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- PDB-4j0c: tannin acyl hydrolase from Lactobacillus plantarum (native structure) -

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Basic information

Entry
Database: PDB / ID: 4j0c
Titletannin acyl hydrolase from Lactobacillus plantarum (native structure)
ComponentsTannase
KeywordsHYDROLASE / tannin / tannase
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
DI(HYDROXYETHYL)ETHER / Tannase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.65 Å
AuthorsWu, 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 30, 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)107,3588
Polymers106,5892
Non-polymers7696
Water12,232679
1
A: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,5073
Polymers53,2951
Non-polymers2122
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,8515
Polymers53,2951
Non-polymers5574
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.458, 62.791, 83.803
Angle α, β, γ (deg.)70.39, 86.01, 79.41
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-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C4H10O3
#3: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 679 / 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: 2.12 Å3/Da / Density % sol: 42.08 %
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 / Date: Nov 1, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionHighest resolution: 1.65 Å / Num. obs: 100941 / Redundancy: 3.9 % / Biso Wilson estimate: 14.61 Å2 / Rmerge(I) obs: 0.077
Reflection shellResolution: 1.65→1.74 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.55 / % possible all: 88.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHENIXmodel building
PHENIX(phenix.refine: 1.7_650)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MIR / Resolution: 1.65→19.677 Å / Occupancy max: 1 / Occupancy min: 0.12 / FOM work R set: 0.8745 / SU ML: 0.17 / σ(F): 1.98 / Phase error: 20.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1919 5038 4.99 %RANDOM
Rwork0.1647 ---
obs0.1661 100915 95.73 %-
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.689 Å2 / ksol: 0.428 e/Å3
Displacement parametersBiso max: 86.66 Å2 / Biso mean: 20.8516 Å2 / Biso min: 5.59 Å2
Baniso -1Baniso -2Baniso -3
1-9.4533 Å2-4.5168 Å22.8299 Å2
2---7.5568 Å2-1.2857 Å2
3----0.691 Å2
Refinement stepCycle: LAST / Resolution: 1.65→19.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6945 0 51 679 7675
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097221
X-RAY DIFFRACTIONf_angle_d1.1879850
X-RAY DIFFRACTIONf_dihedral_angle_d13.2662571
X-RAY DIFFRACTIONf_chiral_restr0.0781109
X-RAY DIFFRACTIONf_plane_restr0.0051292
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.65-1.7090.29484620.2693870687
1.709-1.77730.2674860.219955395
1.7773-1.85820.23244900.1866966196
1.8582-1.9560.20254770.1591958196
1.956-2.07850.17925200.1453962796
2.0785-2.23870.17315140.1356968397
2.2387-2.46370.17275150.1379974097
2.4637-2.81930.17655300.1466969597
2.8193-3.54860.185550.1544978098
3.5486-19.67820.1884890.1788985198
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)
10.0935-0.12330.00410.22130.03710.28820.04510.0010.05850.24360.0247-0.0162-0.2333-0.0291-0.00680.3410.0057-0.00090.10610.00140.130126.7688115.021987.3948
20.19060.0481-0.00850.51860.09490.431-0.01650.00590.0390.19310.0245-0.0266-0.2607-0.06010.06430.20160.0142-0.01680.08460.00260.088324.2251106.322884.8521
30.0982-0.1257-0.14820.58380.06840.52430.01090.04250.0139-0.00630.0079-0.0813-0.09590.0092-0.00870.12260.0077-0.01540.10060.00420.100430.122598.769674.0389
40.23390.12280.19410.4471-0.15980.6225-0.091-0.0016-0.0476-0.17340.05710.04170.2805-0.07710.05710.16050.02280.00750.1234-0.00450.082325.153478.599361.3381
50.25470.07950.03840.54030.2050.5834-0.02280.02350.00270.04090.0227-0.02280.0908-0.0159-0.00090.11330.0077-0.0020.09450.00080.081423.423684.653871.4276
61.4833-0.0032-0.11150.0012-0.00440.1515-0.0309-0.25450.09460.11190.0902-0.0985-0.03480.08370.00860.26260.0171-0.06810.1329-0.02170.120932.32692.866393.4296
70.30860.0883-0.22530.4668-0.15020.638-0.04760.0488-0.0787-0.15030.00180.01290.139-0.02930.03380.11610.00470.01220.1042-0.00920.14539.533234.751628.1963
80.10470.04020.01860.90620.11150.2177-0.0013-0.0373-0.149-0.3607-0.00050.03190.0892-0.06520.0432-0.05130.06080.03790.0431-0.02630.098238.927444.26129.2237
90.1481-0.13790.01651.20110.2960.19980.0142-0.0312-0.0509-0.08-0.0274-0.0240.0108-0.0335-0.01180.02090.0075-0.01370.08940.00540.082436.041351.230441.0819
100.2337-0.12750.05550.50070.05110.51770.0290.1-0.0719-0.09180.0035-0.0347-0.1080.1264-0.1170.04850.0001-0.00480.0835-0.04180.071828.655672.831347.0239
110.4267-0.1082-0.01810.86120.30270.34970.0048-0.07950.0013-0.1120.023-0.0245-0.07480.0114-0.00890.04510.0062-0.00670.06810.00160.069534.760666.480240.564
120.0267-0.028-0.15130.03350.18321.245-0.04340.0123-0.1624-0.07370.049-0.24480.00680.3193-0.04280.07670.01030.02860.1354-0.00620.215754.305453.256532.0311
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 128:228)A128 - 228
4X-RAY DIFFRACTION4(chain A and resid 247:282)A247 - 282
5X-RAY DIFFRACTION5(chain A and resid 283:461)A283 - 461
6X-RAY DIFFRACTION6(chain A and resid 462:469)A462 - 469
7X-RAY DIFFRACTION7(chain B and resid 1:51)B1 - 51
8X-RAY DIFFRACTION8(chain B and resid 52:127)B52 - 127
9X-RAY DIFFRACTION9(chain B and resid 128:231)B128 - 231
10X-RAY DIFFRACTION10(chain B and resid 245:282)B245 - 282
11X-RAY DIFFRACTION11(chain B and resid 283:461)B283 - 461
12X-RAY DIFFRACTION12(chain B and resid 462:469)B462 - 469

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