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- PDB-4j0i: Tannin acyl hydrolase in complex with 3,4-dihydroxybenzoate -

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Basic information

Entry
Database: PDB / ID: 4j0i
TitleTannin acyl hydrolase in complex with 3,4-dihydroxybenzoate
ComponentsTannase
KeywordsHYDROLASE / tannin / hydrolysis
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-DIHYDROXYBENZOIC ACID / DI(HYDROXYETHYL)ETHER / Tannase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.75 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)107,83412
Polymers106,5892
Non-polymers1,24510
Water13,962775
1
A: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,6614
Polymers53,2951
Non-polymers3663
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,1738
Polymers53,2951
Non-polymers8797
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)46.578, 62.852, 83.853
Angle α, β, γ (deg.)70.35, 86.05, 79.48
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-DHB / 3,4-DIHYDROXYBENZOIC ACID / Protocatechuic acid


Mass: 154.120 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H6O4
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 775 / 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: 2.13 Å3/Da / Density % sol: 42.32 %
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

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
ReflectionHighest resolution: 1.75 Å / Num. obs: 328191 / % possible obs: 96.8 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.088 / Net I/σ(I): 10.7
Reflection shellResolution: 1.75→1.84 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.5 / % possible all: 96.2

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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: 1.75→19.741 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8923 / SU ML: 0.4 / σ(F): 1.99 / Phase error: 18.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1875 4315 5.02 %
Rwork0.1547 --
obs0.1563 86020 96.9 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 57.888 Å2 / ksol: 0.415 e/Å3
Displacement parametersBiso max: 84.62 Å2 / Biso mean: 20.3272 Å2 / Biso min: 7.01 Å2
Baniso -1Baniso -2Baniso -3
1-5.3228 Å2-2.5766 Å24.7353 Å2
2---6.2456 Å2-0.3426 Å2
3---0.9228 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.741 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7024 0 84 775 7883
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087507
X-RAY DIFFRACTIONf_angle_d1.08110270
X-RAY DIFFRACTIONf_dihedral_angle_d13.8352706
X-RAY DIFFRACTIONf_chiral_restr0.0721153
X-RAY DIFFRACTIONf_plane_restr0.0041352
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 (%)
1.75-1.76990.27641280.2402270196
1.7699-1.79070.27151410.2321277596
1.7907-1.81250.28471250.2294265096
1.8125-1.83540.26781480.21272596
1.8354-1.85960.24991400.2014275296
1.8596-1.8850.23451270.1834266897
1.885-1.91190.22751500.177272097
1.9119-1.94040.21811460.1686276097
1.9404-1.97070.231540.1631269797
1.9707-2.0030.22211440.1563269397
2.003-2.03750.18431470.1522274397
2.0375-2.07450.18851360.1394270197
2.0745-2.11440.15811390.1467280997
2.1144-2.15750.19461470.1376271997
2.1575-2.20440.1771480.1396271598
2.2044-2.25560.18511350.1422273297
2.2556-2.31190.19291470.1391274897
2.3119-2.37430.17911470.1384271597
2.3743-2.4440.17651340.1343278597
2.444-2.52280.19731570.1437270597
2.5228-2.61270.19821480.1502276098
2.6127-2.71710.17851510.1462272498
2.7171-2.84040.20321400.1549273998
2.8404-2.98970.1751330.1546275897
2.9897-3.17630.18391460.1528270297
3.1763-3.42040.16931410.1472268596
3.4204-3.76240.13861470.1357268696
3.7624-4.30190.16081460.1339270996
4.3019-5.40160.14461700.1367268797
5.4016-19.74250.21671530.1937274298
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)
10.18190.04420.01391.27190.22010.820.01260.00790.03610.14-0.0032-0.0392-0.1505-0.0117-0.00390.12660.0125-0.0120.10560.00730.092827.3119105.021580.4441
20.5650.2546-0.45130.9391-0.29971.7716-0.07820.016-0.0217-0.03850.03960.04060.2892-0.06770.04220.18930.00290.00010.1166-0.00220.113820.939374.28171.1974
30.40780.23170.08850.98690.10561.11780.0080.03830.00110.0450.0344-0.08280.01850.0602-0.03810.09080.0194-0.00580.1167-0.00720.107325.97391.237970.2158
40.426-0.0589-0.18281.14770.2650.528-0.00530.0313-0.0609-0.0754-0.0058-0.04190.0294-0.00590.02180.06270.00370.0020.1004-0.0010.107239.626841.871633.6487
51.2889-0.1212-0.26781.31920.10630.85890.01250.04040.0256-0.21630.01590.0396-0.0698-0.0846-0.04030.1211-0.0076-0.00730.0979-0.01460.097230.662471.79440.0784
60.4894-0.0656-0.02690.89050.10770.29370.009-0.0315-0.0015-0.0770.0064-0.0329-0.03930.0227-0.01160.0733-0.005-0.00490.1059-0.00610.081634.736863.744939.9373
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 247:340)A247 - 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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