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- PDB-6vmv: Crystal structure of the H767A mutant of GoxA soaked with glycine -

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Basic information

Entry
Database: PDB / ID: 6vmv
TitleCrystal structure of the H767A 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 / FOURIER SYNTHESIS / Resolution: 2.2 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 / 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

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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)367,10117
Polymers366,1394
Non-polymers96213
Water17,312961
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22110 Å2
ΔGint-253 kcal/mol
Surface area105520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.965, 93.081, 187.642
Angle α, β, γ (deg.)90.000, 95.070, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Glycine oxidase


Mass: 91534.781 Da / Num. of mol.: 4 / Mutation: H767A
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-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 961 / 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: 2.62 Å3/Da / Density % sol: 53.04 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: Protein at 10 mg/mL was combined at a 1:1 ratio with precipitation solution containing 23% PEG 3350, 0.1 M HEPES pH 7.5, 0.1 M ammonium sulfate

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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 PILATUS 6M / Detector: PIXEL / Date: Oct 26, 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: 2.2→48.2 Å / Num. obs: 189420 / % possible obs: 98.9 % / Redundancy: 3.5 % / CC1/2: 0.993 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.067 / Rrim(I) all: 0.129 / Net I/σ(I): 5.9
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.513 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 9379 / CC1/2: 0.792 / Rpim(I) all: 0.322 / Rrim(I) all: 0.609 / % possible all: 99.6

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimlessdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6BYW

6byw


Resolution: 2.2→48.197 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 29.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2385 1991 1.05 %
Rwork0.1867 186975 -
obs0.1873 188966 98.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 169.6 Å2 / Biso mean: 52.1637 Å2 / Biso min: 16.96 Å2
Refinement stepCycle: final / Resolution: 2.2→48.197 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24446 0 49 961 25456
Biso mean--97.86 44.31 -
Num. residues----3090
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.2-2.2550.35591440.332313400100
2.255-2.3160.40221420.298713394100
2.316-2.38410.33581430.26381340099
2.3841-2.46110.27021440.235713431100
2.4611-2.5490.28621430.218413423100
2.549-2.65110.2461430.208613500100
2.6511-2.77170.26411450.203413418100
2.7717-2.91790.30611410.20511337099
2.9179-3.10060.29931430.20751338399
3.1006-3.340.27931410.20061328598
3.34-3.6760.21671410.17981315897
3.676-4.20770.21391360.14751306396
4.2077-5.30010.16961390.13591311196
5.3001-48.1970.17241460.15251363998
Refinement TLS params.Method: refined / Origin x: 15.8768 Å / Origin y: -142.6968 Å / Origin z: 232.1241 Å
111213212223313233
T0.1305 Å2-0.0029 Å2-0.0161 Å2-0.2472 Å20.004 Å2--0.2336 Å2
L0.1062 °20.0201 °2-0.06 °2-0.5797 °2-0.0803 °2--0.5748 °2
S0.0048 Å °0.0133 Å °0.0043 Å °-0.0669 Å °0.0206 Å °0.059 Å °0.0276 Å °-0.1419 Å °-0.0003 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 816
2X-RAY DIFFRACTION1allB4 - 816
3X-RAY DIFFRACTION1allC4 - 812
4X-RAY DIFFRACTION1allD4 - 813
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF1
7X-RAY DIFFRACTION1allG1
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allS1 - 981
10X-RAY DIFFRACTION1allI1 - 9

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