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- PDB-6vl7: Crystal structure of the H583C mutant of GoxA soaked with glycine -

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Basic information

Entry
Database: PDB / ID: 6vl7
TitleCrystal structure of the H583C 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 / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Uncharacterized protein
Function and homology information
Biological speciesPseudoalteromonas luteoviolacea DSM 6061 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.14 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 22, 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: Advisory / Data collection ...Advisory / 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_unobs_or_zero_occ_atoms / 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
B: Glycine oxidase
C: Glycine oxidase
D: Glycine oxidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,58222
Polymers365,9674
Non-polymers1,61418
Water27,8151544
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24300 Å2
ΔGint-249 kcal/mol
Surface area105150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.811, 93.285, 188.572
Angle α, β, γ (deg.)90.000, 95.080, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Glycine oxidase


Mass: 91491.781 Da / Num. of mol.: 4 / Mutation: H583C
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, 1562 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.: 10 / 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-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1544 / 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: 2.63 Å3/Da / Density % sol: 53.21 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: 1uL protein was combined with 1uL precipitant solution containing 25% PEG 3350, 0.1 M HEPES pH 7.5 and 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: 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: 2.14→49.191 Å / Num. obs: 207973 / % possible obs: 99.4 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.051 / Rrim(I) all: 0.101 / Net I/σ(I): 9.2
Reflection shellResolution: 2.14→2.18 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.605 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 10307 / CC1/2: 0.783 / Rpim(I) all: 0.354 / Rrim(I) all: 0.703 / % possible all: 100

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Processing

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

6byw


Resolution: 2.14→49.191 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 23.73
RfactorNum. reflection% reflection
Rfree0.2112 1999 0.96 %
Rwork0.1565 --
obs0.157 207903 99.42 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 162.47 Å2 / Biso mean: 47.6067 Å2 / Biso min: 18.09 Å2
Refinement stepCycle: final / Resolution: 2.14→49.191 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24548 0 143 1545 26236
Biso mean--93.19 44.55 -
Num. residues----3104
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.14-2.19350.31341440.253814746100
2.1935-2.25280.28171420.221614693100
2.2528-2.31910.26461420.204114660100
2.3191-2.3940.27161440.18614745100
2.394-2.47950.23551430.177614702100
2.4795-2.57880.24771430.17214769100
2.5788-2.69620.22881430.163314698100
2.6962-2.83830.24671420.169314726100
2.8383-3.01610.25641430.169914715100
3.0161-3.24890.24031420.169714688100
3.2489-3.57580.22351430.15611472299
3.5758-4.0930.15481420.12731455598
4.093-5.15590.15411410.1181458198
5.1559-49.1910.19131450.14541490498
Refinement TLS params.Method: refined / Origin x: 16.1741 Å / Origin y: -142.5305 Å / Origin z: 233.4471 Å
111213212223313233
T0.2346 Å2-0.0136 Å2-0.0115 Å2-0.2412 Å20.0036 Å2--0.2336 Å2
L0.1326 °20.0156 °2-0.0596 °2-0.5264 °2-0.1101 °2--0.5713 °2
S-0.0016 Å °0.0209 Å °-0.0008 Å °-0.0573 Å °0.0224 Å °0.0629 Å °0.0503 Å °-0.1446 Å °-0.0068 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allA4 - 816
2X-RAY DIFFRACTION1allB4 - 816
3X-RAY DIFFRACTION1allC4 - 816
4X-RAY DIFFRACTION1allD4 - 816
5X-RAY DIFFRACTION1allE1
6X-RAY DIFFRACTION1allF1
7X-RAY DIFFRACTION1allG1
8X-RAY DIFFRACTION1allH1
9X-RAY DIFFRACTION1allI1 - 2
10X-RAY DIFFRACTION1allI3 - 8
11X-RAY DIFFRACTION1allI9 - 10
12X-RAY DIFFRACTION1allS1 - 1516
13X-RAY DIFFRACTION1allS1517 - 1544
14X-RAY DIFFRACTION1allS1545 - 1570
15X-RAY DIFFRACTION1allS1571 - 1578
16X-RAY DIFFRACTION1allJ1 - 3
17X-RAY DIFFRACTION1allK1

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