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- PDB-5zgo: Crystal structure of APRT2 from Thermus thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 5zgo
TitleCrystal structure of APRT2 from Thermus thermophilus HB8
ComponentsAdenine phosphoribosyltransferase
KeywordsTRANSFERASE / Phosphoribosyltransferase / Thermostable / Enzyme / Nucleic acid
Function / homologyRossmann fold - #2020 / Phosphoribosyl transferase domain / Phosphoribosyltransferase-like / Phosphoribosyltransferase domain / glycosyltransferase activity / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Adenine phosphoribosyltransferase
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKunishima, N. / Naitow, H. / Matsuura, Y.
CitationJournal: Bioresour. Technol. / Year: 2019
Title: Structural and functional characterization of thermostable biocatalysts for the synthesis of 6-aminopurine nucleoside-5'-monophospate analogues.
Authors: Arco, J.D. / Perez, E. / Naitow, H. / Matsuura, Y. / Kunishima, N. / Fernandez-Lucas, J.
History
DepositionMar 9, 2018Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Adenine phosphoribosyltransferase
B: Adenine phosphoribosyltransferase
C: Adenine phosphoribosyltransferase
D: Adenine phosphoribosyltransferase
E: Adenine phosphoribosyltransferase
F: Adenine phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)113,4736
Polymers113,4736
Non-polymers00
Water2,792155
1
A: Adenine phosphoribosyltransferase
B: Adenine phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)37,8242
Polymers37,8242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-15 kcal/mol
Surface area16410 Å2
MethodPISA
2
C: Adenine phosphoribosyltransferase
D: Adenine phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)37,8242
Polymers37,8242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2250 Å2
ΔGint-19 kcal/mol
Surface area16270 Å2
MethodPISA
3
E: Adenine phosphoribosyltransferase
F: Adenine phosphoribosyltransferase


Theoretical massNumber of molelcules
Total (without water)37,8242
Polymers37,8242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2050 Å2
ΔGint-14 kcal/mol
Surface area16100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.084, 83.179, 91.488
Angle α, β, γ (deg.)90.00, 102.07, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Adenine phosphoribosyltransferase


Mass: 18912.135 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Strain: HB8 / ATCC 27634 / DSM 579 / Gene: TTHA1614 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SHW6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 155 / 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: 2.3 Å3/Da / Density % sol: 46.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6 / Details: 19% PEG 20K, 0.1 M Citrate-NaOH pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.6→45 Å / Num. obs: 31724 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 46.17 Å2 / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.044 / Rrim(I) all: 0.086 / Χ2: 1.611 / Net I/av σ(I): 24.64 / Net I/σ(I): 16.95
Reflection shellResolution: 2.6→2.64 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 4.03 / Num. unique obs: 1569 / CC1/2: 0.907 / Rpim(I) all: 0.204 / Rrim(I) all: 0.392 / Χ2: 0.868 / % possible all: 98.9

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Processing

Software
NameVersionClassification
PHENIXv1.9-1692refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXv1.9-1692phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1VCH

1vch


Resolution: 2.6→45 Å / Cross valid method: THROUGHOUT / Phase error: 30.03
RfactorNum. reflection% reflectionSelection details
Rfree0.2636 1534 4.86 %Random selection
Rwork0.201 ---
obs0.204 31535 99.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 47.39 Å2
Refinement stepCycle: LAST / Resolution: 2.6→45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7980 0 0 155 8135
LS refinement shellResolution: 2.6→2.68 Å
RfactorNum. reflection% reflection
Rfree0.3693 145 5.09 %
Rwork0.2755 2704 -
obs--99 %

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