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- PDB-4jui: crystal structure of tannase from from Lactobacillus plantarum -

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Basic information

Entry
Database: PDB / ID: 4jui
Titlecrystal structure of tannase from from Lactobacillus plantarum
ComponentsTannase
KeywordsHYDROLASE / gallate / hydrolysis / tannins
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: 1.7 Å
AuthorsRen, B. / Wu, M. / Wang, Q. / Peng, X. / Wen, H. / McKinstry, W.J. / Chen, Q.
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
DepositionMar 24, 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

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Assembly

Deposited unit
A: Tannase
B: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,35415
Polymers101,6142
Non-polymers1,74013
Water20,3931132
1
A: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,7748
Polymers50,8071
Non-polymers9677
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5807
Polymers50,8071
Non-polymers7736
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.212, 62.943, 84.412
Angle α, β, γ (deg.)70.66, 85.49, 79.51
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: 50806.883 Da / Num. of mol.: 2 / Mutation: S163A
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, 1145 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-PG4 / TETRAETHYLENE GLYCOL


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


Mass: 106.120 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1132 / 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: 2.29 Å3/Da / Density % sol: 46.29 %
Crystal growTemperature: 281 K / Method: vapor diffusion / pH: 5.5
Details: 20% (w/v) PEG 3000, 0.1M tri-sodium citrate pH 5.5, VAPOR DIFFUSION, temperature 281K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.7→65 Å / Num. all: 99532 / Num. obs: 90575 / % possible obs: 91 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.5 % / Rmerge(I) obs: 0.051 / Net I/σ(I): 23.3
Reflection shellResolution: 1.7→1.79 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 4.9 / % possible all: 83.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.8.1_1168)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→19.523 Å / Occupancy max: 1 / Occupancy min: 0.24 / FOM work R set: 0.8858 / SU ML: 0.16 / σ(F): 1.97 / Phase error: 18.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1796 1530 1.69 %RANDOM
Rwork0.1528 ---
all0.1533 99532 --
obs0.1533 90551 91.37 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 154.33 Å2 / Biso mean: 20.8356 Å2 / Biso min: 3.61 Å2
Refinement stepCycle: LAST / Resolution: 1.7→19.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7172 0 117 1132 8421
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067533
X-RAY DIFFRACTIONf_angle_d1.05810264
X-RAY DIFFRACTIONf_dihedral_angle_d14.3132707
X-RAY DIFFRACTIONf_chiral_restr0.0711147
X-RAY DIFFRACTIONf_plane_restr0.0041340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.7-1.75480.25291240.1904733883
1.7548-1.81750.21851300.1851749785
1.8175-1.89020.24791260.1754760986
1.8902-1.97620.20221360.1723785589
1.9762-2.08030.19761370.1583795890
2.0803-2.21040.20921370.152812092
2.2104-2.38080.14111400.1542830994
2.3808-2.61990.19091440.155844395
2.6199-2.99780.22961480.16852596
2.9978-3.77250.1611520.1426866598
3.7725-19.52410.13411560.1346870298
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)
10.7483-0.1334-0.06641.136-0.14912.06230.0108-0.06410.07630.0870.01510.0424-0.39540.07710.00180.3165-0.0104-0.01480.1065-0.0070.09827.3614114.807388.16
20.74940.00970.69510.83620.03073.0143-0.0431-0.0290.09020.0825-0.00370.0405-0.3161-0.12120.04440.2090.0121-0.0090.08190.00260.081324.6439106.299284.8485
30.29580.40380.29691.92810.93081.58140.00210.03040.0369-0.0260.0008-0.0198-0.11610.14850.00040.13240.0126-0.00050.12790.00790.052729.907898.738174.0715
47.04613.60494.10193.6852-0.37585.7136-0.1339-1.03190.84550.3667-0.14740.0039-0.6308-0.19840.21360.77560.03380.0221.0871-0.31.30613.8068104.167476.2288
51.05750.85580.13241.7610.26412.3428-0.2267-0.31860.18430.16940.09470.03090.0482-0.10980.07990.1990.06530.00280.1434-0.04170.065322.593580.220462.3439
60.48740.17270.06131.00250.25431.3120.0138-0.00590.02010.08480.018-0.00860.25670.0294-0.01150.19830.0152-0.0110.1063-0.00650.056923.394584.92371.8328
74.1776-0.1291-1.06593.264-1.33036.2783-0.0564-0.40290.05930.32380.0211-0.2939-0.10170.53010.10020.25930.0321-0.07230.15540.00320.114134.199792.426493.4088
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain A and resid 1:51)A1 - 51
2X-RAY DIFFRACTION2(chain A and resid 52:127)A52 - 127
3X-RAY DIFFRACTION3(chain A and resid 128:229)A128 - 229
4X-RAY DIFFRACTION4(chain A and resid 230:242)A230 - 242
5X-RAY DIFFRACTION5(chain A and resid 243:282)A243 - 282
6X-RAY DIFFRACTION6(chain A and resid 283:461)A283 - 461
7X-RAY DIFFRACTION7(chain A and resid 462:469)A462 - 469

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