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- PDB-6xo3: ScoE with alpha-ketoglutarate in an off-site -

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Basic information

Entry
Database: PDB / ID: 6xo3
TitleScoE with 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
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: 1.85 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 6, 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)37,1204
Polymers36,8821
Non-polymers2373
Water3,009167
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)61.454, 61.454, 167.271
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#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
#2: 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
#3: Chemical ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O
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: 2.14 Å3/Da / Density % sol: 42.55 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 24% PEG 4000, 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: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Aug 4, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.85→49.52 Å / Num. obs: 28221 / % possible obs: 99.9 % / Redundancy: 12.656 % / Biso Wilson estimate: 34.822 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.099 / Rrim(I) all: 0.103 / Χ2: 0.827 / Net I/σ(I): 15.93 / Num. measured all: 357160
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
1.85-1.9612.8370.772.8156828444844270.9530.80299.5
1.96-2.112.5530.5194.3352747420242020.9730.541100
2.1-2.2713.370.3127.3252529392939290.990.324100
2.27-2.4812.6860.22310.0546315365136510.9940.232100
2.48-2.7713.0810.15115.3843206330333030.9960.157100
2.77-3.212.5430.123.5737066295529550.9980.104100
3.2-3.9212.4140.06636.4831358252625260.9990.068100
3.92-5.5211.6880.05342.7523516201320120.9990.055100
5.52-49.5211.180.04745.0213595121712160.9990.0599.9

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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: 1.85→49.52 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 22.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2068 1813 6.43 %
Rwork0.1685 26369 -
obs0.1709 28182 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 99.33 Å2 / Biso mean: 31.2632 Å2 / Biso min: 18.38 Å2
Refinement stepCycle: final / Resolution: 1.85→49.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2316 0 12 167 2495
Biso mean--32.44 36.01 -
Num. residues----296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062456
X-RAY DIFFRACTIONf_angle_d0.7953353
X-RAY DIFFRACTIONf_dihedral_angle_d14.894342
X-RAY DIFFRACTIONf_chiral_restr0.055363
X-RAY DIFFRACTIONf_plane_restr0.006448
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.85-1.90.30631350.22881953208899
1.9-1.960.26831290.207419752104100
1.96-2.020.26121420.201419862128100
2.02-2.090.25751340.194919972131100
2.09-2.180.23251420.18819882130100
2.18-2.280.2611350.173720102145100
2.28-2.40.23041370.177419962133100
2.4-2.550.20891390.182320292168100
2.55-2.740.28191360.189720152151100
2.74-3.020.23461420.193620332175100
3.02-3.450.20091440.184620522196100
3.45-4.350.16391430.135721052248100
4.35-49.520.16271550.142222302385100

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