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- PDB-6ubz: Crystal structure of D678A GoxA bound to glycine at pH 5.5 -

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Basic information

Entry
Database: PDB / ID: 6ubz
TitleCrystal structure of D678A GoxA bound to glycine at pH 5.5
ComponentsUncharacterized protein GoxA
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 / GLYCINE / Uncharacterized protein
Function and homology information
Biological speciesPseudoalteromonas luteoviolacea DSM 6061 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 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 13, 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 GoxA
A: Uncharacterized protein GoxA
C: Uncharacterized protein GoxA
D: Uncharacterized protein GoxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,32912
Polymers365,9314
Non-polymers3978
Water44,2092454
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area21630 Å2
ΔGint-124 kcal/mol
Surface area106390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.325, 93.403, 187.987
Angle α, β, γ (deg.)90.000, 95.200, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Uncharacterized protein GoxA


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
#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 / Glycine


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


Mass: 18.015 Da / Num. of mol.: 2454 / 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: 2.74 Å3/Da / Density % sol: 55.14 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 5.5
Details: Protein at 10 mg/mL was combined at 1:1 with 21% 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: 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: 1.83→48.35 Å / Num. obs: 332023 / % possible obs: 99.3 % / Redundancy: 3.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.057 / Rpim(I) all: 0.034 / Rrim(I) all: 0.067 / Net I/σ(I): 13.6 / Num. measured all: 1203064 / Scaling rejects: 750
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
1.83-1.863.40.52456220163410.7720.3260.622.399.3
10.02-48.353.60.023769821150.9990.0130.02738.997.7

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Processing

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

6byw


Resolution: 1.83→47.352 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.67
RfactorNum. reflection% reflection
Rfree0.1894 16599 5 %
Rwork0.1617 --
obs0.1631 331919 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 130.33 Å2 / Biso mean: 33.3217 Å2 / Biso min: 9.01 Å2
Refinement stepCycle: final / Resolution: 1.83→47.352 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24811 0 4 2455 27270
Biso mean--19.54 35.16 -
Num. residues----3143
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.83-1.85080.33625470.2971039699
1.8508-1.87260.27815570.25261057199
1.8726-1.89540.26715510.236510475100
1.8954-1.91940.24825510.22541047599
1.9194-1.94470.26785540.216310525100
1.9447-1.97130.23825520.202910501100
1.9713-1.99950.22775540.197610529100
1.9995-2.02930.23255570.194110561100
2.0293-2.0610.22865530.193510521100
2.061-2.09480.22215520.19241046899
2.0948-2.13090.2175540.181610527100
2.1309-2.16970.20695550.173910552100
2.1697-2.21140.20655550.173510544100
2.2114-2.25650.20175510.17061044299
2.2565-2.30560.20115510.16731047499
2.3056-2.35920.19835530.16171050999
2.3592-2.41820.20565510.16681047299
2.4182-2.48360.21395530.17021048699
2.4836-2.55670.21675500.17081046299
2.5567-2.63920.20245530.16271049999
2.6392-2.73350.19435520.16181050099
2.7335-2.8430.20285530.1691048799
2.843-2.97230.19445510.16661048699
2.9723-3.1290.19315510.16761044399
3.129-3.3250.19315520.1611048799
3.325-3.58170.17365530.14941052199
3.5817-3.94190.14575510.1311047998
3.9419-4.5120.14855550.12091053499
4.512-5.68310.14855580.13261058099
5.6831-47.3520.15635690.14971081499
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.293-0.08390.00610.75440.15890.80460.0023-0.03350.00820.05330.0090.1153-0.0893-0.0633-0.00890.1279-0.00270.02420.1066-0.00280.1453-21.823-14.808251.395
20.4029-0.0566-0.08230.70520.17110.96830.0022-0.06420.00260.22860.0654-0.19330.18720.33760.0360.18270.0989-0.09480.2703-0.01350.181111.739-48.225262.987
30.30260.0315-0.13460.74250.20120.9292-0.01830.0514-0.0111-0.05730.0030.10770.1345-0.0889-0.01370.1649-0.0065-0.0150.1107-0.00460.1347-18.857-59.275216.303
40.3211-0.0061-0.00390.69920.16890.97980.01570.01350.0193-0.19480.0873-0.2319-0.11250.34520.05310.1285-0.07090.0840.2802-0.0390.221216.149-25.67211.117
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN B AND RESID 4:816 )B4 - 816
2X-RAY DIFFRACTION2( CHAIN A AND RESID 4:816 )A4 - 816
3X-RAY DIFFRACTION3( CHAIN C AND RESID 4:816 )C4 - 816
4X-RAY DIFFRACTION4( CHAIN D AND RESID 4:816 )D4 - 816

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