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- PDB-6xpa: ScoE with oxovanadium and the CABA substrate bound and His299 and... -

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Basic information

Entry
Database: PDB / ID: 6xpa
TitleScoE with oxovanadium and the CABA substrate bound and His299 and Arg157 flipped out
ComponentsScoE protein
KeywordsOXIDOREDUCTASE / isonitrile formation mononuclear iron dioxygenase
Function / homology
Function and homology information


(R)-3-[(carboxymethyl)amino]fatty acid dioxygenase/decarboxylase / dioxygenase activity / metal ion binding
Similarity search - Function
: / TauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily
Similarity search - Domain/homology
Chem-7UC / ACETATE ION / oxovanadium(2+) / (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase
Similarity search - Component
Biological speciesStreptomyces coeruleorubidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsJonnalagadda, R. / Drennan, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: J.Biol.Chem. / Year: 2021
Title: Biochemical and crystallographic investigations into isonitrile formation by a nonheme iron-dependent oxidase/decarboxylase.
Authors: Jonnalagadda, R. / Del Rio Flores, A. / Cai, W. / Mehmood, R. / Narayanamoorthy, M. / Ren, C. / Zaragoza, J.P.T. / Kulik, H.J. / Zhang, W. / Drennan, C.L.
History
DepositionJul 8, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 6, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: 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 1.2Jul 14, 2021Group: 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.year / _citation_author.identifier_ORCID
Revision 1.3Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ScoE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,2406
Polymers36,8821
Non-polymers3585
Water2,414134
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)61.820, 61.820, 167.483
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ScoE protein


Mass: 36882.316 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces coeruleorubidus (bacteria)
Gene: ScoE / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A3B6UEU3

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Non-polymers , 5 types, 139 molecules

#2: Chemical ChemComp-7UC / (3~{R})-3-(2-hydroxy-2-oxoethylamino)butanoic acid


Mass: 161.156 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H11NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-VVO / oxovanadium(2+)


Mass: 66.941 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: OV / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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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: 2.17 Å3/Da / Density % sol: 43.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 24% PEG4000 0.205 M Sodium acetate 0.1 M Tris pH 8.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2→49.74 Å / Num. obs: 22816 / % possible obs: 99.8 % / Redundancy: 15.712 % / Biso Wilson estimate: 34.273 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.125 / Rrim(I) all: 0.129 / Χ2: 1.189 / Net I/σ(I): 17.42 / Num. measured all: 358483
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2-2.1214.6780.8473.152240359535590.930.87799
2.12-2.2715.8380.584.9353501337933780.9620.599100
2.27-2.4516.8060.4217.0653511318531840.9820.434100
2.45-2.6816.4660.29110.2548344293629360.9890.301100
2.68-315.6560.18115.441865267426740.9960.188100
3-3.4615.580.10625.9637189238723870.9980.109100
3.46-4.2416.3170.06940.6133254203820380.9990.071100
4.24-5.9714.6820.05347.2224167164716460.9990.05599.9
5.97-49.7414.2130.04152.7614412102010140.9990.04299.4

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DCH

6dch


Resolution: 2.1→49.74 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 20.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2132 1268 6.45 %
Rwork0.171 18406 -
obs0.1737 19674 99.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.81 Å2 / Biso mean: 25.5313 Å2 / Biso min: 13.57 Å2
Refinement stepCycle: final / Resolution: 2.1→49.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2302 0 19 134 2455
Biso mean--32.48 28.86 -
Num. residues----296
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.190.27671370.20661956209398
2.19-2.290.23651380.184820142152100
2.29-2.410.25911350.18919952130100
2.41-2.560.24291390.194920132152100
2.56-2.760.27691390.199520182157100
2.76-3.030.23971400.203620302170100
3.03-3.470.23091430.187420602203100
3.47-4.370.17541430.139520902233100
4.37-49.740.16071540.14122302384100

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