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- PDB-6ubr: Crystal structure of D678A GoxA bound to glycine at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 6ubr
TitleCrystal structure of D678A GoxA bound to glycine at pH 7.5
ComponentsUncharacterized protein
KeywordsOXIDOREDUCTASE / tryotiophylquinone / 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 / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological speciesPseudoalteromonas luteoviolacea DSM 6061 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsYukl, E.T. / Avalos, D.
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 12, 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
B: Uncharacterized protein
A: Uncharacterized protein
C: Uncharacterized protein
D: Uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,62715
Polymers365,9314
Non-polymers69611
Water39,0022165
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22020 Å2
ΔGint-147 kcal/mol
Surface area105760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.679, 93.348, 187.853
Angle α, β, γ (deg.)90.000, 94.950, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules BACD

#1: Protein
Uncharacterized protein


Mass: 91482.781 Da / Num. of mol.: 4 / Mutation: D678A
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

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Non-polymers , 5 types, 2176 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical
ChemComp-GLY / GLYCINE


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


Mass: 18.015 Da / Num. of mol.: 2165 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.76 Å3/Da / Density % sol: 55.46 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: Protein at 10 mg/mL was combined in a 1:1 ratio with a solution containing 21% PEG 3350, 0.1 M ammonium sulfate, 0.1 M HEPES pH 7.5

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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: Jun 30, 2018
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: 1.96→48.29 Å / Num. obs: 271688 / % possible obs: 99.5 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.042 / Rrim(I) all: 0.081 / Net I/σ(I): 11.5 / Num. measured all: 951567 / Scaling rejects: 402
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
1.96-1.993.30.48244639134780.7780.3060.5742.299.8
10.74-48.293.60.023627217220.9990.0130.02734.396.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
XDSdata reduction
Aimless0.7.1data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BYW

6byw


Resolution: 1.96→48.288 Å / SU ML: 0.24 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.54
RfactorNum. reflection% reflection
Rfree0.2094 1998 0.74 %
Rwork0.1753 --
obs0.1755 270739 99.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 196.81 Å2 / Biso mean: 43.4925 Å2 / Biso min: 9.91 Å2
Refinement stepCycle: final / Resolution: 1.96→48.288 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24694 0 31 2165 26890
Biso mean--75.18 37.18 -
Num. residues----3127
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.96-2.0090.28891460.248519287100
2.009-2.06330.29281420.229419202100
2.0633-2.12410.27851380.222919311100
2.1241-2.19260.23391390.210819174100
2.1926-2.2710.37321530.32321835395
2.271-2.36190.23541490.197819281100
2.3619-2.46940.24331200.180319307100
2.4694-2.59960.20251540.17619251100
2.5996-2.76240.23531420.176919317100
2.7624-2.97570.21891410.177819246100
2.9757-3.27510.21031500.1691928099
3.2751-3.74880.1841430.15631913399
3.7488-4.72250.13551350.12781914298
4.7225-48.2880.1811460.15411945798

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