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- PDB-7tlr: Structure of Atopobium parvulum SufS A34Y mutant -

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Basic information

Entry
Database: PDB / ID: 7tlr
TitleStructure of Atopobium parvulum SufS A34Y mutant
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: 2.1 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)99,0564
Polymers98,5622
Non-polymers4942
Water3,099172
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6830 Å2
ΔGint-23 kcal/mol
Surface area27100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.314, 86.780, 133.438
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab

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Components

#1: Protein Cysteine desulfurase


Mass: 49280.938 Da / Num. of mol.: 2 / Mutation: A34Y
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.: 172 / 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: 2.24 Å3/Da / Density % sol: 45.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 24% 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: Nov 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.1→36.3 Å / Num. obs: 52321 / % possible obs: 99.62 % / Redundancy: 7.2 % / Biso Wilson estimate: 21.38 Å2 / CC1/2: 0.99 / Net I/σ(I): 26.1
Reflection shellResolution: 2.1→2.175 Å / Redundancy: 6.1 % / Num. unique obs: 5123 / CC1/2: 0.976 / % possible all: 99.07

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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: 2.1→36.3 Å / SU ML: 0.2133 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.492
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2506 1997 3.82 %
Rwork0.2109 50264 -
obs0.2124 52261 99.55 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.29 Å2
Refinement stepCycle: LAST / Resolution: 2.1→36.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6108 0 30 172 6310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00256275
X-RAY DIFFRACTIONf_angle_d0.57798559
X-RAY DIFFRACTIONf_chiral_restr0.04541003
X-RAY DIFFRACTIONf_plane_restr0.00381107
X-RAY DIFFRACTIONf_dihedral_angle_d5.2715886
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.150.26311370.21553456X-RAY DIFFRACTION97.34
2.15-2.210.24811410.21093550X-RAY DIFFRACTION99.81
2.21-2.270.27111420.22143559X-RAY DIFFRACTION99.97
2.27-2.350.26151410.21963526X-RAY DIFFRACTION99.08
2.35-2.430.2841400.22183554X-RAY DIFFRACTION99.92
2.43-2.530.26751410.22463564X-RAY DIFFRACTION99.6
2.53-2.640.2881430.22163588X-RAY DIFFRACTION99.95
2.64-2.780.27621420.2293570X-RAY DIFFRACTION99.87
2.78-2.960.2361430.23513591X-RAY DIFFRACTION99.76
2.96-3.190.24361420.22923599X-RAY DIFFRACTION99.97
3.19-3.510.27581430.2253607X-RAY DIFFRACTION99.52
3.51-4.010.24061440.19693623X-RAY DIFFRACTION99.76
4.01-5.060.22611460.18123659X-RAY DIFFRACTION99.61
5.06-36.30.21861520.19493818X-RAY DIFFRACTION99.55
Refinement TLS params.Method: refined / Origin x: -32.0133314139 Å / Origin y: -7.29326450651 Å / Origin z: 21.6523906551 Å
111213212223313233
T0.0492328705335 Å2-0.00140334633042 Å20.00607686377489 Å2-0.0766426883306 Å2-0.00840029982243 Å2--0.0720455936121 Å2
L0.0948794215914 °2-0.0898287624968 °20.108663300962 °2-0.723347682571 °2-0.103386036438 °2--0.612160142285 °2
S-0.0474905457654 Å °-0.031683575036 Å °0.0453203660214 Å °-0.0284472628946 Å °0.028452715254 Å °-0.0309614028687 Å °-0.0418082146744 Å °-0.0291613084578 Å °-0.047565635049 Å °
Refinement TLS groupSelection details: all

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