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- PDB-6ufq: Crystal structure of D678N GoxA bound to glycine -

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Basic information

Entry
Database: PDB / ID: 6ufq
TitleCrystal structure of D678N GoxA bound to glycine
ComponentsGlycine Oxidase GoxA
KeywordsOXIDOREDUCTASE / oxidase
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 / GLYCINE / Uncharacterized protein
Function and homology information
Biological speciesPseudoalteromonas luteoviolacea DSM 6061 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.51 Å
AuthorsYukl, E.T.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R37GM41574 United States
CitationJournal: J.Biol.Chem. / Year: 2019
Title: Kinetic and structural evidence that Asp-678 plays multiple roles in catalysis by the quinoprotein glycine oxidase.
Authors: Mamounis, K.J. / Avalos, D. / Yukl, E.T. / Davidson, V.L.
History
DepositionSep 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2019Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Nov 27, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
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 / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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
A: Glycine Oxidase GoxA
B: Glycine Oxidase GoxA
C: Glycine Oxidase GoxA
D: Glycine Oxidase GoxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,50112
Polymers366,1034
Non-polymers3978
Water14,898827
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22760 Å2
ΔGint-129 kcal/mol
Surface area104720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.141, 91.573, 178.409
Angle α, β, γ (deg.)90.000, 91.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycine Oxidase GoxA


Mass: 91525.805 Da / Num. of mol.: 4 / Mutation: D678N
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-GLY / GLYCINE


Type: peptide linking / Mass: 75.067 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H5NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 827 / 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: 2.44 Å3/Da / Density % sol: 49.49 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 5.5
Details: Protein at 10 mg/mL was mixed in a 1:1 ratio with crystallization cocktail containing 21% w/v PEG 3350, 0.1 M sodium 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: 2.51→47.1 Å / Num. obs: 119962 / % possible obs: 99.6 % / Redundancy: 3.7 % / CC1/2: 0.99 / Rmerge(I) obs: 0.13 / Rpim(I) all: 0.078 / Rrim(I) all: 0.152 / Net I/σ(I): 8.9 / Num. measured all: 443732 / Scaling rejects: 19
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.51-2.553.70.6182193259290.6680.3720.7232.299.9
13.75-47.13.50.03424477010.9980.020.0423.488.4

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimless0.1.27data scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BYW

6byw


Resolution: 2.51→46.866 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 23.13
RfactorNum. reflection% reflection
Rfree0.2309 6022 5.02 %
Rwork0.1757 --
obs0.1785 119927 99.56 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 141.97 Å2 / Biso mean: 40.0036 Å2 / Biso min: 14.75 Å2
Refinement stepCycle: final / Resolution: 2.51→46.866 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24716 0 14 827 25557
Biso mean--45.03 34.85 -
Num. residues----3130
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.51-2.53850.33152283821100
2.5385-2.56840.29382063700100
2.5684-2.59970.28562083853100
2.5997-2.63260.29762053699100
2.6326-2.66720.3142203797100
2.6672-2.70380.30252103766100
2.7038-2.74240.30731893815100
2.7424-2.78330.32892063810100
2.7833-2.82680.28531883756100
2.8268-2.87320.2712083847100
2.8732-2.92270.28981823769100
2.9227-2.97580.24991883806100
2.9758-3.03310.25491923836100
3.0331-3.0950.24641823801100
3.095-3.16220.25822173766100
3.1622-3.23580.26431933827100
3.2358-3.31670.25642123759100
3.3167-3.40630.24142073818100
3.4063-3.50650.23021860.17623789100
3.5065-3.61970.23182000.16323787100
3.6197-3.7490.2092330.15383779100
3.749-3.8990.19721990.1512378099
3.899-4.07640.18541980.1466378499
4.0764-4.29120.19622150.142377999
4.2912-4.55980.19751840.1401383999
4.5598-4.91150.18521810.1404381199
4.9115-5.40510.18622020.1438379399
5.4051-6.18580.19831940.155382399
6.1858-7.78760.20381900.1479385399
7.7876-46.8660.18441990.1614384297

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