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

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Basic information

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


cysteine-S-conjugate beta-lyase / L-aspartate:2-oxoglutarate aminotransferase activity / biosynthetic process / pyridoxal phosphate binding / lyase activity
Similarity search - Function
: / Putative C-S lyase / Aminotransferase, class I/classII / Aminotransferase class I and II / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase
Similarity search - Domain/homology
PYRIDOXAL-5'-PHOSPHATE / cysteine-S-conjugate beta-lyase
Similarity search - Component
Biological speciesBacillus cereus ATCC 14579 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 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 1.1Dec 18, 2024Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._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 / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Aspartate aminotransferase
B: Aspartate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)91,0984
Polymers90,6032
Non-polymers4942
Water4,143230
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, dimer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-37 kcal/mol
Surface area28080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.670, 85.233, 167.965
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Aspartate aminotransferase


Mass: 45301.645 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus cereus ATCC 14579 (bacteria) / Gene: BC_4906 / Plasmid: pET28
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q816F3
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 230 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.08 Å3/Da / Density % sol: 40.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: PET3350, Magnesium formate dihydrate

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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: Apr 12, 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: 1.99→50 Å / Num. obs: 50383 / % possible obs: 95.7 % / Redundancy: 11.7 % / CC1/2: 0.996 / CC star: 0.999 / Rmerge(I) obs: 0.079 / Rpim(I) all: 0.024 / Rrim(I) all: 0.083 / Χ2: 2.489 / Net I/σ(I): 13.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2CC starRpim(I) allRrim(I) allΧ2% possible all
2-2.0311.90.29923710.9750.9940.0880.3132.09790.5
2.03-2.0711.90.25123420.9810.9950.0740.2632.11992
2.07-2.1111.80.22723650.9860.9960.0670.2372.18790.9
2.11-2.1511.80.20523710.9860.9960.060.2142.24291.8
2.15-2.211.80.18223910.990.9970.0540.192.26191.1
2.2-2.2511.70.17224110.990.9970.0510.182.2593.6
2.25-2.3111.60.16224150.9910.9980.0480.1692.33992.2
2.31-2.3711.60.14724180.9930.9980.0440.1532.36493.7
2.37-2.4411.50.1424400.9940.9980.0420.1462.34193.7
2.44-2.5211.40.12725060.9940.9980.0380.1332.39794.5
2.52-2.6111.40.11624650.9940.9990.0350.1222.44396.7
2.61-2.7111.20.10225650.9960.9990.0310.1072.52497.6
2.71-2.8411.30.09425810.9960.9990.0290.0982.50899
2.84-2.9911.30.08226020.9970.9990.0250.0862.52299.3
2.99-3.1711.50.07326310.9970.9990.0220.0772.63799.7
3.17-3.4211.70.06626520.9980.9990.020.0692.73999.9
3.42-3.7611.80.05926650.9980.9990.0180.0612.902100
3.76-4.3112.20.05426620.99910.0160.0572.95499.8
4.31-5.4312.80.05227130.99910.0150.0542.81699.6
5.43-5011.90.05328170.99810.0160.0562.81998.2

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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: 6QP3

6qp3


Resolution: 1.99→33.15 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.909 / SU B: 4.206 / SU ML: 0.118 / Cross valid method: THROUGHOUT / ESU R: 0.209 / ESU R Free: 0.179 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23929 2488 5 %RANDOM
Rwork0.19257 ---
obs0.19493 47707 95.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.305 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3----0.05 Å2
Refinement stepCycle: 1 / Resolution: 1.99→33.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6004 0 32 230 6266
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136192
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175652
X-RAY DIFFRACTIONr_angle_refined_deg1.5411.6418425
X-RAY DIFFRACTIONr_angle_other_deg1.3091.56413162
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0925737
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.98123.406323
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.923151063
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7111528
X-RAY DIFFRACTIONr_chiral_restr0.0730.2832
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.026834
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021264
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_it1.6761.9762954
X-RAY DIFFRACTIONr_mcbond_other1.6751.9762953
X-RAY DIFFRACTIONr_mcangle_it2.4632.9553689
X-RAY DIFFRACTIONr_mcangle_other2.4632.9553690
X-RAY DIFFRACTIONr_scbond_it2.5092.3373238
X-RAY DIFFRACTIONr_scbond_other2.4982.3363235
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.8943.3874737
X-RAY DIFFRACTIONr_long_range_B_refined8.37224.0726968
X-RAY DIFFRACTIONr_long_range_B_other8.37624.0536951
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.993→2.044 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.284 168 -
Rwork0.207 3301 -
obs--89.99 %

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