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- PDB-6le4: Crystal structure of cystathionine gamma-lyase from Lactobacillus... -

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Basic information

Entry
Database: PDB / ID: 6le4
TitleCrystal structure of cystathionine gamma-lyase from Lactobacillus plantarum complexed with cystathionine
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-E9U / 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: 3.1 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 24, 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)254,48715
Polymers251,4936
Non-polymers2,9939
Water5,332296
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)169,75311
Polymers167,6624
Non-polymers2,0907
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19150 Å2
ΔGint-113 kcal/mol
Surface area43310 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)169,4688
Polymers167,6624
Non-polymers1,8064
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
Buried area18720 Å2
ΔGint-98 kcal/mol
Surface area43480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)216.568, 200.738, 114.883
Angle α, β, γ (deg.)90.000, 117.210, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11E-1249-

HOH

21E-1255-

HOH

31F-1286-

HOH

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Components

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


Mass: 41915.562 Da / Num. of mol.: 6 / Fragment: Cystathionine gamma-lyase / 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-E9U / (2~{S})-4-[(2~{R})-2-azanyl-3-oxidanyl-3-oxidanylidene-propyl]sulfanyl-2-[(~{E})-[2-methyl-3-oxidanyl-5-(phosphonooxymethyl)pyridin-4-yl]methylideneamino]butanoic acid


Mass: 451.389 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H22N3O9PS / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 296 / 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: May 30, 2014 / Details: mirros
RadiationMonochromator: SINGLE WAVELENGTH / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.083→100 Å / Num. obs: 72733 / % possible obs: 91.4 % / Redundancy: 2 % / Rmerge(I) obs: 0.142 / Rpim(I) all: 0.123 / Rrim(I) all: 0.189 / Χ2: 1.01 / Net I/σ(I): 4.1
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
3.1-3.2120.43474690.7610.3740.5750.7894.2
3.21-3.3420.34173870.8170.2940.4520.85493.6
3.34-3.4920.25774210.8940.2210.340.9493.5
3.49-3.6820.21174000.9150.1810.2790.93493.1
3.68-3.9120.17173080.9410.1470.2271.04592.4
3.91-4.2120.13573030.9590.1160.1791.06191.8
4.21-4.6320.11172430.970.0960.1471.1991
4.63-5.32.10.09871770.9780.0840.131.11390.1
5.3-6.6820.10870900.9720.0930.1430.9888.8
6.68-1002.20.06169350.990.0520.0811.18386.1

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Processing

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

4l0o


Resolution: 3.1→36.257 Å / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 27.63
RfactorNum. reflection% reflection
Rfree0.2725 3656 5.03 %
Rwork0.2457 --
obs0.2471 72703 90.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 341.95 Å2 / Biso mean: 39.3219 Å2 / Biso min: 0.77 Å2
Refinement stepCycle: final / Resolution: 3.1→36.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17208 0 189 297 17694
Biso mean--38.43 19.31 -
Num. residues----2280
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
3.1-3.12370.36461170.3085208672
3.1237-3.16650.31031270.2997277594
3.1665-3.21170.31291570.295275294
3.2117-3.25960.32341380.2946272094
3.2596-3.31050.32751360.2819273494
3.3105-3.36480.33281490.2696274894
3.3648-3.42270.24751400.2573273093
3.4227-3.48490.27171530.2537272093
3.4849-3.55190.3041400.2522269993
3.5519-3.62430.28821520.2568271593
3.6243-3.70310.27391050.2427276193
3.7031-3.78910.24241210.2437274192
3.7891-3.88380.26791580.2405267392
3.8838-3.98860.26551220.2253272192
3.9886-4.10590.24251470.2272268491
4.1059-4.23820.26381430.2302266592
4.2382-4.38940.2391650.2247265991
4.3894-4.56480.26431420.2079263591
4.5648-4.77220.22631590.215263590
4.7722-5.02320.23141450.2145263390
5.0232-5.33690.23821330.2243263390
5.3369-5.74750.26061460.2202264289
5.7475-6.32320.27051400.2418260389
6.3232-7.23180.26811440.2573257588
7.2318-9.08760.26851260.233259987
9.0876-36.2570.31211510.287250984

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