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- PDB-3q9t: Crystal structure analysis of formate oxidase -

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Basic information

Entry
Database: PDB / ID: 3q9t
TitleCrystal structure analysis of formate oxidase
ComponentsCholine dehydrogenase and related flavoproteins
KeywordsOXIDOREDUCTASE / glucose-methanol-choline oxidoreductase family / Formate oxidase / 8-formyl-FAD
Function / homology
Function and homology information


choline dehydrogenase activity / glycine betaine biosynthetic process from choline / flavin adenine dinucleotide binding / mitochondrial inner membrane
Similarity search - Function
Glucose Oxidase; domain 3 / Glucose Oxidase, domain 3 / GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain ...Glucose Oxidase; domain 3 / Glucose Oxidase, domain 3 / GMC oxidoreductases signature 1. / Glucose-methanol-choline oxidoreductase / Glucose-methanol-choline oxidoreductase, N-terminal / GMC oxidoreductase / Glucose-methanol-choline oxidoreductase, C-terminal / GMC oxidoreductase / FAD/NAD(P)-binding domain / FAD/NAD(P)-binding domain / 3-Layer(bba) Sandwich / FAD/NAD(P)-binding domain superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Chem-FAY / DI(HYDROXYETHYL)ETHER / Glucose-methanol-choline oxidoreductase N-terminal domain-containing protein
Similarity search - Component
Biological speciesAspergillus oryzae (mold)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.24 Å
AuthorsDoubayashi, D. / Ootake, T. / Maeda, Y. / Oki, M. / Tokunaga, Y. / Sakurai, A. / Nagaosa, Y. / Mikami, B. / Uchida, H.
Citation
Journal: Biosci.Biotechnol.Biochem. / Year: 2011
Title: Formate oxidase, an enzyme of the glucose-methanol-choline oxidoreductase family, has a His-Arg pair and 8-formyl-FAD at the catalytic site.
Authors: Doubayashi, D. / Ootake, T. / Maeda, Y. / Oki, M. / Tokunaga, Y. / Sakurai, A. / Nagaosa, Y. / Mikami, B. / Uchida, H.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and preliminary X-ray analysis of formate oxidase, an enzyme of the glucose-methanol-choline oxidoreductase family
Authors: Maeda, Y. / Doubayashi, D. / Ootake, T. / Oki, M. / Mikami, B. / Uchida, H.
History
DepositionJan 9, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 21, 2011Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software
Revision 1.3Oct 16, 2019Group: Data collection / Database references / Category: citation / Item: _citation.pdbx_database_id_DOI / _citation.title
Revision 1.4Nov 1, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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: Choline dehydrogenase and related flavoproteins
B: Choline dehydrogenase and related flavoproteins
C: Choline dehydrogenase and related flavoproteins
hetero molecules


Theoretical massNumber of molelcules
Total (without water)195,86911
Polymers192,9503
Non-polymers2,9188
Water16,214900
1
A: Choline dehydrogenase and related flavoproteins
hetero molecules

A: Choline dehydrogenase and related flavoproteins
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,82310
Polymers128,6342
Non-polymers2,1908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
2
B: Choline dehydrogenase and related flavoproteins
C: Choline dehydrogenase and related flavoproteins
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,4576
Polymers128,6342
Non-polymers1,8234
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)156.679, 156.019, 184.696
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-592-

HOH

21A-663-

HOH

31A-793-

HOH

41A-806-

HOH

51A-811-

HOH

61A-832-

HOH

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Choline dehydrogenase and related flavoproteins


Mass: 64316.754 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Aspergillus oryzae (mold) / Strain: RIB40 / Gene: AO090012000349 / Plasmid: pET-FOD / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q2UD26

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Non-polymers , 6 types, 908 molecules

#2: Chemical ChemComp-FAY / [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-(8-formyl-7-methyl-2,4-dioxo-3,4-dihydrobenzo[g]pteridin-10(2H)-yl)-2,3,4-trihydroxypentyl dihydrogen diphosphate / 8-FORMYL-FLAVIN-ADENINE DINUCLEOTIDE


Mass: 799.533 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C27H31N9O16P2
#3: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#6: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 900 / 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: 2.92 Å3/Da / Density % sol: 57.95 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 6% PEG 4000, 0.1M sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 5, 2010 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. all: 108042 / Num. obs: 106962 / % possible obs: 99 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Biso Wilson estimate: 31.49 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.3
Reflection shellResolution: 2.24→2.28 Å / Redundancy: 4 % / Rmerge(I) obs: 0.395 / Mean I/σ(I) obs: 4.03 / Num. unique all: 4838 / % possible all: 90.8

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1GAL

1gal


Resolution: 2.24→49.525 Å / FOM work R set: 0.8133 / SU ML: 0.32 / σ(F): 1.33 / Phase error: 25.32 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.236 5333 5.01 %RANDOM
Rwork0.1839 ---
obs0.1865 106543 98.35 %-
all-108330 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 32.372 Å2 / ksol: 0.306 e/Å3
Displacement parametersBiso mean: 30.6813 Å2
Baniso -1Baniso -2Baniso -3
1--1.4194 Å20 Å20 Å2
2---0.2271 Å20 Å2
3---1.6465 Å2
Refinement stepCycle: LAST / Resolution: 2.24→49.525 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13581 0 197 900 14678
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00714290
X-RAY DIFFRACTIONf_angle_d1.19219441
X-RAY DIFFRACTIONf_dihedral_angle_d15.2195363
X-RAY DIFFRACTIONf_chiral_restr0.082083
X-RAY DIFFRACTIONf_plane_restr0.0052539
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2403-2.26580.33451550.26492816X-RAY DIFFRACTION82
2.2658-2.29240.29931560.23943133X-RAY DIFFRACTION92
2.2924-2.32040.36121570.26153180X-RAY DIFFRACTION94
2.3204-2.34980.34311470.25453299X-RAY DIFFRACTION96
2.3498-2.38070.35371870.26363273X-RAY DIFFRACTION98
2.3807-2.41330.32421900.2493370X-RAY DIFFRACTION99
2.4133-2.44780.34951760.24983414X-RAY DIFFRACTION99
2.4478-2.48430.30151800.23133371X-RAY DIFFRACTION100
2.4843-2.52310.28871880.23363377X-RAY DIFFRACTION99
2.5231-2.56450.30932000.22783368X-RAY DIFFRACTION100
2.5645-2.60870.28361870.21543373X-RAY DIFFRACTION100
2.6087-2.65610.27511900.22083405X-RAY DIFFRACTION100
2.6561-2.70720.26471670.22323384X-RAY DIFFRACTION100
2.7072-2.76250.29061750.22083416X-RAY DIFFRACTION99
2.7625-2.82250.27651710.22033392X-RAY DIFFRACTION99
2.8225-2.88820.31031950.233388X-RAY DIFFRACTION100
2.8882-2.96040.27781700.22123390X-RAY DIFFRACTION100
2.9604-3.04040.2191640.20033428X-RAY DIFFRACTION100
3.0404-3.12990.27861910.20413408X-RAY DIFFRACTION100
3.1299-3.23090.26152050.19643368X-RAY DIFFRACTION100
3.2309-3.34630.22671890.18573439X-RAY DIFFRACTION100
3.3463-3.48030.23311500.18123416X-RAY DIFFRACTION99
3.4803-3.63860.2311700.17773439X-RAY DIFFRACTION100
3.6386-3.83040.19661910.16173428X-RAY DIFFRACTION100
3.8304-4.07030.19351490.14713458X-RAY DIFFRACTION99
4.0703-4.38440.1961970.13143429X-RAY DIFFRACTION100
4.3844-4.82530.14032240.12173426X-RAY DIFFRACTION100
4.8253-5.52270.19031800.14123485X-RAY DIFFRACTION100
5.5227-6.9550.23421560.16193530X-RAY DIFFRACTION100
6.955-49.53730.14131760.13273607X-RAY DIFFRACTION99

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