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- PDB-6qp1: Crystal structure of the PLP-bound C-S lyase in the external aldi... -

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Basic information

Entry
Database: PDB / ID: 6qp1
TitleCrystal structure of the PLP-bound C-S lyase in the external aldimine form from Staphylococcus hominis complexed with an inhibitor, L-cycloserine.
ComponentsAminotransferase
KeywordsLYASE / pyridoxal phosphate binding / cystathionine beta-lyase / inhibitor / complex / L-cycloserine / external aldimine
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 / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-LCS / Putative C-S lyase
Similarity search - Component
Biological speciesStaphylococcus hominis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.42 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aminotransferase
B: Aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,5204
Polymers96,8572
Non-polymers6622
Water6,990388
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6290 Å2
ΔGint-31 kcal/mol
Surface area29920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.466, 115.456, 118.962
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: This sequence contains additional residues introduced by the expression vector (MGGGFA.....ENLYFQGHHHHHHHHHH)
Source: (gene. exp.) Staphylococcus hominis (bacteria) / Gene: BUZ46_10400 / Plasmid: pBADcLIC / Production host: Escherichia coli MC1061 (bacteria) / References: UniProt: A0A533IVU2*PLUS
#2: Chemical ChemComp-LCS / [5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate


Mass: 331.219 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H14N3O7P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 388 / 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: 1.97 Å3/Da / Density % sol: 37.45 %
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, Hampton Research), 20mM L-cycloserine

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 23, 2018
RadiationMonochromator: 0.9762 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.42→52.88 Å / Num. obs: 143873 / % possible obs: 99.6 % / Redundancy: 7.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.103 / Rpim(I) all: 0.039 / Rrim(I) all: 0.11 / Net I/σ(I): 9.8
Reflection shellResolution: 1.42→1.44 Å / Redundancy: 8 % / Rmerge(I) obs: 2.503 / Num. unique obs: 7011 / CC1/2: 0.331 / Rpim(I) all: 0.929 / Rrim(I) all: 2.673 / % possible all: 99.1

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
REFMAC5.8.0230refinement
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DQ6

4dq6


Resolution: 1.42→51.99 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.956 / SU B: 1.577 / SU ML: 0.059 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.071
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2189 7085 4.9 %RANDOM
Rwork0.1907 ---
obs0.1921 136702 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 394.56 Å2 / Biso mean: 22.723 Å2 / Biso min: 10.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å20 Å2
2--1.11 Å2-0 Å2
3----1.18 Å2
Refinement stepCycle: final / Resolution: 1.42→51.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6341 0 44 388 6773
Biso mean--26.77 26.83 -
Num. residues----784
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0146711
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175971
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.6559097
X-RAY DIFFRACTIONr_angle_other_deg1.0571.64513967
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1695816
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.19823.807352
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.608151151
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.511523
X-RAY DIFFRACTIONr_chiral_restr0.0860.2862
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.027561
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021343
LS refinement shellResolution: 1.42→1.457 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 526 -
Rwork0.335 9937 -
all-10463 -
obs--98.74 %

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