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- PDB-6eer: Structure of glycine-bound GoxA from Pseudoalteromonas luteoviolacea -

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Basic information

Entry
Database: PDB / ID: 6eer
TitleStructure of glycine-bound GoxA from Pseudoalteromonas luteoviolacea
ComponentsGoxA
KeywordsUNKNOWN FUNCTION / glycine oxidase / tryptophylquinone
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 / TRIETHYLENE GLYCOL / Uncharacterized protein
Function and homology information
Biological speciesPseudoalteromonas luteoviolacea DSM 6061 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 Å
AuthorsYukl, E.T. / Avalos, D.
CitationJournal: Biochemistry / Year: 2019
Title: Structural and Spectroscopic Characterization of a Product Schiff Base Intermediate in the Reaction of the Quinoprotein Glycine Oxidase, GoxA.
Authors: Avalos, D. / Sabuncu, S. / Mamounis, K.J. / Davidson, V.L. / Moenne-Loccoz, P. / Yukl, E.T.
History
DepositionAug 15, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / 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.identifier_ORCID
Revision 1.2Oct 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 / pdbx_struct_conn_angle / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _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: GoxA
B: GoxA
C: GoxA
D: GoxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)366,85115
Polymers366,3434
Non-polymers50811
Water53,1802952
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.242, 93.464, 187.903
Angle α, β, γ (deg.)90.00, 95.02, 90.00
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
GoxA


Mass: 91585.852 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 , 6 types, 2963 molecules

#2: Chemical
ChemComp-MG / MAGNESIUM ION


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


Mass: 22.990 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H10O3
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 2952 / 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: 2.64 Å3/Da / Density % sol: 53.42 %
Crystal growTemperature: 292 K / Method: batch mode / pH: 7.5
Details: 22% w/v PEG 3350, 0.1 M ammonium sulfate, 0.1 M HEPES pH 7.5 mixed 1:1 with protein at 10 mg/mL

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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: Oct 6, 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: 1.82→48.3 Å / Num. obs: 338105 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.062 / Rsym value: 0.092 / Net I/σ(I): 10
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.405 / Num. unique obs: 16759 / Rpim(I) all: 0.365 / Rsym value: 0.547 / % possible all: 99.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BYW

6byw


Resolution: 1.82→48.295 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.91 / Phase error: 21.95 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2127 17049 5.05 %RANDOM
Rwork0.1755 ---
obs0.1774 337928 99.41 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.82→48.295 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24637 0 29 2952 27618
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00625558
X-RAY DIFFRACTIONf_angle_d0.88534844
X-RAY DIFFRACTIONf_dihedral_angle_d14.65715278
X-RAY DIFFRACTIONf_chiral_restr0.0553774
X-RAY DIFFRACTIONf_plane_restr0.0064625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.84070.29645400.25210791X-RAY DIFFRACTION100
1.8407-1.86230.28325550.242310660X-RAY DIFFRACTION100
1.8623-1.88510.27655390.231610721X-RAY DIFFRACTION100
1.8851-1.90890.27145840.227510745X-RAY DIFFRACTION100
1.9089-1.9340.27615450.224910655X-RAY DIFFRACTION100
1.934-1.96050.25326080.213910673X-RAY DIFFRACTION100
1.9605-1.98850.25965570.208610719X-RAY DIFFRACTION100
1.9885-2.01820.24325980.200910643X-RAY DIFFRACTION100
2.0182-2.04980.24866080.203110686X-RAY DIFFRACTION100
2.0498-2.08340.25155220.204610735X-RAY DIFFRACTION100
2.0834-2.11930.23525820.190110722X-RAY DIFFRACTION100
2.1193-2.15780.23685600.18710693X-RAY DIFFRACTION100
2.1578-2.19930.22265480.184810702X-RAY DIFFRACTION100
2.1993-2.24420.22795810.184610662X-RAY DIFFRACTION99
2.2442-2.2930.22435620.185810726X-RAY DIFFRACTION100
2.293-2.34640.22735970.180410696X-RAY DIFFRACTION100
2.3464-2.4050.22235810.177510712X-RAY DIFFRACTION100
2.405-2.47010.225730.1810660X-RAY DIFFRACTION100
2.4701-2.54270.23025600.181110671X-RAY DIFFRACTION99
2.5427-2.62480.2165900.175310721X-RAY DIFFRACTION100
2.6248-2.71860.21955830.170810655X-RAY DIFFRACTION99
2.7186-2.82740.21585610.175110737X-RAY DIFFRACTION99
2.8274-2.95610.20545220.172610726X-RAY DIFFRACTION99
2.9561-3.11190.21156160.172710630X-RAY DIFFRACTION99
3.1119-3.30690.19345940.164210613X-RAY DIFFRACTION99
3.3069-3.56210.20565360.16510638X-RAY DIFFRACTION98
3.5621-3.92040.17665170.149710632X-RAY DIFFRACTION98
3.9204-4.48740.17765420.142410638X-RAY DIFFRACTION98
4.4874-5.65220.1765710.151110722X-RAY DIFFRACTION98
5.6522-48.3120.1926170.174210895X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 16.3453 Å / Origin y: -142.6933 Å / Origin z: 232.4121 Å
111213212223313233
T0.0332 Å20.0004 Å2-0.0108 Å2-0.1512 Å20.0041 Å2--0.1719 Å2
L0.0552 °20.0102 °2-0.0307 °2-0.3266 °2-0.0959 °2--0.4544 °2
S0.002 Å °0.0027 Å °0.0032 Å °-0.0122 Å °0.0181 Å °0.0413 Å °0.0087 Å °-0.1152 Å °0.0022 Å °
Refinement TLS groupSelection details: all

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