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- PDB-1cl1: CYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI -

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Basic information

Entry
Database: PDB / ID: 1cl1
TitleCYSTATHIONINE BETA-LYASE (CBL) FROM ESCHERICHIA COLI
ComponentsCYSTATHIONINE BETA-LYASE
KeywordsMETHIONINE BIOSYNTHESIS / PLP-DEPENDENT ENZYMES / C-S BETA LYASE
Function / homology
Function and homology information


L-cysteine desulfidase / L-cysteine catabolic process to pyruvate / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / alanine racemase activity / L-cysteine desulfhydrase activity / transsulfuration / methionine biosynthetic process / pyridoxal phosphate binding / protein homotetramerization ...L-cysteine desulfidase / L-cysteine catabolic process to pyruvate / cysteine-S-conjugate beta-lyase activity / cysteine-S-conjugate beta-lyase / alanine racemase activity / L-cysteine desulfhydrase activity / transsulfuration / methionine biosynthetic process / pyridoxal phosphate binding / protein homotetramerization / protein-containing complex / identical protein binding / cytoplasm
Similarity search - Function
Cystathionine beta-lyase, bacterial / : / 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, bacterial / : / 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
BICARBONATE ION / Cystathionine beta-lyase MetC
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.83 Å
AuthorsClausen, T. / Huber, R. / Messerschmidt, A.
Citation
Journal: J.Mol.Biol. / Year: 1996
Title: Crystal structure of the pyridoxal-5'-phosphate dependent cystathionine beta-lyase from Escherichia coli at 1.83 A.
Authors: Clausen, T. / Huber, R. / Laber, B. / Pohlenz, H.D. / Messerschmidt, A.
#1: Journal: FEBS Lett. / Year: 1996
Title: Cloning, Purification, and Crystallization of Escherichia Coli Cystathionine Beta-Lyase
Authors: Laber, B. / Clausen, T. / Huber, R. / Messerschmidt, A. / Egner, U. / Muller-Fahrnow, A. / Pohlenz, H.D.
History
DepositionSep 2, 1997Processing site: BNL
Revision 1.0Sep 9, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Source and taxonomy / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Other / Refinement description
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / software / struct_conn / struct_ref_seq_dif / struct_site
Item: _atom_site.Cartn_x / _atom_site.Cartn_y ..._atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site.occupancy / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _software.name / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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
B: CYSTATHIONINE BETA-LYASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1014
Polymers86,9792
Non-polymers1222
Water11,259625
1
A: CYSTATHIONINE BETA-LYASE
B: CYSTATHIONINE BETA-LYASE
hetero molecules

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


Theoretical massNumber of molelcules
Total (without water)174,2028
Polymers173,9584
Non-polymers2444
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area19240 Å2
ΔGint-94 kcal/mol
Surface area45220 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)60.900, 154.700, 152.700
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-591-

HOH

21A-660-

HOH

31B-623-

HOH

Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.997, 0.001, -0.125), (0.001, -1), (-0.125, -0.997)
Vector: 4.75, 57.71, 76.27)

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Components

#1: Protein CYSTATHIONINE BETA-LYASE / BETA CYSTATHIONASE


Mass: 43489.387 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PLP BOUND AS COFACTOR TO LYS 210 / Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: METC / Production host: Escherichia coli (E. coli) / Strain (production host): DH5 / References: UniProt: P06721, cystathionine beta-lyase
#2: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CHO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 625 / 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: 3

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Sample preparation

CrystalDensity Matthews: 2.1 Å3/Da / Density % sol: 40.49 %
Crystal growpH: 8.2 / Details: 20% PEG400, 0.15M CACL2, 0.1 M HEPES/NAOH (PH 8.2)
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop / pH: 7.3
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
15 mg/mlenzyme1drop
210-14 %PEG4001reservoir
3100 mMHEPES1reservoirpH7.3
4150 mM1reservoirCaCl2

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.07
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 1995 / Details: MIRRORS
RadiationMonochromator: SINGLE CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.07 Å / Relative weight: 1
ReflectionResolution: 1.83→15 Å / Num. obs: 58238 / % possible obs: 92.6 % / Observed criterion σ(I): 1.5 / Redundancy: 3.2 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.042 / Rsym value: 0.041
Reflection shellResolution: 1.83→1.87 Å / Redundancy: 3 % / Rmerge(I) obs: 0.21 / Rsym value: 0.23 / % possible all: 95
Reflection
*PLUS
Num. obs: 58549 / Num. measured all: 152322
Reflection shell
*PLUS
% possible obs: 95 %

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
MOSFLMdata reduction
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MIR / Resolution: 1.83→8 Å / Rfactor Rfree error: 0.019 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.221 5824 10 %RANDOM
Rwork0.151 ---
obs0.151 186362 92.6 %-
Displacement parametersBiso mean: 23.7 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å / Luzzati d res low obs: 8 Å
Refinement stepCycle: LAST / Resolution: 1.83→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5989 0 8 625 6622
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.76
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Num. reflection obs: 58549
Solvent computation
*PLUS
Displacement parameters
*PLUS

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