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- PDB-6dch: Structure of isonitrile biosynthesis enzyme ScoE -

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Basic information

Entry
Database: PDB / ID: 6dch
TitleStructure of isonitrile biosynthesis enzyme ScoE
ComponentsScoE protein
KeywordsOXIDOREDUCTASE / Isonitrile / non-heme iron / enzyme / metalloenzyme
Function / homology
Function and homology information


(R)-3-[(carboxymethyl)amino]fatty acid dioxygenase/decarboxylase / organic cyclic compound metabolic process / : / 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
ACETATE ION / CHOLINE ION / (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase
Similarity search - Component
Biological speciesStreptomyces coeruleorubidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsBorn, D.A. / Drennan, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
Howard Hughes Medical Institute (HHMI) United States
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2018
Title: Isonitrile Formation by a Non-Heme Iron(II)-Dependent Oxidase/Decarboxylase.
Authors: Harris, N.C. / Born, D.A. / Cai, W. / Huang, Y. / Martin, J. / Khalaf, R. / Drennan, C.L. / Zhang, W.
History
DepositionMay 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 27, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 29, 2018Group: Data collection / 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_author.identifier_ORCID / _citation_author.name
Revision 1.2Nov 20, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 11, 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)37,1465
Polymers36,8821
Non-polymers2644
Water5,963331
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area880 Å2
ΔGint-45 kcal/mol
Surface area13240 Å2
2
A: ScoE protein
hetero molecules

A: ScoE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,29310
Polymers73,7652
Non-polymers5288
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_557y,x,-z+21
Buried area3430 Å2
ΔGint-105 kcal/mol
Surface area24810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.100, 62.100, 167.850
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-831-

HOH

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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 (E. coli) / References: UniProt: A0A3B6UEU3*PLUS

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Non-polymers , 5 types, 335 molecules

#2: Chemical ChemComp-ACT / ACETATE ION / Acetate


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


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-CHT / CHOLINE ION / Choline


Mass: 104.171 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H14NO
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 331 / Source method: isolated from a natural source / Formula: H2O

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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: 2.19 Å3/Da / Density % sol: 43.93 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 200 mM sodium acetate, 100 mM Tris pH 8.5, 30% (w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 14, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 1.8→58.242 Å / Num. obs: 31084 / % possible obs: 99 % / Redundancy: 24.417 % / Biso Wilson estimate: 22.09 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.215 / Rrim(I) all: 0.22 / Χ2: 0.911 / Net I/σ(I): 14.22 / Num. measured all: 758976 / Scaling rejects: 78
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.8-1.8526.1621.662.5622710.7391.693100
1.85-1.926.1371.3923.0422200.7261.42100
1.9-1.9524.6781.3063.4421510.821.33499.9
1.95-2.0123.3871.034.3721040.8421.054100
2.01-2.0824.9250.8475.6320380.9360.865100
2.08-2.1525.0470.5967.7319720.9760.608100
2.15-2.2324.3440.4739.2119080.9820.484100
2.23-2.3223.5320.45310.1618330.9850.46399.9
2.32-2.4323.0780.36512.3317630.990.373100
2.43-2.5524.9390.31314.8816910.9940.319100
2.55-2.6825.4540.27517.2816280.9950.281100
2.68-2.8525.7850.2519.3315490.9960.255100
2.85-3.0425.2220.20122.3314410.9970.205100
3.04-3.2923.6570.15625.5913670.9970.16100
3.29-3.625.0960.12331.0312520.9980.12699.9
3.6-4.0221.9860.10232.548370.9980.10572.7
4.02-4.6521.4060.08635.410320.9970.089100
4.65-5.6923.2190.08537.28860.9980.087100
5.69-8.0522.5130.08336.217080.9980.08499.9
8.05-58.24218.7690.06138.354330.9990.06399.8

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIX1.13_2998refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PVJ

3pvj


Resolution: 1.8→58.242 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 19.35
RfactorNum. reflection% reflection
Rfree0.2071 2000 6.44 %
Rwork0.1787 --
obs0.1805 31077 98.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 62.87 Å2 / Biso mean: 24.4133 Å2 / Biso min: 11.45 Å2
Refinement stepCycle: final / Resolution: 1.8→58.242 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2336 0 20 331 2687
Biso mean--22.14 34.52 -
Num. residues----296
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8001-1.84520.24231420.211920512193100
1.8452-1.8950.26791400.231120452185100
1.895-1.95080.32561420.278620742216100
1.9508-2.01380.25551410.224920482189100
2.0138-2.08580.27351410.233820462187100
2.0858-2.16930.25341430.229120722215100
2.1693-2.2680.27231410.231220662207100
2.268-2.38760.19981440.179520982242100
2.3876-2.53720.23151420.16920622204100
2.5372-2.73310.19231450.16520942239100
2.7331-3.00810.21081450.174121142259100
3.0081-3.44330.18831460.160621352281100
3.4433-4.3380.15431300.13881863199386
4.338-58.27220.16711580.15423092467100

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