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- PDB-7tlq: Structure of Atopobium parvulum SufS C375S -

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Basic information

Entry
Database: PDB / ID: 7tlq
TitleStructure of Atopobium parvulum SufS C375S
ComponentsCysteine desulfurase
KeywordsTRANSFERASE / Cysteine desulferase
Function / homology
Function and homology information


cysteine desulfurase / cysteine desulfurase activity / cysteine metabolic process / pyridoxal phosphate binding
Similarity search - Function
Cysteine desulfurase, SufS / Cysteine desulfurase / Aminotransferase class-V, pyridoxal-phosphate binding site / Aminotransferases class-V pyridoxal-phosphate attachment site. / Aminotransferase class V domain / Aminotransferase class-V / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Cysteine desulfurase
Similarity search - Component
Biological speciesLancefieldella parvula (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsKarunakaran, G. / Couture, J.F.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Febs Lett. / Year: 2022
Title: Structural analysis of Atopobium parvulum SufS cysteine desulfurase linked to Crohn's disease.
Authors: Karunakaran, G. / Yang, Y. / Tremblay, V. / Ning, Z. / Martin, J. / Belaouad, A. / Figeys, D. / Brunzelle, J.S. / Giguere, P.M. / Stintzi, A. / Couture, J.F.
History
DepositionJan 18, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine desulfurase
B: Cysteine desulfurase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,8404
Polymers98,3462
Non-polymers4942
Water6,287349
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7270 Å2
ΔGint-29 kcal/mol
Surface area26590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.120, 110.612, 122.343
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP22121
Space group name HallP22ab(z,x,y)

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Components

#1: Protein Cysteine desulfurase


Mass: 49172.777 Da / Num. of mol.: 2 / Mutation: C375S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lancefieldella parvula (bacteria) / Gene: Apar_0399 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C8W9P2, cysteine desulfurase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2.56 Å3/Da / Density % sol: 51.97 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 22% PEG3350, 50 mM sodium malate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: May 5, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→29.8 Å / Num. obs: 47832 / % possible obs: 97.2 % / Redundancy: 2.9 % / Biso Wilson estimate: 27.31 Å2 / CC1/2: 0.99 / Net I/σ(I): 17.1
Reflection shellResolution: 2.2→2.28 Å / Mean I/σ(I) obs: 3.9 / Num. unique obs: 2393 / CC1/2: 0.955

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
d*TREKdata scaling
PDB_EXTRACT3.27data extraction
d*TREKdata reduction
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5J8Q

5j8q


Resolution: 2.2→29.8 Å / SU ML: 0.2636 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.4939
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2413 2893 4.2 %
Rwork0.1952 65945 -
obs0.1971 47798 72.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 30.19 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6135 0 30 349 6514
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00226332
X-RAY DIFFRACTIONf_angle_d0.55678665
X-RAY DIFFRACTIONf_chiral_restr0.04311020
X-RAY DIFFRACTIONf_plane_restr0.0041126
X-RAY DIFFRACTIONf_dihedral_angle_d5.6669902
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2-2.230.2875860.23281954X-RAY DIFFRACTION45.2
2.23-2.270.2904920.23212131X-RAY DIFFRACTION49.19
2.27-2.310.3107970.22282223X-RAY DIFFRACTION51.46
2.31-2.360.2631030.21232342X-RAY DIFFRACTION54.01
2.36-2.410.25631070.20932417X-RAY DIFFRACTION55.95
2.41-2.460.24551110.20892509X-RAY DIFFRACTION57.84
2.46-2.520.2571090.19962622X-RAY DIFFRACTION61.22
2.52-2.580.23961230.19412868X-RAY DIFFRACTION65.64
2.58-2.650.19491340.20822964X-RAY DIFFRACTION68.6
2.65-2.730.24931420.20833147X-RAY DIFFRACTION72.86
2.73-2.820.26791470.19933361X-RAY DIFFRACTION77.96
2.82-2.920.27091630.20853562X-RAY DIFFRACTION82.74
2.92-3.030.25991520.20493736X-RAY DIFFRACTION85.81
3.03-3.170.26541720.2063817X-RAY DIFFRACTION88.37
3.17-3.340.28451690.21093817X-RAY DIFFRACTION88.4
3.34-3.550.22721590.21283808X-RAY DIFFRACTION87.34
3.55-3.820.26991650.18893816X-RAY DIFFRACTION88.21
3.82-4.20.22561700.18263761X-RAY DIFFRACTION87.3
4.2-4.810.19451740.16253785X-RAY DIFFRACTION87.69
4.81-6.050.21431580.1843743X-RAY DIFFRACTION86.44
6.05-29.80.22211600.1813562X-RAY DIFFRACTION82.31
Refinement TLS params.Method: refined / Origin x: 17.5255447009 Å / Origin y: 23.594227358 Å / Origin z: 28.1017908651 Å
111213212223313233
T0.161233826827 Å2-9.52073845241E-5 Å20.0226931333655 Å2-0.129458690518 Å20.00154297427234 Å2--0.166903118117 Å2
L0.727580758634 °20.0779652118788 °20.329544008373 °2-0.20613832871 °20.00282111333755 °2--0.829715662622 °2
S-0.0641848488241 Å °0.0251250473631 Å °0.00728646021325 Å °-0.00293189086149 Å °-0.0182059256954 Å °-0.00266339097603 Å °0.00695428530304 Å °0.0412902011342 Å °-6.7287633475E-5 Å °
Refinement TLS groupSelection details: all

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