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

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Basic information

Entry
Database: PDB / ID: 7xgl
TitleQuinolinate Phosphoribosyl Transferase (QAPRTase) from Streptomyces pyridomyceticus NRRL B-2517 in Apo form
ComponentsQuinolinate Phosphoribosyl Transferase
KeywordsTRANSFERASE / nicotinamide adenine dinucleotide / pyridomycin / quinolinic acid
Function / homologyAldolase class I / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / hexanedioic acid / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM
Function and homology information
Biological speciesStreptomyces pyridomyceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 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)66,05316
Polymers64,8252
Non-polymers1,22714
Water5,116284
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8460 Å2
ΔGint-154 kcal/mol
Surface area21880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)120.046, 150.929, 55.181
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 , 6 types, 298 molecules

#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-0L1 / hexanedioic acid / Adipic acid


Mass: 146.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H10O4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-144 / TRIS-HYDROXYMETHYL-METHYL-AMMONIUM


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 284 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.86 Å3/Da / Density % sol: 68.1 %
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: 2.11→37.73 Å / Num. obs: 58249 / % possible obs: 99.4 % / Redundancy: 6.5 % / Biso Wilson estimate: 27.63 Å2 / CC1/2: 0.993 / Net I/σ(I): 11.1
Reflection shellResolution: 2.11→2.14 Å / Num. unique obs: 5409 / CC1/2: 0.838

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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: 2.11→37.73 Å / SU ML: 0.212 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 19.4934
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2073 2985 5.12 %
Rwork0.1764 55264 -
obs0.178 58249 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.33 Å2
Refinement stepCycle: LAST / Resolution: 2.11→37.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4328 0 69 284 4681
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00664454
X-RAY DIFFRACTIONf_angle_d0.81746064
X-RAY DIFFRACTIONf_chiral_restr0.0473733
X-RAY DIFFRACTIONf_plane_restr0.0074799
X-RAY DIFFRACTIONf_dihedral_angle_d14.1181609
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.11-2.140.2741360.22872207X-RAY DIFFRACTION85.11
2.14-2.180.24881480.21052595X-RAY DIFFRACTION100
2.18-2.220.24441510.20992625X-RAY DIFFRACTION100
2.22-2.260.2591280.2042597X-RAY DIFFRACTION99.96
2.26-2.310.24861430.19712657X-RAY DIFFRACTION100
2.31-2.360.27241460.2062590X-RAY DIFFRACTION99.96
2.36-2.410.24781290.19282639X-RAY DIFFRACTION100
2.41-2.470.22381530.18662598X-RAY DIFFRACTION100
2.47-2.540.25831500.1912622X-RAY DIFFRACTION100
2.54-2.620.23441240.192643X-RAY DIFFRACTION100
2.62-2.70.22471430.192623X-RAY DIFFRACTION100
2.7-2.80.21211430.18792642X-RAY DIFFRACTION100
2.8-2.910.22011370.18412659X-RAY DIFFRACTION100
2.91-3.040.20251470.17972629X-RAY DIFFRACTION100
3.04-3.20.19511120.18072673X-RAY DIFFRACTION99.93
3.2-3.40.20271610.18772644X-RAY DIFFRACTION100
3.4-3.660.18291430.16272675X-RAY DIFFRACTION100
3.66-4.030.17531450.15332670X-RAY DIFFRACTION100
4.03-4.610.16931390.14262712X-RAY DIFFRACTION100
4.62-5.810.17281490.16272723X-RAY DIFFRACTION100
5.81-37.730.20721580.17132841X-RAY DIFFRACTION99.04

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