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32

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Components

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


Mass: 32401.914 Da / Num. of mol.: 2
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) / Strain (production host): bl21*
References: UniProt: P43619, nicotinate-nucleotide diphosphorylase (carboxylating)
#2: Chemical ChemComp-PHT / PHTHALIC ACID


Mass: 166.131 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H6O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.17 Å3/Da / Density % sol: 43.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 20% PEG 3350, 0.2 M potassium formate, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Aug 5, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.4→46.932 Å / Num. all: 22088 / Num. obs: 22088 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 10.9 % / Biso Wilson estimate: 50 Å2 / Rmerge(I) obs: 0.099 / Rsym value: 0.099 / Net I/σ(I): 6.4
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 11 % / Rmerge(I) obs: 0.578 / Mean I/σ(I) obs: 1.3 / Num. measured all: 17785 / Num. unique all: 1622 / Rsym value: 0.578 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
SCALAdata scaling
PHASERphasing
REFMAC5.2.0005refinement
PDB_EXTRACT3.004data extraction
Blu-Icedata collection
MOSFLMdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→46.93 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.934 / SU B: 7.034 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.593 / ESU R Free: 0.263 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.225 2189 10.2 %RANDOM
Rwork0.183 ---
obs0.188 21560 97.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 50.701 Å2
Baniso -1Baniso -2Baniso -3
1--1.28 Å2-0.64 Å20 Å2
2---1.28 Å20 Å2
3---1.92 Å2
Refinement stepCycle: LAST / Resolution: 2.4→46.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4082 0 24 101 4207
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224174
X-RAY DIFFRACTIONr_angle_refined_deg1.9371.9635646
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.0795528
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.52624.828174
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.41215714
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.91518
X-RAY DIFFRACTIONr_chiral_restr0.1230.2648
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023100
X-RAY DIFFRACTIONr_nbd_refined0.3060.22279
X-RAY DIFFRACTIONr_nbtor_refined0.340.22873
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2050.2228
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.2122
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1810.214
X-RAY DIFFRACTIONr_mcbond_it15.3991.52703
X-RAY DIFFRACTIONr_mcangle_it17.2724224
X-RAY DIFFRACTIONr_scbond_it24.87231662
X-RAY DIFFRACTIONr_scangle_it25.3894.51422
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 153 -
Rwork0.217 1362 -
all-1515 -
obs--93.52 %

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