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- PDB-4i9a: Crystal Structure of Sus scrofa Quinolinate Phosphoribosyltransfe... -

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Basic information

Entry
Database: PDB / ID: 4i9a
TitleCrystal Structure of Sus scrofa Quinolinate Phosphoribosyltransferase in Complex with Nicotinate Mononucleotide
Componentsquinolinate phosphoribosyltransferase
KeywordsTRANSFERASE
Function / homology
Function and homology information


Nicotinate metabolism / quinolinate catabolic process / nicotinate-nucleotide diphosphorylase (carboxylating) / nicotinate-nucleotide diphosphorylase (carboxylating) activity / NAD biosynthetic process / catalytic complex / nucleotide binding / identical protein binding / cytoplasm
Similarity search - Function
Nicotinate-nucleotide pyrophosphorylase / Nicotinate-nucleotide pyrophosphorylase/Putative pyrophosphorylase ModD / Quinolinate phosphoribosyl transferase, N-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-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 / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, N-terminal domain / Quinolinate phosphoribosyl transferase, C-terminal / Quinolinate phosphoribosyl transferase, N-terminal domain superfamily / Quinolinate phosphoribosyl transferase, C-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 MONONUCLEOTIDE / Nicotinate-nucleotide pyrophosphorylase [carboxylating]
Similarity search - Component
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.096 Å
AuthorsYoun, H.-S. / Kim, M.-K. / Kang, K.B. / Kim, T.G. / Lee, J.-G. / An, J.Y. / Park, K.R. / Lee, Y. / Kang, J.Y. / Song, H.E. ...Youn, H.-S. / Kim, M.-K. / Kang, K.B. / Kim, T.G. / Lee, J.-G. / An, J.Y. / Park, K.R. / Lee, Y. / Kang, J.Y. / Song, H.E. / Park, I. / Cho, C. / Fukuoka, S. / Eom, S.H.
CitationJournal: Plos One / Year: 2013
Title: Crystal structure of Sus scrofa quinolinate phosphoribosyltransferase in complex with nicotinate mononucleotide
Authors: Youn, H.-S. / Kim, M.-K. / Kang, G.B. / Kim, T.G. / Lee, J.-G. / An, J.Y. / Park, K.R. / Lee, Y. / Kang, J.Y. / Song, H.E. / Park, I. / Cho, C. / Fukuoka, S. / Eom, S.H.
History
DepositionDec 5, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 1, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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: quinolinate phosphoribosyltransferase
B: quinolinate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,4794
Polymers59,8092
Non-polymers6702
Water1,74797
1
A: quinolinate phosphoribosyltransferase
B: quinolinate phosphoribosyltransferase
hetero molecules

A: quinolinate phosphoribosyltransferase
B: quinolinate phosphoribosyltransferase
hetero molecules

A: quinolinate phosphoribosyltransferase
B: quinolinate phosphoribosyltransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)181,43812
Polymers179,4266
Non-polymers2,0116
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area31040 Å2
ΔGint-165 kcal/mol
Surface area55410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.106, 119.106, 93.737
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321
Components on special symmetry positions
IDModelComponents
11B-424-

HOH

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Components

#1: Protein quinolinate phosphoribosyltransferase


Mass: 29904.389 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sus scrofa (pig) / Production host: Sus scrofa (pig)
References: UniProt: I3LK75*PLUS, nicotinate-nucleotide diphosphorylase (carboxylating)
#2: Chemical ChemComp-NCN / NICOTINATE MONONUCLEOTIDE / NAMN / Nicotinamide mononucleotide


Mass: 335.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14NO9P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE PROTEIN WAS DIRECTLY PURIFIED FROM PORCINE KIDNEY. THE SEQUENCE DATABASE REFERENCES FOR THIS ...THE PROTEIN WAS DIRECTLY PURIFIED FROM PORCINE KIDNEY. THE SEQUENCE DATABASE REFERENCES FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 3.21 Å3/Da / Density % sol: 61.67 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorDate: Feb 17, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.096→50 Å / Num. obs: 45417 / Biso Wilson estimate: 37.19 Å2

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Processing

SoftwareName: PHENIX / Version: (phenix.refine: 1.8.1_1168) / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JBM

2jbm


Resolution: 2.096→34.686 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8185 / SU ML: 0.19 / σ(F): 0 / Phase error: 25.05 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2587 2222 4.92 %
Rwork0.2149 --
obs0.217 45199 99.63 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.22 Å2 / Biso mean: 32.4461 Å2 / Biso min: 10 Å2
Refinement stepCycle: LAST / Resolution: 2.096→34.686 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4202 0 44 97 4343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0084336
X-RAY DIFFRACTIONf_angle_d1.3515920
X-RAY DIFFRACTIONf_chiral_restr0.079688
X-RAY DIFFRACTIONf_plane_restr0.008772
X-RAY DIFFRACTIONf_dihedral_angle_d16.4631542
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0964-2.1420.21941490.1642580272998
2.142-2.19180.22381330.167927002833100
2.1918-2.24660.23351210.182826962817100
2.2466-2.30740.26291620.186626092771100
2.3074-2.37520.23091320.182826792811100
2.3752-2.45190.23251130.174326872800100
2.4519-2.53950.24771490.194426842833100
2.5395-2.64110.25341240.207126992823100
2.6411-2.76130.28041480.209626822830100
2.7613-2.90680.29821290.229326982827100
2.9068-3.08880.28921330.244826782811100
3.0888-3.32710.28891590.250426852844100
3.3271-3.66160.29891340.239427042838100
3.6616-4.19070.24191590.196527142873100
4.1907-5.27690.24161420.200327372879100
5.2769-34.69040.24281350.23872745288096

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