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- PDB-6vmw: Crystal structure of the F316A mutant of GoxA soaked with glycine -

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Basic information

Entry
Database: PDB / ID: 6vmw
TitleCrystal structure of the F316A mutant of GoxA soaked with glycine
ComponentsGlycine oxidase
KeywordsOXIDOREDUCTASE / CTQ
Function / homologyL-Lysine epsilon oxidase, N-terminal / L-lysine epsilon oxidase, C-terminal / L-Lysine epsilon oxidase N-terminal / L-lysine epsilon oxidase C-terminal domain / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesPseudoalteromonas luteoviolacea DSM 6061 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsYukl, E.T.
CitationJournal: J.Biol.Chem. / Year: 2020
Title: Roles of active-site residues in catalysis, substrate binding, cooperativity, and the reaction mechanism of the quinoprotein glycine oxidase.
Authors: Mamounis, K.J. / Yukl, E.T. / Davidson, V.L.
History
DepositionJan 28, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 8, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 15, 2020Group: Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed ..._citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2May 20, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3May 27, 2020Group: Database references / Category: citation_author / Item: _citation_author.identifier_ORCID
Revision 1.4Oct 11, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _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.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_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_conn.ptnr2_label_seq_id / _struct_conn_type.id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)366,1599
Polymers366,0394
Non-polymers1205
Water38,8402156
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22570 Å2
ΔGint-139 kcal/mol
Surface area102830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.607, 91.883, 178.786
Angle α, β, γ (deg.)90.000, 91.370, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycine oxidase


Mass: 91509.758 Da / Num. of mol.: 4 / Mutation: F316A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudoalteromonas luteoviolacea DSM 6061 (bacteria)
Gene: N475_19905 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A161XU12
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 5.5
Details: Protein at 10 mg/mL was combined in a 1:1 ratio with precipitant containing 19% PEG 3350, 0.1 M citrate pH 5.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Apr 15, 2019
RadiationMonochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.99→47.21 Å / Num. obs: 240912 / % possible obs: 99.1 % / Redundancy: 3.5 % / CC1/2: 0.994 / Rmerge(I) obs: 0.1 / Rpim(I) all: 0.061 / Rrim(I) all: 0.117 / Net I/σ(I): 9
Reflection shellResolution: 1.99→2.02 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 11746 / CC1/2: 0.535 / Rpim(I) all: 0.359 / Rrim(I) all: 0.669 / % possible all: 98.5

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3BYW

3byw


Resolution: 1.99→45.941 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 21.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2231 12075 5.01 %
Rwork0.1716 228775 -
obs0.1741 240850 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 168.93 Å2 / Biso mean: 32.2642 Å2 / Biso min: 4.48 Å2
Refinement stepCycle: final / Resolution: 1.99→45.941 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24282 0 5 2157 26444
Biso mean--27.12 32.48 -
Num. residues----3076
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.99-2.01260.35943990.2962746698
2.0126-2.03630.32033990.2612759299
2.0363-2.06110.29093910.2467752799
2.0611-2.08720.31144010.2515756599
2.0872-2.11470.29844180.2343760299
2.1147-2.14360.28393790.2232764199
2.1436-2.17430.26884350.2094755399
2.1743-2.20670.27954080.20867660100
2.2067-2.24120.27813960.2184766699
2.2412-2.27790.30874350.2476752099
2.2779-2.31720.27794200.19927623100
2.3172-2.35940.22843780.17837711100
2.3594-2.40470.23663980.18117663100
2.4047-2.45380.26624170.18367661100
2.4538-2.50720.26043930.18867671100
2.5072-2.56550.24624210.17797662100
2.5655-2.62960.22244060.17427650100
2.6296-2.70070.25184350.17487681100
2.7007-2.78020.24194040.18327649100
2.7802-2.86990.24194260.17227651100
2.8699-2.97250.22523810.1697710100
2.9725-3.09150.23183590.1698767699
3.0915-3.23210.20614190.1646762599
3.2321-3.40250.22274140.1611762198
3.4025-3.61560.2063650.1551755698
3.6156-3.89460.18253960.1413756898
3.8946-4.28630.15823970.128757098
4.2863-4.90590.16013900.1263758998
4.9059-6.17850.18243910.1366765898
6.1785-45.9410.16584040.1501778898

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