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- PDB-7q6y: The X-ray crystal structure of CbTan2, a tannase enzyme from Clos... -

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Basic information

Entry
Database: PDB / ID: 7q6y
TitleThe X-ray crystal structure of CbTan2, a tannase enzyme from Clostridium butyricum
ComponentsAlpha/beta hydrolase
KeywordsHYDROLASE / Tannase / Serine hydrolase / Gallate / Tannic acid
Function / homology: / : / BD-FAE / Alpha/Beta hydrolase fold / DI(HYDROXYETHYL)ETHER / Alpha/beta hydrolase
Function and homology information
Biological speciesClostridium butyricum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.22 Å
AuthorsColeman, T. / Mazurkewich, S. / Larsbrink, J.
Funding support Sweden, 3items
OrganizationGrant numberCountry
Swedish Energy Agency2018-004339 Sweden
Swedish Research Council2018-004339 Sweden
Carl Trygger FoundationCTS 19:195 Sweden
Citation
Journal: J.Biol.Chem. / Year: 2022
Title: Structural diversity and substrate preferences of three tannase enzymes encoded by the anaerobic bacterium Clostridium butyricum.
Authors: Ristinmaa, A.S. / Coleman, T. / Cesar, L. / Langborg Weinmann, A. / Mazurkewich, S. / Branden, G. / Hasani, M. / Larsbrink, J.
#1: Journal: J.Biol.Chem. / Year: 2022
Title: The X-ray crystal structure of CbTan2, a tannase enzyme from Clostridium butyricum
Authors: Coleman, T. / Mazurkewich, S.
History
DepositionNov 9, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 2, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 3, 2022Group: Database references / Category: citation / citation_author
Revision 1.2Jan 31, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Alpha/beta hydrolase
B: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)111,14718
Polymers109,9342
Non-polymers1,21316
Water4,107228
1
A: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,82612
Polymers54,9671
Non-polymers85911
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Alpha/beta hydrolase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3216
Polymers54,9671
Non-polymers3545
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)90.675, 95.003, 131.586
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein Alpha/beta hydrolase / CbTan2


Mass: 54966.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Clostridium butyricum (bacteria) / Gene: CBLFYP62_01769, FF104_18625 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6M0U600
#2: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Formula: C4H10O3
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: isolated from a natural source / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationY

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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: 2.58 Å3/Da / Density % sol: 52.28 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 0.2 M calcium chloride dihydrate 0.1 M sodium acetate, pH 5.0 20 % PEG 6,000 25 mg/mL protein
PH range: 4.75-5.75 / Temp details: 25 C

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8731 Å
DetectorType: DECTRIS PILATUS3 X 2M / Detector: PIXEL / Date: Sep 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8731 Å / Relative weight: 1
ReflectionResolution: 2.22→46.45 Å / Num. obs: 56815 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 43.04 Å2 / Rmerge(I) obs: 0.196 / Net I/σ(I): 11.93
Reflection shellResolution: 2.22→2.3 Å / Redundancy: 13.5 % / Rmerge(I) obs: 2.463 / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5560 / % possible all: 99.7

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4J0C

4j0c


Resolution: 2.22→46.45 Å / SU ML: 0.334 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.825
Stereochemistry target values: GEOSTD + MONOMER LIBRARY + CDL V1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.257 1993 3.51 %Random selection, 5%
Rwork0.2 ---
obs0.202 56785 99.9 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54.34 Å2
Refinement stepCycle: LAST / Resolution: 2.22→46.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7353 0 79 228 7660
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087593
X-RAY DIFFRACTIONf_angle_d0.91610226
X-RAY DIFFRACTIONf_dihedral_angle_d17.3992833
X-RAY DIFFRACTIONf_chiral_restr0.0571098
X-RAY DIFFRACTIONf_plane_restr0.0071323
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.22-2.280.40151390.35783843X-RAY DIFFRACTION100
2.28-2.340.37341420.32893847X-RAY DIFFRACTION100
2.34-2.410.39771310.30273855X-RAY DIFFRACTION100
2.41-2.480.31381470.27573883X-RAY DIFFRACTION100
2.48-2.570.31121360.25973893X-RAY DIFFRACTION100
2.57-2.680.29411460.23993861X-RAY DIFFRACTION100
2.68-2.80.33461440.24483890X-RAY DIFFRACTION100
2.8-2.940.28751380.2263880X-RAY DIFFRACTION100
2.94-3.130.28081460.21993917X-RAY DIFFRACTION100
3.13-3.370.24841410.18753905X-RAY DIFFRACTION100
3.37-3.710.26951430.18363915X-RAY DIFFRACTION100
3.71-4.250.21231430.16353956X-RAY DIFFRACTION100
4.25-5.350.19651460.15013992X-RAY DIFFRACTION100
5.35-46.450.2251510.18054155X-RAY DIFFRACTION100

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