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- PDB-5b1h: Crystal structure of cystathionine beta-synthase from Lactobacill... -

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Basic information

Entry
Database: PDB / ID: 5b1h
TitleCrystal structure of cystathionine beta-synthase from Lactobacillus plantarum
ComponentsCystathionine beta-synthase
KeywordsLYASE / Enzyme / PLP
Function / homology
Function and homology information


cystathionine beta-synthase activity / cysteine synthase / transferase activity, transferring alkyl or aryl (other than methyl) groups / cysteine biosynthetic process from serine
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
Biological speciesLactobacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsMatoba, Y. / Sugiyama, M.
CitationJournal: Protein Sci. / Year: 2017
Title: Crystallographic and mutational analyses of cystathionine beta-synthase in the H2 S-synthetic gene cluster in Lactobacillus plantarum
Authors: Matoba, Y. / Yoshida, T. / Izuhara-Kihara, H. / Noda, M. / Sugiyama, M.
History
DepositionDec 4, 2015Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Database references
Revision 1.2Apr 5, 2017Group: Database references
Revision 1.3Feb 26, 2020Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cystathionine beta-synthase
B: Cystathionine beta-synthase
C: Cystathionine beta-synthase
D: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)136,59030
Polymers134,1484
Non-polymers2,44226
Water7,314406
1
A: Cystathionine beta-synthase
C: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,48717
Polymers67,0742
Non-polymers1,41315
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6650 Å2
ΔGint-151 kcal/mol
Surface area22510 Å2
MethodPISA
2
B: Cystathionine beta-synthase
hetero molecules

B: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,19514
Polymers67,0742
Non-polymers1,12112
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area5650 Å2
ΔGint-87 kcal/mol
Surface area22680 Å2
MethodPISA
3
D: Cystathionine beta-synthase
hetero molecules

D: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,01112
Polymers67,0742
Non-polymers93710
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_553-x,y,-z-21
Buried area4950 Å2
ΔGint-89 kcal/mol
Surface area22830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)139.890, 146.340, 82.790
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Cystathionine beta-synthase


Mass: 33537.008 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum WCFS1 (bacteria)
Strain: WCFS1 / Gene: cbs, lp_0256 / Plasmid: pET-21a(+) / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: F9UT54, cystathionine beta-synthase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 3.16 Å3/Da / Density % sol: 61.06 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8 / Details: lithium sulfate, hepes

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 21, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.39→100 Å / Num. obs: 62935 / % possible obs: 97.6 % / Redundancy: 3.4 % / Biso Wilson estimate: 42.4 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 19.8
Reflection shellResolution: 2.39→2.48 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.412 / Mean I/σ(I) obs: 2 / % possible all: 85

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Processing

Software
NameVersionClassification
CNS1.2refinement
AMoREdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2Q3D

2q3d


Resolution: 2.4→29.49 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3284001.65 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.221 3155 5 %RANDOM
Rwork0.189 ---
obs0.189 62494 96.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 69.557 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 52.5 Å2
Baniso -1Baniso -2Baniso -3
1--9.1 Å20 Å27.06 Å2
2---12.33 Å20 Å2
3---21.43 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.29 Å
Refinement stepCycle: 1 / Resolution: 2.4→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9040 0 240 406 9686
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.5
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.69
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.371.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.122.5
LS refinement shellResolution: 2.39→2.54 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.334 379 4.6 %
Rwork0.3 7917 -
obs--75.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep-3.paramtophcsdx-3.pro
X-RAY DIFFRACTION2CNS_TOPPAR/water_rep.paramCNS_TOPPAR/water.top
X-RAY DIFFRACTION3gol.paramgol.top
X-RAY DIFFRACTION4CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top

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