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- PDB-1ibj: Crystal structure of cystathionine beta-lyase from Arabidopsis th... -

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Basic information

Entry
Database: PDB / ID: 1ibj
TitleCrystal structure of cystathionine beta-lyase from Arabidopsis thaliana
ComponentsCYSTATHIONINE BETA-LYASE
KeywordsLYASE / PLP-dependent enzyme / Methionine biosynthesis / Transsulfuration
Function / homology
Function and homology information


L-methionine biosynthetic process from L-homoserine via cystathionine / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / methionine metabolic process / transsulfuration / chloroplast stroma / chloroplast / pyridoxal phosphate binding / molecular adaptor activity / protein homodimerization activity
Similarity search - Function
Cystathionine beta-lyase, eukaryotic / : / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Cystathionine beta-lyase, eukaryotic / : / Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / Cys/Met metabolism, pyridoxal phosphate-dependent enzyme / Cys/Met metabolism PLP-dependent enzyme / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / 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 / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
CARBONATE ION / PYRIDOXAL-5'-PHOSPHATE / Cystathionine beta-lyase, chloroplastic
Similarity search - Component
Biological speciesArabidopsis thaliana (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsBreitinger, U. / Clausen, T. / Messerschmidt, A.
CitationJournal: Plant Physiol. / Year: 2001
Title: The three-dimensional structure of cystathionine beta-lyase from Arabidopsis and its substrate specificity
Authors: Breitinger, U. / Clausen, T. / Ehlert, S. / Huber, R. / Laber, B. / Schmidt, F. / Pohl, E. / Messerschmidt, A.
History
DepositionMar 28, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CYSTATHIONINE BETA-LYASE
C: CYSTATHIONINE BETA-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,6917
Polymers100,9812
Non-polymers7105
Water4,558253
1
A: CYSTATHIONINE BETA-LYASE
C: CYSTATHIONINE BETA-LYASE
hetero molecules

A: CYSTATHIONINE BETA-LYASE
C: CYSTATHIONINE BETA-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)203,38314
Polymers201,9624
Non-polymers1,42110
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-x+1,y,-z+1/21
Buried area23210 Å2
ΔGint-148 kcal/mol
Surface area47230 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)107.750, 154.332, 118.763
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
DetailsTwo active dimers, related by 2-fold crystallographic symmetry, form the homotetramer.

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Components

#1: Protein CYSTATHIONINE BETA-LYASE / CBL


Mass: 50490.480 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Plasmid: PACBL1 / Production host: Escherichia coli (E. coli) / Strain (production host): JM83/PACBL1 / References: UniProt: P53780, cystathionine beta-lyase
#2: Chemical ChemComp-CO3 / CARBONATE ION


Mass: 60.009 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CO3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


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


Mass: 18.015 Da / Num. of mol.: 253 / 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: 2.44 Å3/Da / Density % sol: 49.69 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6
Details: Ammonium sulfate, Mes-NaOH, PLP, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMHEPES1drop
30.01 mMPLP1drop
5100 mMMES/NaOH1reservoir
6300 mMammonium sulfate1reservoir
4reservoir solution1drop2 micro litter

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.83 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 25, 1999
RadiationMonochromator: Si 111 Channel / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.83 Å / Relative weight: 1
ReflectionResolution: 2.3→15 Å / Num. all: 108362 / Num. obs: 102185 / % possible obs: 94.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Rsym value: 0.072 / Net I/σ(I): 22.3
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 3.1 / Num. unique all: 39111 / Rsym value: 0.141 / % possible all: 81.6
Reflection
*PLUS
Num. obs: 37727 / Num. measured all: 102185
Reflection shell
*PLUS
% possible obs: 81.6 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALAdata scaling
AMoREphasing
CNS1refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1QGN

1qgn


Resolution: 2.3→6 Å / Isotropic thermal model: Anisotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.3089 1891 -RANDOM
Rwork0.2487 ---
all0.255 43105 --
obs0.2495 37727 87.5 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.45 Å20 Å20 Å2
2--15.477 Å20 Å2
3----17.927 Å2
Refinement stepCycle: LAST / Resolution: 2.3→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5669 0 43 253 5965
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.015
X-RAY DIFFRACTIONc_angle_deg1.87
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.309 / Rfactor Rwork: 0.249
Solvent computation
*PLUS
Displacement parameters
*PLUS

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