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- PDB-5b1i: Crystal structure of K42A mutant of cystathionine beta-synthase f... -

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Basic information

Entry
Database: PDB / ID: 5b1i
TitleCrystal structure of K42A mutant of cystathionine beta-synthase from Lactobacillus plantarum in a complex with L-methionine
ComponentsCystathionine beta-synthase
KeywordsLYASE / Enzyme / PLP
Function / homology
Function and homology information


cystathionine beta-synthase / cystathionine beta-synthase activity / transferase activity, transferring alkyl or aryl (other than methyl) groups / cysteine biosynthetic process from serine / cytoplasm
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 / Tryptophan synthase beta subunit-like PLP-dependent enzyme / Pyridoxal-phosphate dependent enzyme / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-AA5 / Cystathionine beta-synthase
Similarity search - Component
Biological speciesLactobacillus plantarum WCFS1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 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

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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
E: Cystathionine beta-synthase
F: Cystathionine beta-synthase
G: Cystathionine beta-synthase
H: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)270,57032
Polymers266,0068
Non-polymers4,56424
Water00
1
A: Cystathionine beta-synthase
B: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6428
Polymers66,5022
Non-polymers1,1416
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5690 Å2
ΔGint-91 kcal/mol
Surface area21760 Å2
MethodPISA
2
C: Cystathionine beta-synthase
D: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6428
Polymers66,5022
Non-polymers1,1416
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-92 kcal/mol
Surface area21710 Å2
MethodPISA
3
E: Cystathionine beta-synthase
F: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6428
Polymers66,5022
Non-polymers1,1416
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5770 Å2
ΔGint-93 kcal/mol
Surface area21750 Å2
MethodPISA
4
G: Cystathionine beta-synthase
H: Cystathionine beta-synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,6428
Polymers66,5022
Non-polymers1,1416
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5700 Å2
ΔGint-92 kcal/mol
Surface area21780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)165.940, 165.940, 259.490
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Cystathionine beta-synthase


Mass: 33250.785 Da / Num. of mol.: 8 / Mutation: K42A
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-AA5 / N-[(3-HYDROXY-2-METHYL-5-{[(TRIHYDROXYPHOSPHORANYL)OXY]METHYL}PYRIDIN-4-YL)METHYLENE]METHIONINE


Mass: 378.338 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C13H19N2O7PS
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: SO4

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.36 Å3/Da / Density % sol: 63.37 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6 / Details: lithium sulfate, ammonium sulfate, sodium citrate

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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: May 30, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.3→100 Å / Num. obs: 55046 / % possible obs: 99.9 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.072 / Net I/σ(I): 26.2
Reflection shellResolution: 3.3→3.42 Å / Redundancy: 6 % / Rmerge(I) obs: 0.498 / Mean I/σ(I) obs: 3.8 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2q3d

2q3d


Resolution: 3.3→29.98 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 5499089.78 / 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
Rfree0.283 2714 5 %RANDOM
Rwork0.238 ---
obs0.238 53762 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.9359 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 45.6 Å2
Baniso -1Baniso -2Baniso -3
1--5.36 Å20 Å20 Å2
2---5.36 Å20 Å2
3---10.71 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.51 Å0.42 Å
Luzzati d res low-5 Å
Luzzati sigma a0.61 Å0.54 Å
Refinement stepCycle: LAST / Resolution: 3.3→29.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18120 0 272 0 18392
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.211.5
X-RAY DIFFRACTIONc_mcangle_it2.142
X-RAY DIFFRACTIONc_scbond_it1.632
X-RAY DIFFRACTIONc_scangle_it2.72.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 3.3→3.51 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 456 5.3 %
Rwork0.306 8140 -
obs--95 %
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 DIFFRACTION3pme.parampme.top
X-RAY DIFFRACTION4CNS_TOPPAR/ion.paramCNS_TOPPAR/ion.top

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