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- PDB-6l86: The structure of SfaA -

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Basic information

Entry
Database: PDB / ID: 6l86
TitleThe structure of SfaA
ComponentsTaurine catabolism dioxygenase
KeywordsOXIDOREDUCTASE / iron(II) and 2-oxoglutarate dependent oxygenases
Function / homologyTauD/TfdA-like domain / Taurine catabolism dioxygenase TauD, TfdA family / Taurine dioxygenase TauD-like superfamily / dioxygenase activity / : / (2S)-2-hydroxybutanedioic acid / D-MALATE / Taurine catabolism dioxygenase
Function and homology information
Biological speciesStreptomyces thioluteus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.23 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
DepositionNov 5, 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.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _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: Taurine catabolism dioxygenase
B: Taurine catabolism dioxygenase
C: Taurine catabolism dioxygenase
D: Taurine catabolism dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)144,54214
Polymers143,5144
Non-polymers1,02810
Water10,503583
1
A: Taurine catabolism dioxygenase
hetero molecules

C: Taurine catabolism dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2717
Polymers71,7572
Non-polymers5145
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area2400 Å2
ΔGint-44 kcal/mol
Surface area25130 Å2
MethodPISA
2
B: Taurine catabolism dioxygenase
hetero molecules

D: Taurine catabolism dioxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,2717
Polymers71,7572
Non-polymers5145
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
Buried area2040 Å2
ΔGint-46 kcal/mol
Surface area24880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.173, 150.173, 387.859
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number155
Space group name H-MH32
Space group name HallR32"
Symmetry operation#1: x,y,z
#2: -y,x-y,z
#3: -x+y,-x,z
#4: x-y,-y,-z
#5: -x,-x+y,-z
#6: y,x,-z
#7: x+1/3,y+2/3,z+2/3
#8: -y+1/3,x-y+2/3,z+2/3
#9: -x+y+1/3,-x+2/3,z+2/3
#10: x-y+1/3,-y+2/3,-z+2/3
#11: -x+1/3,-x+y+2/3,-z+2/3
#12: y+1/3,x+2/3,-z+2/3
#13: x+2/3,y+1/3,z+1/3
#14: -y+2/3,x-y+1/3,z+1/3
#15: -x+y+2/3,-x+1/3,z+1/3
#16: x-y+2/3,-y+1/3,-z+1/3
#17: -x+2/3,-x+y+1/3,-z+1/3
#18: y+2/3,x+1/3,-z+1/3
Components on special symmetry positions
IDModelComponents
11B-527-

HOH

21B-545-

HOH

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Components

#1: Protein
Taurine catabolism dioxygenase


Mass: 35878.512 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces thioluteus (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A2H4T920
#2: Chemical
ChemComp-FE2 / FE (II) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-LMR / (2S)-2-hydroxybutanedioic acid / L-Malate


Mass: 134.087 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID


Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H6O5 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 583 / 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: 2.93 Å3/Da / Density % sol: 58.05 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / Details: 2.1M D/L-malic pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 27, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.23→50 Å / Num. obs: 82024 / % possible obs: 100 % / Redundancy: 19.6 % / Biso Wilson estimate: 30.57 Å2 / CC1/2: 0.704 / Net I/σ(I): 30.556
Reflection shellResolution: 2.23→2.27 Å / Num. unique obs: 1390 / CC1/2: 0.709

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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: 2.23→43.1 Å / SU ML: 0.2689 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 23.8584 / Stereochemistry target values: GeoStd + Monomer Library
RfactorNum. reflection% reflection
Rfree0.2281 3993 4.91 %
Rwork0.1902 77275 -
obs0.1921 81268 99.08 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.8 Å2
Refinement stepCycle: LAST / Resolution: 2.23→43.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9369 0 58 583 10010
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00239684
X-RAY DIFFRACTIONf_angle_d0.558213144
X-RAY DIFFRACTIONf_chiral_restr0.04591420
X-RAY DIFFRACTIONf_plane_restr0.00451703
X-RAY DIFFRACTIONf_dihedral_angle_d8.11075752
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.23-2.260.29161240.26272234X-RAY DIFFRACTION84.73
2.26-2.280.30861300.24562481X-RAY DIFFRACTION93.02
2.28-2.310.28681400.24352594X-RAY DIFFRACTION97.61
2.31-2.340.28881420.24672635X-RAY DIFFRACTION99.64
2.34-2.380.29471370.24672642X-RAY DIFFRACTION99.96
2.38-2.410.29051390.23222661X-RAY DIFFRACTION100
2.41-2.450.27711450.24022683X-RAY DIFFRACTION100
2.45-2.480.27721420.23732665X-RAY DIFFRACTION100
2.48-2.530.28561430.23272671X-RAY DIFFRACTION100
2.53-2.570.30111570.23012609X-RAY DIFFRACTION99.96
2.57-2.620.26841420.23092687X-RAY DIFFRACTION99.96
2.62-2.670.27551530.22982655X-RAY DIFFRACTION100
2.67-2.720.2951290.24182689X-RAY DIFFRACTION99.96
2.72-2.780.28581370.25112692X-RAY DIFFRACTION99.96
2.78-2.840.30351290.23592667X-RAY DIFFRACTION100
2.84-2.920.27721420.23512664X-RAY DIFFRACTION100
2.92-2.990.26871340.2312712X-RAY DIFFRACTION99.96
2.99-3.080.25041220.2162670X-RAY DIFFRACTION100
3.08-3.180.3021180.2262720X-RAY DIFFRACTION100
3.18-3.290.26521440.21522675X-RAY DIFFRACTION100
3.29-3.430.25881360.19672697X-RAY DIFFRACTION100
3.43-3.580.2331340.182688X-RAY DIFFRACTION100
3.58-3.770.17891150.17262724X-RAY DIFFRACTION100
3.77-4.010.21081410.15862710X-RAY DIFFRACTION100
4.01-4.320.181200.13582741X-RAY DIFFRACTION100
4.32-4.750.15171510.12792691X-RAY DIFFRACTION100
4.75-5.440.16111350.13722736X-RAY DIFFRACTION99.97
5.44-6.850.16361710.16272750X-RAY DIFFRACTION100
6.85-43.10.16291410.14962832X-RAY DIFFRACTION98.54

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