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- PDB-6l6x: The structure of ScoE with substrate -

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Basic information

Entry
Database: PDB / ID: 6l6x
TitleThe structure of ScoE with substrate
ComponentsScoE protein
KeywordsOXIDOREDUCTASE / ScoE / iron(II) and 2-oxoglutarate (Fe/2OG) dependent enzymes.
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 / : / D(-)-TARTARIC ACID / (3R)-3-[(carboxymethyl)amino]fatty acid oxygenase/decarboxylase
Similarity search - Component
Biological speciesStreptomyces coeruleorubidus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.18 Å
AuthorsChen, T.Y. / Chen, J. / Zhou, J. / Chang, W.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: Pathway from N-Alkylglycine to Alkylisonitrile Catalyzed by Iron(II) and 2-Oxoglutarate-Dependent Oxygenases.
Authors: Chen, T.Y. / Chen, J. / Tang, Y. / Zhou, J. / Guo, Y. / Chang, W.C.
History
DepositionOct 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: 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.name
Revision 1.2Nov 22, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id

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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)39,4214
Polymers39,0541
Non-polymers3673
Water4,558253
1
A: ScoE protein
hetero molecules

A: ScoE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,8428
Polymers78,1072
Non-polymers7346
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area2840 Å2
ΔGint-52 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.200, 97.200, 70.030
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number77
Space group name H-MP42
Space group name HallP4c
Symmetry operation#1: x,y,z
#2: -y,x,z+1/2
#3: y,-x,z+1/2
#4: -x,-y,z
Components on special symmetry positions
IDModelComponents
11A-753-

HOH

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Components

#1: Protein ScoE protein


Mass: 39053.664 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(DE3) (bacteria) / References: UniProt: A0A3B6UEU3
#2: Chemical ChemComp-7UC / (3~{R})-3-(2-hydroxy-2-oxoethylamino)butanoic acid


Mass: 161.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H11NO4 / 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 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O6 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / 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: 4.24 Å3/Da / Density % sol: 70.96 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 1.3M Na/K tartrate, 0.1M Tris/HCl (pH 8.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 2.18→50 Å / Num. obs: 33911 / % possible obs: 99.1 % / Redundancy: 3.7 % / Biso Wilson estimate: 35.03 Å2 / CC1/2: 0.522 / Net I/σ(I): 11.462
Reflection shellResolution: 2.18→2.22 Å / Num. unique obs: 1688 / CC1/2: 0.54

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Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6dch

6dch


Resolution: 2.18→36.93 Å / SU ML: 0.2243 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 20.6529 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.1879 1574 4.71 %
Rwork0.1704 31838 -
obs0.1712 33412 97.72 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.33 Å2
Refinement stepCycle: LAST / Resolution: 2.18→36.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2369 0 22 253 2644
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00772455
X-RAY DIFFRACTIONf_angle_d0.85613331
X-RAY DIFFRACTIONf_chiral_restr0.0532358
X-RAY DIFFRACTIONf_plane_restr0.0062441
X-RAY DIFFRACTIONf_dihedral_angle_d6.72592067
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.18-2.250.23561160.24682698X-RAY DIFFRACTION91.63
2.25-2.330.25431270.21292883X-RAY DIFFRACTION97.19
2.33-2.420.21561460.1942900X-RAY DIFFRACTION99.06
2.42-2.530.22021370.18752922X-RAY DIFFRACTION98.87
2.53-2.670.25431440.21222867X-RAY DIFFRACTION97.25
2.67-2.840.23331520.20832885X-RAY DIFFRACTION98.38
2.84-3.050.22061230.19162995X-RAY DIFFRACTION99.71
3.05-3.360.19671350.17632940X-RAY DIFFRACTION99.39
3.36-3.850.18271810.16092838X-RAY DIFFRACTION96.7
3.85-4.850.13251500.1322915X-RAY DIFFRACTION97.99
4.85-36.930.17271630.1472995X-RAY DIFFRACTION98.75

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