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- PDB-7cyx: Crystal strcuture of Glycine oxidase from Bacillus cereus ATCC 14579 -

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Basic information

Entry
Database: PDB / ID: 7cyx
TitleCrystal strcuture of Glycine oxidase from Bacillus cereus ATCC 14579
ComponentsGlycine oxidase
KeywordsFLAVOPROTEIN / oxidase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor / thiamine diphosphate biosynthetic process / flavin adenine dinucleotide binding / oxidoreductase activity / 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 / Glycine oxidase
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.41 Å
AuthorsSeok, J. / Kim, K.-J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2020
Title: Structural basis for stereospecificity to d-amino acid of glycine oxidase from Bacillus cereus ATCC 14579.
Authors: Seok, J. / Kim, Y.J. / Kim, I.K. / Kim, K.J.
History
DepositionSep 5, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 14, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 30, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)86,2034
Polymers84,6322
Non-polymers1,5712
Water57632
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4520 Å2
ΔGint-16 kcal/mol
Surface area29740 Å2
Unit cell
Length a, b, c (Å)82.180, 132.810, 165.212
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein Glycine oxidase /


Mass: 42315.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Strain: ATCC 14579 / Gene: BC_0747 / Plasmid: pET30a / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q81HQ7, Oxidoreductases; Acting on the CH-NH group of donors; With oxygen as acceptor
#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE / 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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 32 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.66 Å3/Da / Density % sol: 53.82 % / Mosaicity: 1.27 °
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: Tacsimate, HEPES, PEG 3350

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Data collection

DiffractionMean temperature: 297 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 12, 2020
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.36→30 Å / Num. obs: 36198 / % possible obs: 98.8 % / Redundancy: 12.9 % / Rmerge(I) obs: 0.102 / Rpim(I) all: 0.031 / Rrim(I) all: 0.107 / Χ2: 3.121 / Net I/σ(I): 11
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.41-2.4514.61.35818020.9420.3661.4071.822100
2.45-2.514.70.80418140.9550.2160.8331.861100
2.5-2.5414.70.6717900.9650.180.6941.9100
2.54-2.614.60.618110.9750.1620.6221.98100
2.6-2.6514.70.55318320.9750.1490.5732.04100
2.65-2.7114.60.46318030.9810.1250.4792.163100
2.71-2.7814.50.33217930.9880.090.3442.425100
2.78-2.8614.50.3118320.9890.0840.3222.511100
2.86-2.9414.30.22618270.9930.0620.2352.86100
2.94-3.0414.10.21118010.9940.0580.2193.085100
3.04-3.14140.18318180.9920.0510.193.251100
3.14-3.2713.60.14818170.9950.0420.1533.617100
3.27-3.42130.11918410.9960.0340.1244.068100
3.42-3.6120.1118350.9970.0330.1154.43399.7
3.6-3.826.60.09816190.9910.0390.1064.64688.9
3.82-4.1210.60.08318210.9970.0260.0874.898.9
4.12-4.5310.50.07318200.9970.0230.0774.90599
4.53-5.1810.20.06618580.9970.0210.074.67299.4
5.18-6.5211.90.06718720.9970.020.074.43199.8
6.52-309.60.06117920.9950.0210.0644.590.9

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
REFMAC5.8.0230refinement
HKL-2000data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ysh

4ysh


Resolution: 2.41→29.6 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.906 / SU B: 11.038 / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.43 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2999 1740 5.1 %RANDOM
Rwork0.2232 ---
obs0.2268 32704 92.09 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 162.43 Å2 / Biso mean: 61.32 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å2-0 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: final / Resolution: 2.41→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5666 0 106 32 5804
Biso mean--49.36 49.24 -
Num. residues----720
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0145897
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175309
X-RAY DIFFRACTIONr_angle_refined_deg1.4161.6817999
X-RAY DIFFRACTIONr_angle_other_deg0.8531.64612427
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0915716
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.59122.095296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.37915997
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3831536
X-RAY DIFFRACTIONr_chiral_restr0.0640.2770
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026564
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021094
LS refinement shellResolution: 2.41→2.424 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.485 90 -
Rwork0.37 1644 -
all-1734 -
obs--63.63 %

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