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- PDB-4j0k: Tannin acyl hydrolase in complex with ethyl gallate -

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Basic information

Entry
Database: PDB / ID: 4j0k
TitleTannin acyl hydrolase in complex with ethyl gallate
ComponentsTannase
KeywordsHYDROLASE / tannin / hydrolysis
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
ethyl 3,4,5-trihydroxybenzoate / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Tannase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.05 Å
AuthorsRen, B. / Wu, M. / Wang, Q. / Peng, X. / Wen, H. / Chen, Q. / McKinstry, W.J.
CitationJournal: J.Mol.Biol. / Year: 2013
Title: Crystal structure of tannase from Lactobacillus plantarum.
Authors: Ren, B. / Wu, M. / Wang, Q. / Peng, X. / Wen, H. / McKinstry, W.J. / Chen, Q.
History
DepositionJan 31, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 24, 2022Group: Database references / Derived calculations
Category: citation / database_2 ...citation / database_2 / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Tannase
B: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)102,5998
Polymers101,6462
Non-polymers9536
Water9,494527
1
A: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,1713
Polymers50,8231
Non-polymers3482
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,4285
Polymers50,8231
Non-polymers6054
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.099, 62.734, 83.192
Angle α, β, γ (deg.)70.20, 87.10, 79.19
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Tannase


Mass: 50822.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactobacillus plantarum (bacteria) / Gene: tanLpl / Production host: Escherichia coli (E. coli) / References: UniProt: B3Y018

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Non-polymers , 5 types, 533 molecules

#2: Chemical ChemComp-EGR / ethyl 3,4,5-trihydroxybenzoate / ethyl gallate


Mass: 198.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O5
#3: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H10O3
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 527 / 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: 2.19 Å3/Da / Density % sol: 43.76 %
Crystal growTemperature: 281 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.1M tri-sodium citrate pH 5.5, 20% PEG 3000, VAPOR DIFFUSION, SITTING DROP, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionHighest resolution: 2.05 Å / Num. obs: 52480 / % possible obs: 97 % / Redundancy: 2.9 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 8.1
Reflection shellResolution: 2.05→2.16 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.396 / Mean I/σ(I) obs: 2.5 / % possible all: 96

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.05→19.892 Å / Occupancy max: 1 / Occupancy min: 0.28 / FOM work R set: 0.8079 / SU ML: 0.46 / σ(F): 1.98 / Phase error: 26.63 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2397 2663 5.08 %
Rwork0.1966 --
obs0.1988 52453 97.1 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 47.241 Å2 / ksol: 0.383 e/Å3
Displacement parametersBiso max: 100.39 Å2 / Biso mean: 27.3611 Å2 / Biso min: 9.52 Å2
Baniso -1Baniso -2Baniso -3
1-11.8658 Å2-5.2087 Å28.9124 Å2
2---11.5013 Å2-5.0029 Å2
3----0.3645 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.892 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7054 0 65 527 7646
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077353
X-RAY DIFFRACTIONf_angle_d0.93410036
X-RAY DIFFRACTIONf_dihedral_angle_d15.5522626
X-RAY DIFFRACTIONf_chiral_restr0.0651124
X-RAY DIFFRACTIONf_plane_restr0.0041313
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.05-2.08720.33271330.3005264195
2.0872-2.12730.36981490.2917254196
2.1273-2.17070.31261330.267260096
2.1707-2.21790.27521500.2522260197
2.2179-2.26940.30591430.2421261096
2.2694-2.32610.29481550.2315257097
2.3261-2.38880.30191340.2219262097
2.3888-2.4590.29371230.204264097
2.459-2.53820.22841470.2019263998
2.5382-2.62880.25661490.1903261298
2.6288-2.73380.23941510.1803266598
2.7338-2.85780.2451410.1826263898
2.8578-3.0080.22761290.1798264398
3.008-3.19580.23041310.1843264098
3.1958-3.44130.25681380.1687264998
3.4413-3.78550.2031390.1626262797
3.7855-4.32840.16771320.1599260897
4.3284-5.43480.16061430.1685261297
5.4348-19.89330.23421430.2006263498
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)
10.2837-0.0089-0.0640.72140.2930.51840.0587-0.02880.07910.1519-0.0203-0.0668-0.0823-0.0108-0.04320.2629-0.01760.02150.15010.00160.172926.6857105.142280.3327
20.47280.3769-0.34490.4182-0.16691.5031-0.00760.0066-0.0414-0.0281-0.0390.005-0.01120.00220.0570.3263-0.00490.04210.1368-0.00170.143119.892775.146670.9977
30.31870.0045-0.0960.4013-0.27971.02220.01670.05050.0233-0.01660.0251-0.07170.0335-0.0133-0.03830.284-0.01610.01150.1355-0.01510.145825.416691.152870.2757
40.28130.0947-0.22180.496-0.08770.1794-0.01860.015-0.1021-0.1208-0.008-0.11930.0544-0.0216-0.00270.06390.0244-0.01660.191100.193139.715942.004133.4135
50.9748-0.0766-0.2950.6208-0.20070.61960.01060.0811-0.0287-0.17410.01940.03760.0002-0.0265-0.05550.279-0.0390.040.1741-0.04720.20730.646571.416840.0091
60.47430.0372-0.22310.44310.16540.34520.05440.00610.0714-0.14940.0418-0.1022-0.10280.0126-0.05080.11180.00640.00210.1823-0.00030.188235.110763.68240.0282
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:228)A1 - 228
2X-RAY DIFFRACTION2chain 'A' and (resseq 243:340)A243 - 340
3X-RAY DIFFRACTION3chain 'A' and (resseq 341:469)A341 - 469
4X-RAY DIFFRACTION4chain 'B' and (resseq 1:209)B1 - 209
5X-RAY DIFFRACTION5chain 'B' and (resseq 210:311)B210 - 311
6X-RAY DIFFRACTION6chain 'B' and (resseq 312:469)B312 - 469

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