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- PDB-4j0j: Tannin acyl hydrolase in complex with ethyl 3,5-dihydroxybenzoate -

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Basic information

Entry
Database: PDB / ID: 4j0j
TitleTannin acyl hydrolase in complex with ethyl 3,5-dihydroxybenzoate
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 3,5-dihydroxybenzoate / Tannase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2 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)106,9534
Polymers106,5892
Non-polymers3642
Water9,026501
1
A: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4772
Polymers53,2951
Non-polymers1821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4772
Polymers53,2951
Non-polymers1821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.251, 62.726, 83.466
Angle α, β, γ (deg.)70.47, 86.55, 79.13
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Tannase


Mass: 53294.539 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
#2: Chemical ChemComp-E35 / ethyl 3,5-dihydroxybenzoate


Mass: 182.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H10O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.1 Å3/Da / Density % sol: 41.5 % / Description: STRUCTURE FACTOR FILE CONTAINS FRIEDEL'S PAIRS
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 Å / Num. obs: 113748 / % possible obs: 96.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.096 / Net I/σ(I): 18
Reflection shellResolution: 2→2.11 Å / Redundancy: 7.2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 5.2 / % possible all: 95

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7.2_869)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→19.691 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.8348 / SU ML: 0.4 / σ(F): 1.22 / Phase error: 23.79 / Stereochemistry target values: ML
Details: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS
RfactorNum. reflection% reflection
Rfree0.2168 5659 5.01 %
Rwork0.1845 --
obs0.1861 112872 96.29 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.668 Å2 / ksol: 0.426 e/Å3
Displacement parametersBiso max: 123.74 Å2 / Biso mean: 33.1991 Å2 / Biso min: 11.77 Å2
Baniso -1Baniso -2Baniso -3
1-6.7335 Å2-4.1607 Å212.6453 Å2
2---16.5235 Å2-4.8451 Å2
3----1.3844 Å2
Refinement stepCycle: LAST / Resolution: 2→19.691 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7172 0 26 501 7699
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0057453
X-RAY DIFFRACTIONf_angle_d0.91710193
X-RAY DIFFRACTIONf_dihedral_angle_d14.8152651
X-RAY DIFFRACTIONf_chiral_restr0.0621147
X-RAY DIFFRACTIONf_plane_restr0.0041340
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2-2.02270.31782170.2658347193
2.0227-2.04650.30161820.2574338294
2.0465-2.07140.30442000.2464348894
2.0714-2.09760.24942120.2417351894
2.0976-2.12520.25081710.2174347394
2.1252-2.15430.23191680.2233348294
2.1543-2.1850.27661840.2163350194
2.185-2.21760.24362030.2115352095
2.2176-2.25220.24281690.2039355096
2.2522-2.2890.24861890.2042353595
2.289-2.32840.2911610.2025361995
2.3284-2.37070.23021840.1916349096
2.3707-2.41620.2272260.1818359396
2.4162-2.46550.23972030.1794352396
2.4655-2.5190.22921830.1843360896
2.519-2.57740.2322100.1886359697
2.5774-2.64180.22411640.1792356197
2.6418-2.7130.21712030.1827370798
2.713-2.79260.21051720.1887355497
2.7926-2.88250.22562040.1874365998
2.8825-2.98520.17581720.1763363998
2.9852-3.10430.22391820.173361698
3.1043-3.2450.21621880.176360398
3.245-3.41520.22651850.1694362398
3.4152-3.62790.20691910.163368798
3.6279-3.9060.19581940.1708368598
3.906-4.29540.17971810.1543359498
4.2954-4.90860.14921910.1533366699
4.9086-6.15280.20171860.1868363498
6.1528-19.69240.17881840.1787363697
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)
10.51790.17670.03981.64850.32271.81210.0441-0.02110.07080.14820.0318-0.1427-0.245-0.00370.0020.26440.0113-0.00210.14270.00370.139927.5678108.93983.7433
20.81440.99540.42242.09080.76181.7792-0.09330.02170.3086-0.0881-0.09810.50420.073-0.32820.0590.20770.0344-0.01380.2122-0.01630.234718.449589.408367.243
30.37940.1802-0.21421.61830.02591.3393-0.02780.0108-0.00410.06610.0424-0.09360.1231-0.015-0.01640.1880.0278-0.01880.15840.00270.120623.951885.041973.3173
40.4411-0.1154-0.15750.89630.36680.3221-0.02850.0082-0.1207-0.11630.0138-0.09690.0717-0.0161-0.00240.09920.0068-0.00910.1597-0.00290.16539.295942.458934.372
50.07890.0640.00530.93870.31220.1241-0.01140.1291-0.12-0.54770.07050.1836-0.037-0.01820.06730.2611-0.0127-0.09580.2481-0.02020.16223.583969.185638.2149
60.30850.1985-0.21040.2131-0.11890.21320.1870.071-0.0048-0.144-0.06980.11670.0426-0.02310.01310.30890.065-0.03840.2251-0.03930.20722.9369.021940.1278
70.5325-0.0307-0.11650.97720.14810.27210.0123-0.0380.0656-0.11710.0332-0.1006-0.06510.02990.01030.1301-0.0011-0.02190.1969-0.00810.15436.19166.647641.3061
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 0:188)A0 - 188
2X-RAY DIFFRACTION2chain 'A' and (resseq 189:272)A189 - 272
3X-RAY DIFFRACTION3chain 'A' and (resseq 273:469)A273 - 469
4X-RAY DIFFRACTION4chain 'B' and (resseq 0:208)B0 - 208
5X-RAY DIFFRACTION5chain 'B' and (resseq 209:235)B209 - 235
6X-RAY DIFFRACTION6chain 'B' and (resseq 236:272)B236 - 272
7X-RAY DIFFRACTION7chain 'B' and (resseq 273:469)B273 - 469

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