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- PDB-6ldo: Crystal structure of cystathionine gamma-lyase from Lactobacillus... -

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Basic information

Entry
Database: PDB / ID: 6ldo
TitleCrystal structure of cystathionine gamma-lyase from Lactobacillus plantarum complexed with L-serine
ComponentsCystathionine gamma-lyase
KeywordsLYASE / cystathionine gamma-lyase
Function / homology
Function and homology information


: / cystathionine beta-lyase / cystathionine gamma-lyase / cystathionine gamma-synthase activity / cystathionine gamma-lyase activity / cysteine biosynthetic process via cystathionine / transsulfuration / methionine biosynthetic process / transaminase activity / pyridoxal phosphate binding ...: / cystathionine beta-lyase / cystathionine gamma-lyase / cystathionine gamma-synthase activity / cystathionine gamma-lyase activity / cysteine biosynthetic process via cystathionine / transsulfuration / methionine biosynthetic process / transaminase activity / pyridoxal phosphate binding / lyase activity / cytoplasm
Similarity search - Function
Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
Chem-KOU / PHOSPHATE ION / Aminotransferase class V-fold PLP-dependent enzyme / Cystathionine beta-lyase / cystathionine gamma-lyase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.75 Å
AuthorsOda, K. / Matoba, Y.
CitationJournal: Sci Rep / Year: 2020
Title: Catalytic specificity of the Lactobacillus plantarum cystathionine gamma-lyase presumed by the crystallographic analysis.
Authors: Matoba, Y. / Noda, M. / Yoshida, T. / Oda, K. / Ezumi, Y. / Yasutake, C. / Izuhara-Kihara, H. / Danshiitsoodol, N. / Kumagai, T. / Sugiyama, M.
History
DepositionNov 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 7, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: 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

Downloads & links

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Assembly

Deposited unit
A: Cystathionine gamma-lyase
B: Cystathionine gamma-lyase
C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase
E: Cystathionine gamma-lyase
F: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)254,82826
Polymers251,4936
Non-polymers3,33520
Water11,926662
1
A: Cystathionine gamma-lyase
B: Cystathionine gamma-lyase
C: Cystathionine gamma-lyase
D: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,94918
Polymers167,6624
Non-polymers2,28714
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20820 Å2
ΔGint-162 kcal/mol
Surface area43390 Å2
MethodPISA
2
E: Cystathionine gamma-lyase
F: Cystathionine gamma-lyase
hetero molecules

E: Cystathionine gamma-lyase
F: Cystathionine gamma-lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)169,75916
Polymers167,6624
Non-polymers2,09712
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area20630 Å2
ΔGint-146 kcal/mol
Surface area43410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)217.412, 201.149, 113.938
Angle α, β, γ (deg.)90.000, 117.390, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-516-

HOH

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Components

#1: Protein
Cystathionine gamma-lyase / Cystathionine gamma-synthase


Mass: 41915.562 Da / Num. of mol.: 6 / Mutation: K194A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Gene: BIZ32_00995, Nizo2891_3187 / Plasmid: pET21 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A162EFJ4, UniProt: F9UT53*PLUS
#2: Chemical
ChemComp-KOU / (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine


Mass: 334.219 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H15N2O8P / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 662 / 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: 4.42 Å3/Da / Density % sol: 72.14 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4 / Details: KH2PO4, NaH2PO4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 25, 2014
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.743→100 Å / Num. obs: 112736 / % possible obs: 99.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.065 / Rrim(I) all: 0.127 / Χ2: 1.006 / Net I/σ(I): 6.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.75-2.853.80.436112680.8640.260.5080.685100
2.85-2.963.80.349112290.9070.2070.4070.731100
2.96-3.13.80.286112590.9350.170.3330.753100
3.1-3.263.80.201112680.9650.1190.2340.827100
3.26-3.463.80.142112500.9790.0850.1660.928100
3.46-3.733.80.11112370.9870.0660.1291.0399.9
3.73-4.113.80.088112990.9910.0520.1021.21699.9
4.11-4.73.70.073112580.9920.0440.0861.46399.9
4.7-5.923.70.064113160.9940.0390.0751.20899.9
5.92-1003.70.047113520.9970.0280.0551.25699.4

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
SCALEPACKv1.0data scaling
PDB_EXTRACT3.25data extraction
HKL-2000v1.0data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdbid 4L0O

4l0o


Resolution: 2.75→35.682 Å / SU ML: 0.29 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.66
RfactorNum. reflection% reflection
Rfree0.2018 5634 5 %
Rwork0.1612 --
obs0.1632 112712 99.39 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 257.65 Å2 / Biso mean: 42.2282 Å2 / Biso min: 16.86 Å2
Refinement stepCycle: final / Resolution: 2.75→35.682 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17256 0 202 662 18120
Biso mean--54.6 38.62 -
Num. residues----2286
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.75-2.77370.2931630.241295983
2.7737-2.80640.30591880.22883582100
2.8064-2.84060.28071990.22043602100
2.8406-2.87650.27271950.21233508100
2.8765-2.91430.28091860.20683628100
2.9143-2.95420.23911720.20323608100
2.9542-2.99640.23142000.20543577100
2.9964-3.04110.26371880.19633544100
3.0411-3.08860.22591920.19433595100
3.0886-3.13920.24572120.18933589100
3.1392-3.19330.23431880.19123543100
3.1933-3.25140.21311870.17983588100
3.2514-3.31390.22861770.17453593100
3.3139-3.38140.20491900.16363579100
3.3814-3.45490.20031990.15883611100
3.4549-3.53520.21651510.15923569100
3.5352-3.62350.21962190.15423565100
3.6235-3.72140.19691760.15093602100
3.7214-3.83080.18121940.14773587100
3.8308-3.95430.17541950.14553593100
3.9543-4.09540.17071960.1363578100
4.0954-4.25910.17841890.13483592100
4.2591-4.45260.15451930.12693575100
4.4526-4.68690.16451880.12363594100
4.6869-4.97980.16251950.12753606100
4.9798-5.36310.16171810.13593598100
5.3631-5.90070.17051830.14453597100
5.9007-6.74950.22051840.16573633100
6.7495-8.48480.17661780.14833617100
8.4848-35.6820.19951760.1767366699

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