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- PDB-6qp2: Crystal structure of the PLP-bound C-S lyase from Staphylococcus ... -

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Basic information

Entry
Database: PDB / ID: 6qp2
TitleCrystal structure of the PLP-bound C-S lyase from Staphylococcus hominis
Components
  • Aminotransferase
  • Polyhistidine tag
KeywordsLYASE / pyridoxal phosphate binding / Cysteine-S-conjugate beta-lyase
Function / homology
Function and homology information


biosynthetic process / pyridoxal phosphate binding / lyase activity
Similarity search - Function
Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / Putative C-S lyase
Similarity search - Component
Biological speciesStaphylococcus hominis (bacteria)
unidentified (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsHerman, R. / Rudden, M. / Wilkinson, A.J. / Hanai, S. / Thomas, G.H.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research CouncilBB/N006615/1 United Kingdom
CitationJournal: Sci Rep / Year: 2020
Title: The molecular basis of thioalcohol production in human body odour.
Authors: Rudden, M. / Herman, R. / Rose, M. / Bawdon, D. / Cox, D.S. / Dodson, E. / Holden, M.T.G. / Wilkinson, A.J. / James, A.G. / Thomas, G.H.
History
DepositionFeb 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 5, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: 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 / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase
B: Aminotransferase
C: Polyhistidine tag
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,1985
Polymers97,7043
Non-polymers4942
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7080 Å2
ΔGint-38 kcal/mol
Surface area29450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.751, 113.633, 118.099
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aminotransferase


Mass: 48428.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: Contains a lysine covalently attached to a PLP molecule at position 246. In addition to the protein sequence, this entity also contains additional residues introduced by the expression ...Details: Contains a lysine covalently attached to a PLP molecule at position 246. In addition to the protein sequence, this entity also contains additional residues introduced by the expression vector. (MGGGFA.....ENLYFQGHHHHHHHHHH)
Source: (gene. exp.) Staphylococcus hominis (bacteria) / Gene: BUZ46_10400 / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A533IVU2*PLUS
#2: Protein/peptide Polyhistidine tag


Mass: 846.896 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: Polyhistidine from tag introduced by expression vector but from unknown monomer.
Source: (gene. exp.) unidentified (others) / Production host: Escherichia coli MC1061 (bacteria)
#3: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 1.88 Å3/Da / Density % sol: 34.58 % / Description: Long flat yellow shards.
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 4% Tacsimate pH 6.0, 12% PEG 3,350 (F1: PEG/ION HT)

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 15, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.6→52.4 Å / Num. obs: 97945 / % possible obs: 100 % / Redundancy: 8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.098 / Rpim(I) all: 0.037 / Rrim(I) all: 0.105 / Net I/σ(I): 11.4 / Num. measured all: 784938 / Scaling rejects: 11
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 8.2 % / Rmerge(I) obs: 2.628 / Num. unique obs: 4791 / CC1/2: 0.336 / Rpim(I) all: 0.973 / Rrim(I) all: 2.805 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0222refinement
Aimless0.5.32data scaling
PDB_EXTRACT3.24data extraction
MOLREPphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DQ6

4dq6


Resolution: 1.6→52.4 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.955 / SU B: 2.922 / SU ML: 0.094 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2318 4990 5.1 %RANDOM
Rwork0.1909 ---
obs0.193 92869 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 95.51 Å2 / Biso mean: 29.66 Å2 / Biso min: 15.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2--1.13 Å2-0 Å2
3----1.78 Å2
Refinement stepCycle: final / Resolution: 1.6→52.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6367 0 0 254 6621
Biso mean---29.65 -
Num. residues----780
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0146611
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175878
X-RAY DIFFRACTIONr_angle_refined_deg1.3641.6518958
X-RAY DIFFRACTIONr_angle_other_deg0.9571.6413745
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0115799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.93523.789351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.535151138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.7261522
X-RAY DIFFRACTIONr_chiral_restr0.0720.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027377
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021315
LS refinement shellResolution: 1.6→1.642 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 376 -
Rwork0.352 6746 -
all-7122 -
obs--99.8 %

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