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- PDB-4u2h: The crystal structure of apo CalE6, a methionine gamma lyase from... -

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Basic information

Entry
Database: PDB / ID: 4u2h
TitleThe crystal structure of apo CalE6, a methionine gamma lyase from Micromonospora echinospora
ComponentsCalE6
KeywordsLYASE
Function / homology
Function and homology information


carbon-sulfur lyase activity / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
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 ...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
Biological speciesMicromonospora echinospora (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.85 Å
AuthorsSong, H.G. / Xu, R.
CitationJournal: Chembiochem / Year: 2015
Title: Identification and Characterization of a Methionine gamma-Lyase in the Calicheamicin Biosynthetic Cluster of Micromonospora echinospora
Authors: Song, H. / Xu, R. / Guo, Z.
History
DepositionJul 17, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 7, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Other / Refinement description / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_gen / pdbx_database_status / pdbx_struct_oper_list / pdbx_validate_symm_contact / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_oper_list.symmetry_operation / _pdbx_validate_symm_contact.auth_asym_id_1 / _pdbx_validate_symm_contact.auth_asym_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.dist / _pdbx_validate_symm_contact.site_symmetry_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CalE6
B: CalE6
C: CalE6
D: CalE6
E: CalE6
F: CalE6
G: CalE6
H: CalE6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)335,56324
Polymers334,0268
Non-polymers1,53716
Water46,3352572
1
A: CalE6
B: CalE6
C: CalE6
D: CalE6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,78112
Polymers167,0134
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19220 Å2
ΔGint-232 kcal/mol
Surface area44640 Å2
MethodPISA
2
E: CalE6
F: CalE6
G: CalE6
H: CalE6
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,78112
Polymers167,0134
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19140 Å2
ΔGint-231 kcal/mol
Surface area45120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.2040, 145.3950, 346.1190
Angle α, β, γ (deg.)90.0000, 90.0000, 90.0000
Int Tables number23
Space group name H-MI222

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Components

#1: Protein
CalE6 / METHIONINE GAMMA LYASE


Mass: 41753.219 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calE6 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8KNG3, methionine gamma-lyase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2572 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.73 Å3/Da / Density % sol: 55.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 0.2 M lithium sulfate, 0.1 M Bis-Tris, 25% PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9793 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.85→49.3 Å / Num. obs: 308727 / % possible obs: 99.76 % / Redundancy: 7.4 % / Net I/σ(I): 10.3

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Processing

Software
NameClassification
HKL-2000data collection
HKL-2000data processing
HKL-2000data scaling
PHENIXrefinement
PHASERphasing
Cootmodel building
RefinementResolution: 1.85→49.3 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2316 --
Rwork0.2093 --
obs-286233 99.76 %
Refinement stepCycle: LAST / Resolution: 1.85→49.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21231 0 80 2572 23883

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