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- PDB-1v5e: Crystal Structure of Pyruvate oxidase containing FAD, from Aeroco... -

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Basic information

Entry
Database: PDB / ID: 1v5e
TitleCrystal Structure of Pyruvate oxidase containing FAD, from Aerococcus viridans
ComponentsPyruvate oxidase
KeywordsOXIDOREDUCTASE / Flavoprotein
Function / homology
Function and homology information


pyruvate oxidase / pyruvate oxidase activity / thiamine pyrophosphate binding / nucleotide binding / magnesium ion binding
Similarity search - Function
Arc Repressor Mutant, subunit A - #940 / Pyruvate oxidase / : / : / : / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain ...Arc Repressor Mutant, subunit A - #940 / Pyruvate oxidase / : / : / : / TPP-binding enzyme, conserved site / Thiamine pyrophosphate enzymes signature. / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, central domain / Thiamine pyrophosphate enzyme, N-terminal TPP-binding domain / Thiamine pyrophosphate enzyme, N-terminal TPP binding domain / Thiamine pyrophosphate enzyme, C-terminal TPP-binding / Thiamine pyrophosphate enzyme, C-terminal TPP binding domain / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Thiamin diphosphate-binding fold / DHS-like NAD/FAD-binding domain superfamily / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / Pyruvate oxidase
Similarity search - Component
Biological speciesAerococcus viridans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHossain, M.T. / Suzuki, K. / Yamamoto, T. / Imamura, S. / Sekiguchi, T. / Takenaka, A.
CitationJournal: To be Published
Title: Crystal Structure of Pyruvate oxidase containing FAD, from Aerococcus viridans
Authors: Hossain, M.T. / Suzuki, K. / Yamamoto, T. / Imamura, S. / Sekiguchi, T. / Takenaka, A.
History
DepositionNov 22, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Pyruvate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,5216
Polymers65,3521
Non-polymers1,1705
Water12,953719
1
A: Pyruvate oxidase
hetero molecules

A: Pyruvate oxidase
hetero molecules

A: Pyruvate oxidase
hetero molecules

A: Pyruvate oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)266,08524
Polymers261,4064
Non-polymers4,67920
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_655-x+1,y,-z1
crystal symmetry operation4_555x,-y,-z1
Buried area31250 Å2
ΔGint-378 kcal/mol
Surface area72680 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)77.660, 106.120, 155.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2163-

HOH

21A-2300-

HOH

31A-2301-

HOH

41A-2302-

HOH

51A-2303-

HOH

61A-2304-

HOH

71A-2305-

HOH

DetailsThe biological assembly is a tetramer generated from the monomer in the asymmetric unit by the operations: 1-x, -y, z; 1-x, y, -z and x, -y, -z

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Components

#1: Protein Pyruvate oxidase /


Mass: 65351.508 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aerococcus viridans (bacteria) / References: UniProt: A9X9K8*PLUS, pyruvate oxidase
#2: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 719 / 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: 2.45 Å3/Da / Density % sol: 49.33 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulphate, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2003
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.4→42.17 Å / Num. obs: 110855 / % possible obs: 87.4 %
Reflection shellResolution: 1.4→1.45 Å / % possible all: 85

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1POX

1pox


Resolution: 1.6→10 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflectionSelection details
Rfree0.2501 7341 RANDOM
Rwork0.2308 --
obs0.2308 66079 -
all-73420 -
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.8 Å20 Å20 Å2
2--0.63 Å20 Å2
3----3.44 Å2
Refine analyzeLuzzati coordinate error obs: 0.2 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4598 0 73 719 5390
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d22.5
X-RAY DIFFRACTIONc_improper_angle_d0.78
LS refinement shellResolution: 1.6→1.66 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.311 583 -
Rwork0.296 --
obs-5005 66.9 %

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