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- PDB-2dji: Crystal Structure of Pyruvate Oxidase from Aerococcus viridans co... -

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Basic information

Entry
Database: PDB / ID: 2dji
TitleCrystal Structure of Pyruvate Oxidase from Aerococcus viridans containing FAD
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
AuthorsJuan, E.C.M. / Hossain, M.T. / Suzuki, K. / Yamamoto, T. / Imamura, S. / Sekiguchi, T. / Takenaka, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2007
Title: The structures of pyruvate oxidase from Aerococcus viridans with cofactors and with a reaction intermediate reveal the flexibility of the active-site tunnel for catalysis.
Authors: Juan, E.C.M. / Hoque, M.M. / Hossain, M.T. / Yamamoto, T. / Imamura, S. / Suzuki, K. / Sekiguchi, T. / Takenaka, A.
History
DepositionApr 3, 2006Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 29, 2007Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: 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

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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
Water12,484693
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 area31330 Å2
ΔGint-382 kcal/mol
Surface area71640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.590, 105.250, 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-2189-

HOH

21A-2190-

HOH

31A-2191-

HOH

41A-2192-

HOH

51A-2193-

HOH

61A-2194-

HOH

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Components

#1: Protein Pyruvate oxidase /


Mass: 65351.508 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aerococcus viridans (bacteria) / Production host: Escherichia coli (E. coli) / 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.: 693 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.42 Å3/Da / Density % sol: 49.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 2M ammonium sulfate in 20mM sodium phosphate buffer, pH 7.0., VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 17, 2003
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.58→50 Å / Num. obs: 84186 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.7 % / Rmerge(I) obs: 0.082
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.379 / % possible all: 77.4

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Processing

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

1pox


Resolution: 1.6→10 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Maximum Likelihood
Details: THE AMINO ACID RESIDUES 471-491 HAVE HIGH B-FACTOR VALUES AND MOST OF THEIR ATOMS HAVE LOW OCCUPANCY. THIS REGION, WHICH IS ASSUMED TO HAVE HIGH FLEXIBILITY, IS ALSO FOUND IN OTHER THIAMIN ...Details: THE AMINO ACID RESIDUES 471-491 HAVE HIGH B-FACTOR VALUES AND MOST OF THEIR ATOMS HAVE LOW OCCUPANCY. THIS REGION, WHICH IS ASSUMED TO HAVE HIGH FLEXIBILITY, IS ALSO FOUND IN OTHER THIAMIN DIPHOSPHATE-DEPENDENT ENZYMES.
RfactorNum. reflection% reflectionSelection details
Rfree0.206 6173 -RANDOM
Rwork0.183 ---
all-83505 --
obs-61377 73.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.544 Å20 Å20 Å2
2---3.7 Å20 Å2
3---7.244 Å2
Refinement stepCycle: LAST / Resolution: 1.6→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4598 0 73 693 5364

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