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- PDB-9woz: Crystal structure of the glycine oxidase from Bacillus subtilis w... -

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Basic information

Entry
Database: PDB / ID: 9woz
TitleCrystal structure of the glycine oxidase from Bacillus subtilis with FAD and 2-(Methylthio)acetic acid
ComponentsGlycine oxidase
KeywordsOXIDOREDUCTASE / ThiO (glycine oxidase) / FAD / 2-(Methylthio)acetic acid
Function / homology
Function and homology information


glycine oxidase / glycine oxidase activity / thiamine biosynthetic process / thiamine diphosphate biosynthetic process / response to herbicide / amino acid metabolic process / FAD binding / cytoplasm
Similarity search - Function
Glycine oxidase ThiO / FAD dependent oxidoreductase / FAD dependent oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
FLAVIN-ADENINE DINUCLEOTIDE / [METHYLTHIO]ACETATE / Glycine oxidase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.49 Å
AuthorsWang, Z. / Wang, M.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32125008 China
Citation
Journal: Jacs Au / Year: 2026
Title: Ultrafast Photochemistry of Ligand-Bound Flavoprotein Amine Oxidases: Conformational Insights and Photocatalytic Implications.
Authors: Zhuang, B. / Ran, G. / Wang, M. / Zhou, Y. / Sun, R. / Ren, Y. / Wang, Z. / Zhang, W. / Gai, F.
#1: Journal: To Be Published
Title: Structure of glycine oxidase from Bacillus subtilis
Authors: Wang, Z. / Wang, M.
History
DepositionSep 8, 2025Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Jul 22, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glycine oxidase
B: Glycine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,8286
Polymers87,0472
Non-polymers1,7814
Water2,594144
1
A: Glycine oxidase
B: Glycine oxidase
hetero molecules

A: Glycine oxidase
B: Glycine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,65712
Polymers174,0944
Non-polymers3,5638
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_545x,x-y-1,-z+1/61
Buried area16550 Å2
ΔGint-93 kcal/mol
Surface area51500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.735, 139.735, 213.250
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Space group name HallP612(x,y,z+5/12)
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: x-y,-y,-z
#7: -x,-x+y,-z+2/3
#8: -x,-y,z+1/2
#9: y,x,-z+1/3
#10: -y,-x,-z+5/6
#11: -x+y,y,-z+1/2
#12: x,x-y,-z+1/6

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Components

#1: Protein Glycine oxidase / GO


Mass: 43523.496 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Gene: thiO, goxB, yjbR, BSU11670 / Production host: Escherichia coli (E. coli) / References: UniProt: O31616, glycine oxidase
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-MTG / [METHYLTHIO]ACETATE


Mass: 105.136 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5O2S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 144 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.45 Å3/Da / Density % sol: 64.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M Sodium malonate, pH 7.0, 22% w/v PEG 3350

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97923 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Sep 14, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97923 Å / Relative weight: 1
ReflectionResolution: 2.49→50 Å / Num. obs: 43397 / % possible obs: 100 % / Redundancy: 34.9 % / Biso Wilson estimate: 36.02 Å2 / CC1/2: 1 / Net I/σ(I): 18
Reflection shellResolution: 2.5→2.54 Å / Num. unique obs: 2107 / CC1/2: 1

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.49→24.2 Å / SU ML: 0.3102 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.1489 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2695 2109 5.03 %
Rwork0.2231 39859 -
obs0.2255 41968 96.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41.44 Å2
Refinement stepCycle: LAST / Resolution: 2.49→24.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5688 0 118 144 5950
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00215954
X-RAY DIFFRACTIONf_angle_d0.52528060
X-RAY DIFFRACTIONf_chiral_restr0.043848
X-RAY DIFFRACTIONf_plane_restr0.00331024
X-RAY DIFFRACTIONf_dihedral_angle_d4.87163442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.550.30891270.24582589X-RAY DIFFRACTION96.35
2.55-2.620.26951380.23412684X-RAY DIFFRACTION100
2.62-2.690.32151290.25252747X-RAY DIFFRACTION99.97
2.69-2.770.26191350.22312672X-RAY DIFFRACTION99.96
2.77-2.850.31341560.23452699X-RAY DIFFRACTION99.96
2.85-2.960.27271510.23752706X-RAY DIFFRACTION100
2.96-3.080.35081140.2462741X-RAY DIFFRACTION100
3.08-3.210.31191360.23852712X-RAY DIFFRACTION100
3.21-3.380.3031360.24062743X-RAY DIFFRACTION100
3.38-3.60.34951530.23962732X-RAY DIFFRACTION99.97
3.6-3.870.24491410.21052740X-RAY DIFFRACTION99.86
3.87-4.260.22581610.20142743X-RAY DIFFRACTION99.66
4.26-4.870.20571630.18812710X-RAY DIFFRACTION98.19
4.87-6.120.24481610.22152647X-RAY DIFFRACTION94.13
6.12-24.20.29441080.2271994X-RAY DIFFRACTION66.65
Refinement TLS params.Method: refined / Origin x: 28.8261330659 Å / Origin y: -52.0588942621 Å / Origin z: 3.88971596055 Å
111213212223313233
T0.22603448446 Å2-0.0249793925272 Å2-0.0295374339765 Å2-0.263934833384 Å20.0645074544814 Å2--0.221948591643 Å2
L1.02576297213 °2-0.038016376643 °2-0.129084644716 °2-0.466354173625 °20.0538122596423 °2--0.398719609988 °2
S-0.0421517750672 Å °0.20504107786 Å °0.15134727133 Å °-0.0963272403835 Å °0.00108720981424 Å °0.00479420954335 Å °-0.0507912402139 Å °-0.00400367761089 Å °0.041228441718 Å °
Refinement TLS groupSelection details: all

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