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- PDB-1v5g: Crystal Structure of the Reaction Intermediate between Pyruvate o... -

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Basic information

Entry
Database: PDB / ID: 1v5g
TitleCrystal Structure of the Reaction Intermediate between Pyruvate oxidase containing FAD and TPP, and Substrate Pyruvate
ComponentsPyruvate oxidase
KeywordsOXIDOREDUCTASE / Flavoprotein
Function / homology
Function and homology information


Arc Repressor Mutant, subunit A - #940 / Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains / TPP-binding domain / Arc Repressor Mutant, subunit A / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / 2-ACETYL-THIAMINE DIPHOSPHATE
Similarity search - Component
Biological speciesAerococcus viridans (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsHossain, 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. / Hoque, M.M. / Hossain, M.T. / Yamamoto, T. / Imamura, S. / Suzuki, K. / Sekiguchi, T. / Takenaka, A.
History
DepositionNov 22, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 28, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 17, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3May 31, 2023Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_conn / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 8, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Remark 999SEQUENCE A sequence database reference for this protein does not currently exist.

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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)66,5144
Polymers65,2361
Non-polymers1,2773
Water12,412689
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)266,05416
Polymers260,9464
Non-polymers5,10912
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 area31990 Å2
ΔGint-198 kcal/mol
Surface area69110 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)78.010, 105.500, 155.850
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-2047-

HOH

21A-2170-

HOH

31A-2176-

HOH

41A-2251-

HOH

51A-2252-

HOH

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Components

#1: Protein Pyruvate oxidase


Mass: 65236.414 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Aerococcus viridans (bacteria) / References: pyruvate oxidase
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#4: Chemical ChemComp-HTL / 2-ACETYL-THIAMINE DIPHOSPHATE / 2-ACETYL-3-[(4-AMINO-2-METHYL-5-PYRIMIDINYL)METHYL]-4-METHYL-5-(4,6,6-TRIHYDROXY-3,5-DIOXA-4,6-DIPHOSPHAHEX-1-YL)THIAZO LIUM INNER SALT P,P'-DIOXIDE


Mass: 467.351 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H21N4O8P2S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 689 / 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: 49.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Ammonium sulphate, Thiamine pyrophosphate, Magnesium cloride, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 25, 2003
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.92→38.96 Å / Num. obs: 47691 / % possible obs: 96.5 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 6.5
Reflection shellResolution: 1.92→1.99 Å / Rmerge(I) obs: 0.298 / % possible all: 98.2

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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: 1.96→10 Å / Cross valid method: THROUGHOUT / σ(F): 3
RfactorNum. reflection% reflectionSelection details
Rfree0.244 4353 -RANDOM
Rwork0.195 ---
obs0.195 43485 94.4 %-
all-43488 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.36 Å20 Å20 Å2
2--5.87 Å20 Å2
3----7.23 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.96→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4590 0 83 689 5362
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d22.4
X-RAY DIFFRACTIONc_improper_angle_d0.8
LS refinement shellResolution: 1.96→2.03 Å / Rfactor Rfree error: 0.015
RfactorNum. reflection% reflection
Rfree0.318 441 -
Rwork0.259 --
obs-3799 93.4 %

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