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- PDB-6byw: Structure of GoxA from Pseudoalteromonas luteoviolacea -

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Basic information

Entry
Database: PDB / ID: 6byw
TitleStructure of GoxA from Pseudoalteromonas luteoviolacea
ComponentsGoxA
KeywordsUNKNOWN FUNCTION / cystein tryptophylquinone / glycine 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 / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological speciesPseudoalteromonas luteoviolacea DSM 6061 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsYukl, E.T. / Avalos, D.
CitationJournal: Biochemistry / Year: 2018
Title: Structure and Enzymatic Properties of an Unusual Cysteine Tryptophylquinone-Dependent Glycine Oxidase from Pseudoalteromonas luteoviolacea.
Authors: Andreo-Vidal, A. / Mamounis, K.J. / Sehanobish, E. / Avalos, D. / Campillo-Brocal, J.C. / Sanchez-Amat, A. / Yukl, E.T. / Davidson, V.L.
History
DepositionDec 21, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 14, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: GoxA
A: GoxA
C: GoxA
D: GoxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,98916
Polymers366,1074
Non-polymers88212
Water29,5631641
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22940 Å2
ΔGint-122 kcal/mol
Surface area106300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.843, 93.236, 188.457
Angle α, β, γ (deg.)90.00, 94.88, 90.00
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
GoxA


Mass: 91526.789 Da / Num. of mol.: 4
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, 1653 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1641 / Source method: isolated from a natural source / Formula: H2O

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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: 53.18 %
Crystal growTemperature: 292 K / Method: batch mode / pH: 7.5
Details: Batch mode under paraffin oil. 1:1 mixture of protein at 10 mg/mL with mother liquor containing 0.1 M HEPES pH 7.5, 0.1 M ammonium sulfate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 19, 2017
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: 2.05→48.283 Å / Num. obs: 235829 / % possible obs: 99.3 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.094 / Rpim(I) all: 0.058 / Rrim(I) all: 0.111 / Net I/σ(I): 10.9
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.603 / Mean I/σ(I) obs: 2.7 / Num. unique obs: 11390 / Rpim(I) all: 0.522 / Rrim(I) all: 0.72 / % possible all: 97.5

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→48.283 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.95
RfactorNum. reflection% reflection
Rfree0.2192 11722 4.99 %
Rwork0.1855 --
obs0.1872 234728 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.05→48.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24680 0 53 1641 26374
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00425395
X-RAY DIFFRACTIONf_angle_d0.7834572
X-RAY DIFFRACTIONf_dihedral_angle_d13.69415147
X-RAY DIFFRACTIONf_chiral_restr0.0783750
X-RAY DIFFRACTIONf_plane_restr0.0044561
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.07330.45093800.42787235X-RAY DIFFRACTION96
2.0733-2.09770.40913830.38277361X-RAY DIFFRACTION100
2.0977-2.12330.28064090.26147530X-RAY DIFFRACTION100
2.1233-2.15010.26993830.23337489X-RAY DIFFRACTION100
2.1501-2.17840.24794040.22827436X-RAY DIFFRACTION100
2.1784-2.20830.28063740.2437520X-RAY DIFFRACTION100
2.2083-2.23980.42363580.39926945X-RAY DIFFRACTION93
2.2398-2.27330.54393390.48146617X-RAY DIFFRACTION88
2.2733-2.30880.23764030.21547400X-RAY DIFFRACTION100
2.3088-2.34660.2363900.2027530X-RAY DIFFRACTION100
2.3466-2.38710.2254240.20087505X-RAY DIFFRACTION100
2.3871-2.43050.23263810.19537461X-RAY DIFFRACTION100
2.4305-2.47720.22123990.19327499X-RAY DIFFRACTION100
2.4772-2.52780.223750.19227526X-RAY DIFFRACTION100
2.5278-2.58280.24074050.18817453X-RAY DIFFRACTION100
2.5828-2.64280.22123880.19047493X-RAY DIFFRACTION100
2.6428-2.70890.21153840.18747456X-RAY DIFFRACTION99
2.7089-2.78220.23063950.18617497X-RAY DIFFRACTION100
2.7822-2.8640.22364160.18367457X-RAY DIFFRACTION100
2.864-2.95650.21063800.18187542X-RAY DIFFRACTION100
2.9565-3.06210.21363870.17847534X-RAY DIFFRACTION100
3.0621-3.18470.21474150.17367511X-RAY DIFFRACTION100
3.1847-3.32960.19583800.16327517X-RAY DIFFRACTION100
3.3296-3.50510.20334120.17177408X-RAY DIFFRACTION99
3.5051-3.72460.18023710.15177370X-RAY DIFFRACTION97
3.7246-4.01210.16814020.13767395X-RAY DIFFRACTION98
4.0121-4.41560.15263890.12397535X-RAY DIFFRACTION99
4.4156-5.05390.16733990.1267516X-RAY DIFFRACTION99
5.0539-6.36510.19153970.1537536X-RAY DIFFRACTION99
6.3651-48.29660.19154000.15857732X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -2.1872 Å / Origin y: -36.8445 Å / Origin z: 236.0844 Å
111213212223313233
T0.1504 Å20.0118 Å2-0.0063 Å2-0.2108 Å2-0.0029 Å2--0.206 Å2
L0.1063 °2-0.0098 °2-0.0445 °2-0.3995 °20.1174 °2--0.4362 °2
S0.0044 Å °-0.0082 Å °0.005 Å °0.0278 Å °0.0245 Å °-0.0394 Å °0.0465 Å °0.0875 Å °0.0065 Å °
Refinement TLS groupSelection details: all

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