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- PDB-7xgn: Quinolinate Phosphoribosyl Transferase (QAPRTase) from Streptomyc... -

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Basic information

Entry
Database: PDB / ID: 7xgn
TitleQuinolinate Phosphoribosyl Transferase (QAPRTase) from Streptomyces pyridomyceticus NRRL B-2517 in complex with Nicotinic Acid (NA)
ComponentsQuinolinate Phosphoribosyl Transferase
KeywordsTRANSFERASE / nicotinamide adenine dinucleotide / pyridomycin / quinolinic acid
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / NICOTINIC ACID
Function and homology information
Biological speciesStreptomyces pyridomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsZhou, Z. / Yang, X. / Huang, T. / Wang, X. / Liang, R. / Zheng, J. / Dai, S. / Lin, S. / Deng, Z.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Bifunctional NadC Homologue PyrZ Catalyzes Nicotinic Acid Formation in Pyridomycin Biosynthesis.
Authors: Zhou, Z. / Yang, X. / Huang, T. / Zheng, J. / Deng, Z. / Dai, S. / Lin, S.
History
DepositionApr 5, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 22, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Quinolinate Phosphoribosyl Transferase
B: Quinolinate Phosphoribosyl Transferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,44111
Polymers64,8252
Non-polymers6169
Water88349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7060 Å2
ΔGint-97 kcal/mol
Surface area21960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.208, 150.973, 55.090
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Space group name HallP22ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x+1/2,y+1/2,-z
#4: -x,-y,z

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Components

#1: Protein Quinolinate Phosphoribosyl Transferase


Mass: 32412.721 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces pyridomyceticus (bacteria)
Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H5NO2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 49 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.82 Å3/Da / Density % sol: 67.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M Citric acid, pH 5.0, 1.6M Ammonium sulfate

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Data collection

DiffractionMean temperature: 193 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jun 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.6→40.46 Å / Num. obs: 31172 / % possible obs: 96.3 % / Redundancy: 4.6 % / Biso Wilson estimate: 43.48 Å2 / CC1/2: 0.985 / Net I/σ(I): 12.8
Reflection shellResolution: 2.6→2.7 Å / Num. unique obs: 1506 / CC1/2: 0.787

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QPO

1qpo


Resolution: 2.6→40.46 Å / SU ML: 0.3307 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 22.8927
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.236 1465 4.86 %
Rwork0.1923 28710 -
obs0.1944 30175 96.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 40.77 Å2
Refinement stepCycle: LAST / Resolution: 2.6→40.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4289 0 33 49 4371
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00744364
X-RAY DIFFRACTIONf_angle_d0.91085947
X-RAY DIFFRACTIONf_chiral_restr0.0467731
X-RAY DIFFRACTIONf_plane_restr0.0078785
X-RAY DIFFRACTIONf_dihedral_angle_d14.77951547
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.70.35441100.2872368X-RAY DIFFRACTION81.3
2.7-2.80.28161480.24532660X-RAY DIFFRACTION91.11
2.8-2.930.27461300.22622881X-RAY DIFFRACTION97.54
2.93-3.090.27681830.23712896X-RAY DIFFRACTION98.91
3.09-3.280.2771550.24032886X-RAY DIFFRACTION98.45
3.28-3.530.29621440.20682914X-RAY DIFFRACTION98.49
3.53-3.890.23341460.19282948X-RAY DIFFRACTION98.94
3.89-4.450.20191460.16032979X-RAY DIFFRACTION99.3
4.45-5.60.18821390.15293033X-RAY DIFFRACTION99.5
5.6-40.460.1921640.16813145X-RAY DIFFRACTION99.19

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