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- PDB-6xoj: ScoE with the CABA substrate bound and alpha-ketoglutarate in an ... -

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Basic information

Entry
Database: PDB / ID: 6xoj
TitleScoE with the CABA substrate bound and alpha-ketoglutarate in an off-site
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 / 2-OXOGLUTARIC ACID / : / (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase
Similarity search - Component
Biological speciesStreptomyces coeruleorubidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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 7, 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

Downloads & links

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Assembly

Deposited unit
A: ScoE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3646
Polymers36,8821
Non-polymers4815
Water4,666259
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)62.103, 62.103, 168.083
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, 264 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-AKG / 2-OXOGLUTARIC ACID


Mass: 146.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 259 / 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: 2.2 Å3/Da / Density % sol: 44.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 24% PEG4000 0.205 M Sodium Acetate 0.1 M Tris pH 8.5 1 mM alpha-ketoglutarate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Aug 12, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.45→49.946 Å / Num. obs: 59332 / % possible obs: 99.9 % / Redundancy: 11.606 % / Biso Wilson estimate: 23.872 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.062 / Χ2: 1.143 / Net I/σ(I): 22.21 / Num. measured all: 688622
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
1.45-1.546.4120.4932.659967941793520.8790.53699.3
1.54-1.6411.3440.3555.51100773888388830.9730.372100
1.64-1.7813.1360.249.09109016830382990.9890.25100
1.78-1.9413.0470.1415.5999955766276610.9960.146100
1.94-2.1712.9120.09224.8289622694169410.9980.096100
2.17-2.5113.2130.06834.5481971620462040.9990.07100
2.51-3.0712.6640.05245.3567082529752970.9990.054100
3.07-4.3412.2160.03861.44510284179417710.04100
4.34-49.94611.60.03466.129208252325180.9990.03699.8

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
XSCALEdata scaling
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DCH

6dch


Resolution: 1.45→49.946 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 17.54 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1917 3812 6.44 %
Rwork0.1693 55419 -
obs0.1707 59231 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 79.34 Å2 / Biso mean: 19.784 Å2 / Biso min: 9.78 Å2
Refinement stepCycle: final / Resolution: 1.45→49.946 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2318 0 30 259 2607
Biso mean--28.62 26.9 -
Num. residues----296
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4502-1.46850.25091360.2372197598
1.4685-1.48790.25341380.2202200199
1.4879-1.50820.24561380.20252025100
1.5082-1.52980.1951380.18612020100
1.5298-1.55260.19721390.182011100
1.5526-1.57690.1871390.17812015100
1.5769-1.60270.23231390.16982017100
1.6027-1.63040.18961410.16812049100
1.6304-1.660.21321370.16341990100
1.66-1.6920.21251410.16712050100
1.692-1.72650.19781390.17682023100
1.7265-1.7640.21251390.17482018100
1.764-1.80510.211400.17382025100
1.8051-1.85020.22081380.17092036100
1.8502-1.90020.16781420.16532055100
1.9002-1.95620.20051390.17122047100
1.9562-2.01930.18981410.1712026100
2.0193-2.09150.19111420.17322054100
2.0915-2.17520.22271390.1692045100
2.1752-2.27420.21711420.17012064100
2.2742-2.39410.18081430.17082075100
2.3941-2.54410.17571410.17252054100
2.5441-2.74050.19841440.17822086100
2.7405-3.01630.21181450.18422098100
3.0163-3.45270.21021450.17442126100
3.4527-4.34960.15451480.14742139100
4.3496-49.9460.1611590.15462295100

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