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- PDB-5xw3: Crystal structure of cystathionine beta-synthase from Bacillus an... -

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Basic information

Entry
Database: PDB / ID: 5xw3
TitleCrystal structure of cystathionine beta-synthase from Bacillus anthracis
ComponentsO-acetylserine lyase
KeywordsLYASE / cystathionine beta synthase
Function / homology
Function and homology information


transferase activity, transferring alkyl or aryl (other than methyl) groups / cysteine biosynthetic process from serine / lyase activity
Similarity search - Function
Cysteine synthase/cystathionine beta-synthase, pyridoxal-phosphate attachment site / Cysteine synthase/cystathionine beta-synthase P-phosphate attachment site. / : / Rossmann fold - #1100 / Pyridoxal-phosphate dependent enzyme / Pyridoxal-phosphate dependent enzyme / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
O-acetylserine lyase / O-acetylserine lyase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.17 Å
AuthorsDevi, S. / Tarique, K.F. / Abdul Rehman, S.A. / Gourinath, S.
Funding support India, 1items
OrganizationGrant numberCountry
Department of Biotechnology, Govt. of India India
CitationJournal: FEBS J. / Year: 2017
Title: Structural characterization and functional analysis of cystathionine beta-synthase: an enzyme involved in the reverse transsulfuration pathway of Bacillus anthracis.
Authors: Devi, S. / Abdul Rehman, S.A. / Tarique, K.F. / Gourinath, S.
History
DepositionJun 29, 2017Deposition site: PDBJ / Processing site: PDBJ
SupersessionAug 2, 2017ID: 4QL4
Revision 1.0Aug 2, 2017Provider: repository / Type: Initial release
Revision 1.1Aug 16, 2017Group: Database references / Category: pdbx_related_exp_data_set
Revision 1.2Nov 15, 2017Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.4Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: O-acetylserine lyase
B: O-acetylserine lyase


Theoretical massNumber of molelcules
Total (without water)68,4252
Polymers68,4252
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-22 kcal/mol
Surface area21540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.452, 69.452, 129.670
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein O-acetylserine lyase / cystathionine beta-synthase


Mass: 34212.738 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: cysM, GBAA_4601 / Plasmid: pET21c / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q81LL5, UniProt: A0A6L8PXK0*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / 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: 2.64 Å3/Da / Density % sol: 53.39 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.9
Details: 6% PEG 8000, 12% ethylene glycol, 0.02 M glycine, 0.02 M DL-lysine, 0.02 M DL-serine, 0.02 M DL-alanine and 0.02 M sodium L-glutamate, 0.1 M MES/imidazole pH 6.9

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.978 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: Feb 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.17→50 Å / Num. obs: 37009 / % possible obs: 100 % / Redundancy: 11.6 % / Net I/σ(I): 46.8
Reflection shellResolution: 2.17→2.25 Å / Redundancy: 11.1 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3682 / CC1/2: 0.861 / Rpim(I) all: 0.281 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.7.3_928refinement
HKL-2000data reduction
HKL-2000data scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD / Resolution: 2.17→35.1 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 30.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2567 1761 4.77 %
Rwork0.2228 --
obs0.2245 36942 99.88 %
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 49.511 Å2 / ksol: 0.352 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.4394 Å20 Å20 Å2
2--3.4394 Å20 Å2
3----6.8789 Å2
Refinement stepCycle: LAST / Resolution: 2.17→35.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3890 0 0 37 3927
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0083979
X-RAY DIFFRACTIONf_angle_d1.0785399
X-RAY DIFFRACTIONf_dihedral_angle_d13.8471429
X-RAY DIFFRACTIONf_chiral_restr0.066635
X-RAY DIFFRACTIONf_plane_restr0.005699
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1701-2.22870.45091380.3922698X-RAY DIFFRACTION100
2.2287-2.29430.39131100.36322755X-RAY DIFFRACTION100
2.2943-2.36830.39421580.30622648X-RAY DIFFRACTION100
2.3683-2.4530.3211040.25992772X-RAY DIFFRACTION100
2.453-2.55120.32721320.23912672X-RAY DIFFRACTION100
2.5512-2.66720.24561440.23812729X-RAY DIFFRACTION100
2.6672-2.80780.2881220.2362695X-RAY DIFFRACTION100
2.8078-2.98360.35531220.25282711X-RAY DIFFRACTION100
2.9836-3.21380.32751500.25272732X-RAY DIFFRACTION100
3.2138-3.5370.25631850.23062653X-RAY DIFFRACTION100
3.537-4.04820.23771300.20062696X-RAY DIFFRACTION100
4.0482-5.09770.18821520.17632699X-RAY DIFFRACTION100
5.0977-35.10470.2271140.20732721X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.0888-0.36131.06491.69660.00453.50440.093-0.29410.0742-0.1561-0.1127-0.43410.1140.7356-0.01010.22330.01340.02850.56580.02920.44230.91613.0681-17.6028
22.1981-0.320.75541.6423-1.02643.38120.1396-0.15270.414-0.298-0.15270.1405-0.6093-0.4209-0.01860.50870.1625-0.00340.3239-0.04630.4621-23.828627.4043-24.5524
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:294)
2X-RAY DIFFRACTION2(chain B and resseq 1:294)

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