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- PDB-3if9: Crystal structure of Glycine Oxidase G51S/A54R/H244A mutant in co... -

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Basic information

Entry
Database: PDB / ID: 3if9
TitleCrystal structure of Glycine Oxidase G51S/A54R/H244A mutant in complex with inhibitor glycolate
ComponentsGlycine oxidase
KeywordsOXIDOREDUCTASE / GO structure / G51S/A54R/H244A / glycolate / FAD / Flavoprotein
Function / homology
Function and homology information


glycine oxidase / glycine oxidase activity / thiamine diphosphate biosynthetic process / thiamine biosynthetic process / response to herbicide / amino acid metabolic process / FAD binding / oxidoreductase activity / cytoplasm
Similarity search - Function
Glycine oxidase ThiO / FAD dependent oxidoreductase / FAD dependent oxidoreductase / D-Amino Acid Oxidase, subunit A, domain 2 / D-Amino Acid Oxidase; Chain A, domain 2 / 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
FLAVIN-ADENINE DINUCLEOTIDE / GLYCOLIC ACID / Glycine oxidase
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.6 Å
AuthorsPedotti, M. / Rosini, E. / Molla, G. / Moschetti, T. / Vallone, B. / Savino, C. / Pollegioni, L.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Glyphosate resistance by engineering the flavoenzyme glycine oxidase.
Authors: Pedotti, M. / Rosini, E. / Molla, G. / Moschetti, T. / Savino, C. / Vallone, B. / Pollegioni, L.
History
DepositionJul 24, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Dec 26, 2012Group: Database references
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Category: atom_site / chem_comp_atom / chem_comp_bond
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)174,24612
Polymers170,7994
Non-polymers3,4468
Water2,810156
1
A: Glycine oxidase
B: Glycine oxidase
hetero molecules

A: Glycine oxidase
B: Glycine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,24612
Polymers170,7994
Non-polymers3,4468
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_577x,-y+2,-z+21
Buried area9410 Å2
ΔGint-44 kcal/mol
Surface area53780 Å2
MethodPISA
2
C: Glycine oxidase
D: Glycine oxidase
hetero molecules

C: Glycine oxidase
D: Glycine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,24612
Polymers170,7994
Non-polymers3,4468
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_556-x,y,-z+3/21
Buried area9630 Å2
ΔGint-38 kcal/mol
Surface area54170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)72.344, 215.058, 217.083
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Glycine oxidase /


Mass: 42699.820 Da / Num. of mol.: 4 / Mutation: G51S, A54R, H244A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: goxB, yjbR, BSU11670 / Plasmid: pT7(BH) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: O31616, glycine oxidase
#2: Chemical
ChemComp-GOA / GLYCOLIC ACID / HYDROXYACETIC ACID / HYDROXYETHANOIC ACID / Glycolic acid


Mass: 76.051 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H4O3
#3: Chemical
ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / Flavin adenine dinucleotide


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


Mass: 18.015 Da / Num. of mol.: 156 / 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: 2.47 Å3/Da / Density % sol: 50.24 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 100mM Hepes/Na, pH 7.5, 28 % w/v PEG 400, 200mM CaCl2, 30mM glycolate/Na, 3 % glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.04063 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Apr 23, 2009
RadiationMonochromator: Si 111 CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.04063 Å / Relative weight: 1
ReflectionResolution: 2.6→76.25 Å / Num. obs: 52481 / Observed criterion σ(F): 0 / Observed criterion σ(I): 3 / Redundancy: 10.1 % / Biso Wilson estimate: 43.993 Å2 / Rmerge(I) obs: 0.086
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 10.7 / % possible all: 100

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Processing

Software
NameVersionClassification
MxCuBEdata collection
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 1RYI

1ryi


Resolution: 2.6→76.25 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.872 / SU B: 10.326 / SU ML: 0.224 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 1.16 / ESU R Free: 0.333 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.25654 2639 5.1 %RANDOM
Rwork0.19561 ---
obs0.19866 49195 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.946 Å2
Baniso -1Baniso -2Baniso -3
1--1.18 Å20 Å20 Å2
2--1.02 Å20 Å2
3---0.16 Å2
Refinement stepCycle: LAST / Resolution: 2.6→76.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11332 0 232 156 11720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.02211846
X-RAY DIFFRACTIONr_angle_refined_deg1.3091.97316038
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.02751446
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.00923.652523
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.923151959
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.1381568
X-RAY DIFFRACTIONr_chiral_restr0.0860.21693
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.028976
X-RAY DIFFRACTIONr_nbd_refined0.2090.25312
X-RAY DIFFRACTIONr_nbtor_refined0.3090.27931
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1490.2462
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2020.2115
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2090.220
X-RAY DIFFRACTIONr_mcbond_it0.6111.57326
X-RAY DIFFRACTIONr_mcangle_it1.094211427
X-RAY DIFFRACTIONr_scbond_it1.19935487
X-RAY DIFFRACTIONr_scangle_it1.9664.54610
LS refinement shellResolution: 2.601→2.669 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.326 206 -
Rwork0.26 3420 -
obs--95.3 %

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