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- PDB-2yvs: Crystal structure of glycolate oxidase subunit GlcE from Thermus ... -

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Basic information

Entry
Database: PDB / ID: 2yvs
TitleCrystal structure of glycolate oxidase subunit GlcE from Thermus thermophilus HB8
ComponentsGlycolate oxidase subunit GlcEHydroxyacid oxidase (glycolate oxidase) 1
KeywordsOXIDOREDUCTASE / glycolate oxidase subunit GlcE
Function / homology
Function and homology information


Alpha-Beta Plaits - #2560 / Protein of unknown function DUF5639 / Family of unknown function (DUF5639) / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Alpha-Beta Plaits ...Alpha-Beta Plaits - #2560 / Protein of unknown function DUF5639 / Family of unknown function (DUF5639) / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 - #10 / Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 / FAD-binding domain, PCMH-type / PCMH-type FAD-binding domain profile. / FAD-binding, type PCMH, subdomain 2 / FAD-binding, type PCMH-like superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Glycolate oxidase subunit GlcE
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsYoneda, K. / Sakuraba, H. / Kuramitsu, S. / Ohshima, T.
CitationJournal: To be Published
Title: Crystal structure of glycolate oxidase subunit GlcE from Thermus thermophilus HB8
Authors: Yoneda, K. / Sakuraba, H. / Kuramitsu, S. / Ohshima, T.
History
DepositionApr 15, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycolate oxidase subunit GlcE
B: Glycolate oxidase subunit GlcE


Theoretical massNumber of molelcules
Total (without water)48,4062
Polymers48,4062
Non-polymers00
Water5,278293
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-23 kcal/mol
Surface area19760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.880, 71.690, 89.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Glycolate oxidase subunit GlcE / Hydroxyacid oxidase (glycolate oxidase) 1


Mass: 24202.867 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET11A / Production host: Escherichia coli (E. coli) / References: UniProt: Q5SM78, (S)-2-hydroxy-acid oxidase
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 293 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 47.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.1M Na3 Citrate, 2.2M Na Formate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jun 13, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→55.989 Å / Num. obs: 30844 / Biso Wilson estimate: 21 Å2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
CNS1.1refinement
CrystalCleardata reduction
CrystalCleardata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SeMet crystal of Glycolate oxidase subunit GlcE

Resolution: 2→32.547 Å / Cross valid method: THROUGHOUT
RfactorNum. reflectionSelection details
Rfree0.2493 -RANDOM
Rwork0.2079 --
obs-30844 -
Refinement stepCycle: LAST / Resolution: 2→32.547 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3440 0 0 293 3733
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.89
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.391.5
X-RAY DIFFRACTIONc_mcangle_it2.262
X-RAY DIFFRACTIONc_scbond_it3.012
X-RAY DIFFRACTIONc_scangle_it4.22.5

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