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- PDB-6uc1: Crystal structure of D678A GoxA soaked in glycine at pH 7.5 -

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Basic information

Entry
Database: PDB / ID: 6uc1
TitleCrystal structure of D678A GoxA soaked in glycine at pH 7.5
Components(Uncharacterized protein ...) x 2
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 / metal ion binding / GLYCINE / TRIETHYLENE GLYCOL / Uncharacterized protein
Function and homology information
Biological speciesPseudoalteromonas luteoviolacea DSM 6061 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.19 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
D: Uncharacterized protein GoxA
C: Uncharacterized protein GoxA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)367,68825
Polymers365,9874
Non-polymers1,70021
Water23,3831298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area24240 Å2
ΔGint-286 kcal/mol
Surface area105960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.213, 93.529, 188.334
Angle α, β, γ (deg.)90.000, 95.060, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Uncharacterized protein ... , 2 types, 4 molecules BADC

#1: Protein Uncharacterized protein GoxA


Mass: 91482.781 Da / Num. of mol.: 3 / 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: Protein Uncharacterized protein GoxA


Mass: 91538.828 Da / Num. of mol.: 1 / 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

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Non-polymers , 5 types, 1319 molecules

#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#6: Chemical
ChemComp-GLY / GLYCINE


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


Mass: 18.015 Da / Num. of mol.: 1298 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 293 K / Method: batch mode / pH: 7.5
Details: Protein at 10 mg/mL was combined with 23% PEG 3350, 0.1 M ammonium sulfate, 0.1 M HEPES pH 7.5

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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: 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: 2.19→48.38 Å / Num. obs: 195196 / % possible obs: 99.5 % / Redundancy: 3.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.087 / Rpim(I) all: 0.052 / Rrim(I) all: 0.102 / Net I/σ(I): 10.4 / Num. measured all: 722737 / Scaling rejects: 417
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
2.19-2.233.90.813762596970.6990.4750.9411.999.9
12-48.383.80.026469312420.9990.0150.0332.996.8

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6BYW

6byw


Resolution: 2.19→48.376 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 22.61
RfactorNum. reflection% reflection
Rfree0.2061 9756 5 %
Rwork0.1686 --
obs0.1705 195044 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 407.75 Å2 / Biso mean: 56.0162 Å2 / Biso min: 20 Å2
Refinement stepCycle: final / Resolution: 2.19→48.376 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24548 0 88 1299 25935
Biso mean--95.92 42.86 -
Num. residues----3109
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.19-2.21490.3143260.27536183100
2.2149-2.24090.33313220.2981610299
2.2409-2.26830.41063150.3626598997
2.2683-2.2970.28113250.25476155100
2.297-2.32720.28663260.23926195100
2.3272-2.35910.25123250.23046176100
2.3591-2.39280.26073250.22416199100
2.3928-2.42850.2513230.21386106100
2.4285-2.46650.24873290.20886259100
2.4665-2.50690.24923250.20846161100
2.5069-2.55010.22943240.26171100
2.5501-2.59650.25213240.19686168100
2.5965-2.64640.23483260.19496178100
2.6464-2.70040.21833250.1918617199
2.7004-2.75910.24263260.19276205100
2.7591-2.82330.24713260.18646191100
2.8233-2.89390.23773260.18836172100
2.8939-2.97220.25473250.18046173100
2.9722-3.05960.2253270.1786225100
3.0596-3.15830.21443250.17036174100
3.1583-3.27120.21253250.17066169100
3.2712-3.40210.18623260.16176206100
3.4021-3.55690.19823260.1501618999
3.5569-3.74440.16843210.1386610599
3.7444-3.97890.17373220.1301610898
3.9789-4.28590.15293260.1221619399
4.2859-4.71690.14413240.1136615199
4.7169-5.39870.14993270.1301622099
5.3987-6.79880.19413290.1491624799
6.7988-48.3760.19833350.1702634799
Refinement TLS params.Method: refined / Origin x: -2.8739 Å / Origin y: -37.1004 Å / Origin z: 235.9293 Å
111213212223313233
T0.1786 Å2-0.0042 Å2-0.0089 Å2-0.2774 Å20.007 Å2--0.276 Å2
L0.1883 °2-0.0224 °2-0.0644 °2-0.7042 °20.2305 °2--0.781 °2
S-0.0014 Å °-0.0148 Å °0.0073 Å °0.0126 Å °0.047 Å °-0.0687 Å °0.0171 Å °0.1613 Å °0.0201 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB4 - 815
2X-RAY DIFFRACTION1allA4 - 815
3X-RAY DIFFRACTION1allC5 - 815
4X-RAY DIFFRACTION1allD4 - 815
5X-RAY DIFFRACTION1allE1 - 5
6X-RAY DIFFRACTION1allE6
7X-RAY DIFFRACTION1allE7 - 11
8X-RAY DIFFRACTION1allE12
9X-RAY DIFFRACTION1allH1
10X-RAY DIFFRACTION1allI1
11X-RAY DIFFRACTION1allK1
12X-RAY DIFFRACTION1allL1
13X-RAY DIFFRACTION1allF1
14X-RAY DIFFRACTION1allM1 - 4
15X-RAY DIFFRACTION1allS1 - 1246
16X-RAY DIFFRACTION1allS1247 - 1272
17X-RAY DIFFRACTION1allS1273 - 1285
18X-RAY DIFFRACTION1allS1286 - 1307

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