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- PDB-6qp3: Crystal structure of the PLP-bound C-S lyase from Bacillus subtil... -

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Basic information

Entry
Database: PDB / ID: 6qp3
TitleCrystal structure of the PLP-bound C-S lyase from Bacillus subtilis (strain 168)
ComponentsCystathionine beta-lyase PatB
KeywordsLYASE / pyridoxal phosphate binding / Cysteine-S-conjugate beta-lyase
Function / homology
Function and homology information


cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / methionine biosynthetic process / pyridoxal phosphate binding
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
ACETATE ION / PYRIDOXAL-5'-PHOSPHATE / Cystathionine beta-lyase PatB
Similarity search - Component
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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: Cystathionine beta-lyase PatB
B: Cystathionine beta-lyase PatB
C: Cystathionine beta-lyase PatB
D: Cystathionine beta-lyase PatB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)172,58012
Polymers171,3554
Non-polymers1,2258
Water1,51384
1
A: Cystathionine beta-lyase PatB
D: Cystathionine beta-lyase PatB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2906
Polymers85,6782
Non-polymers6124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6480 Å2
ΔGint-18 kcal/mol
Surface area27200 Å2
MethodPISA
2
B: Cystathionine beta-lyase PatB
C: Cystathionine beta-lyase PatB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,2906
Polymers85,6782
Non-polymers6124
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6550 Å2
ΔGint-17 kcal/mol
Surface area26960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.279, 105.526, 209.576
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
Cystathionine beta-lyase PatB / CBL / Beta-cystathionase PatB / Cysteine lyase PatB / Cysteine-S-conjugate beta-lyase PatB


Mass: 42838.805 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (strain 168) (bacteria)
Strain: 168 / Gene: patB, BSU31440 / Production host: Escherichia coli MC1061 (bacteria)
References: UniProt: Q08432, cysteine-S-conjugate beta-lyase
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 84 / 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: 2.42 Å3/Da / Density % sol: 49.09 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 7.1 / Details: 0.2M Ammonium acetate, 20% PEG 3,350, pH 7.1 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 120 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 18, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.3→61.28 Å / Num. obs: 72159 / % possible obs: 96.1 % / Redundancy: 7.9 % / CC1/2: 0.991 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.071 / Rrim(I) all: 0.21 / Net I/σ(I): 8.7
Reflection shellResolution: 2.3→2.35 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.195 / Num. unique obs: 3803 / CC1/2: 0.574 / Rpim(I) all: 0.479 / Rrim(I) all: 1.295 / % possible all: 82.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
Aimless0.7.3data scaling
PDB_EXTRACT3.24data extraction
MOLREPphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DQ6

4dq6


Resolution: 2.3→61.28 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.894 / SU B: 10.48 / SU ML: 0.236 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.387 / ESU R Free: 0.257
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.257 3601 5 %RANDOM
Rwork0.2076 ---
obs0.2101 68417 95.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 124.43 Å2 / Biso mean: 27.599 Å2 / Biso min: 11.45 Å2
Baniso -1Baniso -2Baniso -3
1-3.07 Å20 Å20 Å2
2---1.41 Å20 Å2
3----1.66 Å2
Refinement stepCycle: final / Resolution: 2.3→61.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12074 0 16 84 12174
Biso mean--44.14 21.88 -
Num. residues----1545
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.01312373
X-RAY DIFFRACTIONr_bond_other_d0.0010.01711436
X-RAY DIFFRACTIONr_angle_refined_deg1.6521.6416767
X-RAY DIFFRACTIONr_angle_other_deg1.2591.57526599
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.651541
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.92522.973592
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.358152096
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.9651560
X-RAY DIFFRACTIONr_chiral_restr0.0720.21585
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213787
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022509
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.311 226 -
Rwork0.301 4347 -
all-4573 -
obs--83.33 %

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