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- PDB-3wa7: Crystal structure of selenomethionine-labeled tannase from Lactob... -

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Basic information

Entry
Database: PDB / ID: 3wa7
TitleCrystal structure of selenomethionine-labeled tannase from Lactobacillus plantarum in the orthorhombic crystal
Componentstannase
KeywordsHYDROLASE / alpha/beta-hydrolase
Function / homology
Function and homology information


: / : / BD-FAE / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Tannase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsMatoba, Y. / Tanaka, N. / Sugiyama, M.
CitationJournal: Proteins / Year: 2013
Title: Crystallographic and mutational analyses of tannase from Lactobacillus plantarum.
Authors: Matoba, Y. / Tanaka, N. / Noda, M. / Higashikawa, F. / Kumagai, T. / Sugiyama, M.
History
DepositionApr 27, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 24, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2013Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,6006
Polymers52,1641
Non-polymers4355
Water6,521362
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.730, 77.820, 199.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-894-

HOH

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Components

#1: Protein tannase


Mass: 52164.184 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Strain: SN35N / Plasmid: pET-21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: B3Y018*PLUS, EC: 3.1.1.20
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 362 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsA SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.

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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: 2.07 Å3/Da / Density % sol: 40.54 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG8000, sodium acetate, ammonium sulfate , pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B2 / Wavelength: 0.9788 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: May 22, 2012
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.7→100 Å / Num. all: 42594 / Num. obs: 42594 / % possible obs: 88.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 20.6
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.159 / Mean I/σ(I) obs: 8.5 / Num. unique all: 4151 / % possible all: 60.6

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Processing

Software
NameVersionClassification
HKL-2000data collection
SHARPphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→29.91 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 5681788.29 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.193 2128 5 %RANDOM
Rwork0.167 ---
all0.168 42347 --
obs0.167 42347 87.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.4213 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 12.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.09 Å20 Å20 Å2
2--0.04 Å20 Å2
3---1.05 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.06 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 26 362 3956
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_d23.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.081.5
X-RAY DIFFRACTIONc_mcangle_it1.622
X-RAY DIFFRACTIONc_scbond_it1.882
X-RAY DIFFRACTIONc_scangle_it2.582.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.249 278 5.8 %
Rwork0.199 4536 -
obs--61.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4ace.paramace.top
X-RAY DIFFRACTION5gol.paramgol.top

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