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- PDB-4j0h: Tannin acyl hydrolase in complex with gallic acid -

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Basic information

Entry
Database: PDB / ID: 4j0h
TitleTannin acyl hydrolase in complex with gallic acid
ComponentsTannase
KeywordsHYDROLASE / tannin / hydrolysis / gallic acid
Function / homology
Function and homology information


aminopeptidase activity
Similarity search - Function
: / : / BD-FAE / Alpha/Beta hydrolase fold, catalytic domain / Alpha/Beta hydrolase fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3,4,5-trihydroxybenzoic acid / DI(HYDROXYETHYL)ETHER / Tannase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.8 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 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

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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)108,06113
Polymers106,5892
Non-polymers1,47211
Water21,8701214
1
A: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9776
Polymers53,2951
Non-polymers6835
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,0837
Polymers53,2951
Non-polymers7896
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)47.551, 62.960, 84.474
Angle α, β, γ (deg.)70.74, 85.18, 79.55
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-GDE / 3,4,5-trihydroxybenzoic acid / Gallate / Gallic acid


Mass: 170.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O5
#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#4: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1214 / 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: 2.2 Å3/Da / Density % sol: 44.14 %
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: 1.8 Å / Num. obs: 82235 / % possible obs: 97.6 % / Redundancy: 3.7 % / Biso Wilson estimate: 11.91 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 11.8
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.456 / Mean I/σ(I) obs: 3.3 / % possible all: 96.7

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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: 1.8→19.68 Å / Occupancy max: 1 / Occupancy min: 0.22 / FOM work R set: 0.9083 / SU ML: 0.4 / σ(F): 2.01 / Phase error: 16.92 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1831 4103 4.99 %
Rwork0.1491 --
obs0.1508 82229 97.65 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.667 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 83.38 Å2 / Biso mean: 15.9204 Å2 / Biso min: 3.34 Å2
Baniso -1Baniso -2Baniso -3
1-3.284 Å20.6113 Å20.4789 Å2
2---2.774 Å2-1.2173 Å2
3----0.51 Å2
Refinement stepCycle: LAST / Resolution: 1.8→19.68 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7170 0 99 1214 8483
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067520
X-RAY DIFFRACTIONf_angle_d110255
X-RAY DIFFRACTIONf_dihedral_angle_d13.522704
X-RAY DIFFRACTIONf_chiral_restr0.0661146
X-RAY DIFFRACTIONf_plane_restr0.0041342
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 29

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.82120.2971420.23622658280097
1.8212-1.84340.26551380.21212663280197
1.8434-1.86670.23911430.19072642278597
1.8667-1.89120.21611440.19322697284197
1.8912-1.91710.20921250.17312659278497
1.9171-1.94450.21411510.16772694284597
1.9445-1.97350.20581320.16342713284597
1.9735-2.00430.20771390.1622630276997
2.0043-2.03710.1751200.15482731285197
2.0371-2.07220.20041290.14852718284797
2.0722-2.10980.20341490.15052618276797
2.1098-2.15040.19121250.14662718284398
2.1504-2.19420.18151470.14742669281697
2.1942-2.24180.18861390.14972722286198
2.2418-2.29390.18291570.14242664282198
2.2939-2.35120.19321300.14062695282598
2.3512-2.41470.17461640.13612699286398
2.4147-2.48560.17581500.14312678282898
2.4856-2.56560.20481560.13972692284898
2.5656-2.65710.19931410.14942699284098
2.6571-2.76320.17781220.14812740286298
2.7632-2.88860.20751590.14692679283898
2.8886-3.04040.14941470.1552707285498
3.0404-3.23010.17691310.14632740287198
3.2301-3.47830.16981380.14292735287398
3.4783-3.8260.1521400.12982698283898
3.826-4.37430.15151510.12142714286598
4.3743-5.49120.13911430.12522731287499
5.4912-19.68090.17911510.1672723287499
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)
10.0615-0.05830.09120.70430.57420.98590.00650.00520.0203-0.0654-0.0068-0.0212-0.15620.0353-0.00020.06-0.01410.00240.06290.00680.044227.4226104.844580.6352
20.42340.23430.10420.4320.10021.20740.0631-0.07230.00750.104-0.06730.04310.1535-0.0819-0.00290.1342-0.00870.00170.0572-0.00970.056418.796377.856472.064
30.32610.0410.16530.64750.29631.08360.03840.03310.0099-0.04570.002-0.03640.09050.0743-0.02160.08020.0217-0.00930.0594-0.00930.058725.983391.305570.2607
40.4066-0.1277-0.0820.98450.3510.4293-0.02720.0316-0.0373-0.030.0195-0.07620.0617-0.00010.01330.0443-0.00430.01480.04430.00750.062239.611741.911133.4411
51.0366-0.0379-0.0440.5097-0.16230.4283-0.0042-0.02880.0211-0.03040.0204-0.0224-0.0292-0.0715-0.03390.02730.004-0.0010.0321-0.01250.041830.317171.62339.4316
60.43390.1218-0.08860.6137-0.05510.2064-0.0065-0.02970.0278-0.01890.01380.00040.003-0.00720.00190.02640.003-0.01290.0483-0.00370.052534.600563.695839.6389
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 1:232)A1 - 232
2X-RAY DIFFRACTION2chain 'A' and (resseq 233:340)A233 - 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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