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- PDB-6xn6: ScoE with the CABA substrate bound and His299 and Arg157 flipped out -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 6xn6
TitleScoE with 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 / : / (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase
Similarity search - Component
Biological speciesStreptomyces coeruleorubidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 2, 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)37,3127
Polymers36,8821
Non-polymers4306
Water3,099172
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)62.090, 62.090, 167.154
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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, 178 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
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-FE2 / FE (II) ION


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


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


Mass: 18.015 Da / Num. of mol.: 172 / 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: 2.18 Å3/Da / Density % sol: 43.68 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop
Details: 205 mM sodium acetate, 100 mM Tris pH 8.5, 24% (w/v) PEG 4000

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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 PILATUS 6M / Detector: PIXEL / Date: Feb 17, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.7→49.841 Å / Num. obs: 36859 / % possible obs: 99.9 % / Redundancy: 12.9 % / Net I/σ(I): 15.9
Reflection shellResolution: 1.7→1.8 Å

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Processing

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

6dch


Resolution: 1.7→49.84 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 17.86 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.196 2373 6.44 %
Rwork0.166 --
obs0.168 36855 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.21 Å2
Refinement stepCycle: LAST / Resolution: 1.7→49.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2333 0 25 172 2530
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062485
X-RAY DIFFRACTIONf_angle_d0.8063385
X-RAY DIFFRACTIONf_dihedral_angle_d6.2752025
X-RAY DIFFRACTIONf_chiral_restr0.057367
X-RAY DIFFRACTIONf_plane_restr0.006451
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7014-1.73610.32861360.29151973X-RAY DIFFRACTION99
1.7361-1.77380.28461370.25721985X-RAY DIFFRACTION100
1.7738-1.81510.25681350.22671967X-RAY DIFFRACTION100
1.8151-1.86050.2631360.21171998X-RAY DIFFRACTION100
1.8605-1.91080.23361400.18462002X-RAY DIFFRACTION100
1.9108-1.9670.19861400.17311994X-RAY DIFFRACTION100
1.967-2.03050.20091330.17331997X-RAY DIFFRACTION100
2.0305-2.10310.21011370.16712007X-RAY DIFFRACTION100
2.1031-2.18730.20841370.16491996X-RAY DIFFRACTION100
2.1873-2.28680.20831410.15232018X-RAY DIFFRACTION100
2.2868-2.40740.19331370.16092011X-RAY DIFFRACTION100
2.4074-2.55820.19141410.15832026X-RAY DIFFRACTION100
2.5582-2.75570.21441420.1662042X-RAY DIFFRACTION100
2.7557-3.0330.18771400.17592050X-RAY DIFFRACTION100
3.033-3.47180.20121410.16142077X-RAY DIFFRACTION100
3.4718-4.37370.16231440.13752097X-RAY DIFFRACTION100
4.3737-49.8410.1691560.15792242X-RAY DIFFRACTION100

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