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- PDB-8jui: Crystal structures of Cystathionine beta lyase from Bacillus cere... -

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Basic information

Entry
Database: PDB / ID: 8jui
TitleCrystal structures of Cystathionine beta lyase from Bacillus cereus ATCC 14579
ComponentsCystathionine beta-lyase
KeywordsLYASE / PLP dependent enzyme
Function / homology
Function and homology information


carbon-sulfur lyase activity / cystathionine beta-lyase / transsulfuration / pyridoxal phosphate binding / cytoplasm
Similarity search - Function
Cys/Met metabolism enzymes pyridoxal-phosphate attachment site. / 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
Cystathionine beta-lyase
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsYu, H. / Kim, K.-J.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2024
Title: Crystal structures of cystathionine beta-lyase and cystathionine beta-lyase like protein from Bacillus cereus ATCC 14579.
Authors: Lee, S.H. / Yu, H. / Hong, J. / Seok, J. / Kim, K.J.
History
DepositionJun 26, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 3, 2024Provider: repository / Type: Initial release
Revision 2.0Dec 18, 2024Group: Atomic model / Author supporting evidence ...Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Polymer sequence / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / citation / citation_author / entity / entity_poly / entity_poly_seq / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_gen / pdbx_struct_mod_residue / pdbx_validate_torsion / struct_asym / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.group_PDB / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.label_seq_id / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _entity_poly.nstd_monomer / _entity_poly.pdbx_seq_one_letter_code / _entity_poly_seq.mon_id / _pdbx_entity_instance_feature.auth_comp_id / _pdbx_entity_instance_feature.comp_id / _pdbx_entry_details.has_protein_modification / _pdbx_poly_seq_scheme.auth_mon_id / _pdbx_poly_seq_scheme.auth_seq_num / _pdbx_poly_seq_scheme.mon_id / _pdbx_poly_seq_scheme.pdb_mon_id / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_torsion.auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystathionine beta-lyase


Theoretical massNumber of molelcules
Total (without water)43,6451
Polymers43,6451
Non-polymers00
Water2,072115
1
A: Cystathionine beta-lyase

A: Cystathionine beta-lyase

A: Cystathionine beta-lyase

A: Cystathionine beta-lyase


Theoretical massNumber of molelcules
Total (without water)174,5814
Polymers174,5814
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_445-x-1,-y-1,z1
crystal symmetry operation7_554y,x,-z-1/31
crystal symmetry operation10_444-y-1,-x-1,-z-1/31
Buried area22540 Å2
ΔGint-100 kcal/mol
Surface area46560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)143.100, 143.100, 80.907
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein Cystathionine beta-lyase


Mass: 43645.176 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Gene: BC_4254 / Plasmid: pET28
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q818J6, cystathionine beta-lyase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 115 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 55.34 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PEG 3350, Lithium citrate tribasic tetrahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 27, 2022
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 25215 / % possible obs: 99.9 % / Redundancy: 41.6 % / CC1/2: 1 / CC star: 1 / Rmerge(I) obs: 0.069 / Rpim(I) all: 0.011 / Rrim(I) all: 0.07 / Χ2: 2.214 / Net I/σ(I): 14
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2.2-2.24420.29812340.9980.9990.0460.3021.938100
2.24-2.2842.20.28112360.99910.0440.2851.976100
2.28-2.3241.90.26312280.9970.9990.0410.2661.961100
2.32-2.3742.30.24212310.9980.9990.0380.2451.973100
2.37-2.4242.10.212390.99910.0310.2032.017100
2.42-2.4842.10.18512450.99910.0290.1882.021100
2.48-2.5442.30.17912450.99810.0280.1811.979100
2.54-2.6142.20.1512520.99910.0230.1512.109100
2.61-2.6942.60.13412350.99910.0210.1352.104100
2.69-2.7742.50.11412370.99910.0180.1162.13100
2.77-2.8742.80.10512560.99910.0160.1072.133100
2.87-2.9942.80.0912570.99910.0140.0912.148100
2.99-3.1242.80.0791256110.0120.082.185100
3.12-3.2942.80.0721250110.0110.0732.233100
3.29-3.4942.80.0621272110.010.0622.369100
3.49-3.7642.30.0561269110.0090.0562.474100
3.76-4.1441.90.0511275110.0080.0522.439100
4.14-4.7440.80.0471293110.0080.0482.493100
4.74-5.9739.80.0491322110.0080.0492.47399.9
5.97-5032.80.05513830.9980.9990.0110.0563.24297.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
MOLREPphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7D7O

7d7o


Resolution: 2.2→32.74 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.933 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.208 / ESU R Free: 0.187 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23291 1235 4.9 %RANDOM
Rwork0.18078 ---
obs0.18343 23904 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.448 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0.01 Å2-0 Å2
2---0.02 Å20 Å2
3---0.08 Å2
Refinement stepCycle: 1 / Resolution: 2.2→32.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2937 0 15 115 3067
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0133009
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172803
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.634081
X-RAY DIFFRACTIONr_angle_other_deg1.3741.576505
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8875379
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.29423.571140
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.18315510
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6321511
X-RAY DIFFRACTIONr_chiral_restr0.080.2398
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023351
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02601
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6744.1991519
X-RAY DIFFRACTIONr_mcbond_other3.6654.1961518
X-RAY DIFFRACTIONr_mcangle_it4.7786.2861897
X-RAY DIFFRACTIONr_mcangle_other4.7776.2891898
X-RAY DIFFRACTIONr_scbond_it4.6294.7171490
X-RAY DIFFRACTIONr_scbond_other4.6334.7211487
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6086.8752185
X-RAY DIFFRACTIONr_long_range_B_refined7.80950.583271
X-RAY DIFFRACTIONr_long_range_B_other7.80550.553263
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.202→2.259 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 85 -
Rwork0.223 1726 -
obs--99.67 %

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