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

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Basic information

Entry
Database: PDB / ID: 7xgm
TitleQuinolinate Phosphoribosyl Transferase (QAPRTase) from Streptomyces pyridomyceticus NRRL B-2517 in complex with Quinolinic Acid (QA)
ComponentsQuinolinate Phosphoribosyl Transferase
KeywordsTRANSFERASE / nicotinamide adenine dinucleotide / pyridomycin / quinolinic acid
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / QUINOLINIC ACID
Function and homology information
Biological speciesStreptomyces pyridomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 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
Revision 1.2Sep 17, 2025Group: Advisory / Derived calculations / Structure summary
Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn
Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)65,84515
Polymers64,8252
Non-polymers1,02013
Water46826
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8160 Å2
ΔGint-112 kcal/mol
Surface area21610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)118.742, 149.079, 54.897
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

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Protein , 1 types, 2 molecules AB

#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)

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Non-polymers , 5 types, 39 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NTM / QUINOLINIC ACID


Mass: 167.119 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H5NO4
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 26 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
Has protein modificationN

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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: 3.75 Å3/Da / Density % sol: 67.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / 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: 2.85→19.13 Å / Num. obs: 23442 / % possible obs: 99.6 % / Redundancy: 6.4 % / Biso Wilson estimate: 51.79 Å2 / CC1/2: 0.99 / Net I/σ(I): 15
Reflection shellResolution: 2.85→2.98 Å / Num. unique obs: 1164 / CC1/2: 0.903

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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: 2.85→19.13 Å / SU ML: 0.3885 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.0663
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2255 1171 5.02 %
Rwork0.178 22156 -
obs0.1805 23327 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.31 Å2
Refinement stepCycle: LAST / Resolution: 2.85→19.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4306 0 57 26 4389
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00834400
X-RAY DIFFRACTIONf_angle_d0.94285993
X-RAY DIFFRACTIONf_chiral_restr0.0469733
X-RAY DIFFRACTIONf_plane_restr0.0083790
X-RAY DIFFRACTIONf_dihedral_angle_d15.67351569
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.980.36131220.27072738X-RAY DIFFRACTION99.65
2.98-3.140.27331490.23942708X-RAY DIFFRACTION100
3.14-3.340.3331560.22252710X-RAY DIFFRACTION100
3.34-3.590.27221390.17662762X-RAY DIFFRACTION100
3.59-3.950.20721360.16332769X-RAY DIFFRACTION100
3.95-4.510.2091640.14482762X-RAY DIFFRACTION100
4.52-5.660.18261580.15572787X-RAY DIFFRACTION100
5.66-19.130.17871470.16992920X-RAY DIFFRACTION99.58

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