[English] 日本語
Yorodumi
- PDB-4j0g: Tannin acyl hydrolase (mercury derivative) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j0g
TitleTannin acyl hydrolase (mercury derivative)
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
: / DI(HYDROXYETHYL)ETHER / Tannase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.5 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 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tannase
B: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,42914
Polymers101,6462
Non-polymers1,78312
Water5,873326
1
A: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,5426
Polymers50,8231
Non-polymers7205
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8878
Polymers50,8231
Non-polymers1,0647
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.357, 62.686, 83.122
Angle α, β, γ (deg.)70.49, 86.93, 79.10
Int Tables number1
Space group name H-MP1

-
Components

#1: Protein Tannase /


Mass: 50822.883 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-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Hg
#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-1PE / PENTAETHYLENE GLYCOL / PEG400 / Polyethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.2 Å3/Da / Density % sol: 44.07 %
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

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9184 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionHighest resolution: 2.5 Å / Num. obs: 25246 / % possible obs: 97.3 % / Biso Wilson estimate: 20.76 Å2
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.233 / Mean I/σ(I) obs: 5.6 / % possible all: 97.6

-
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: MIR / Resolution: 2.5→19.768 Å / Occupancy max: 1 / Occupancy min: 0 / FOM work R set: 0.8445 / SU ML: 0.77 / σ(F): 1.97 / Phase error: 23.31 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.232 1452 4.98 %
Rwork0.1893 --
obs0.1914 29147 97.44 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso max: 84.55 Å2 / Biso mean: 22.5707 Å2 / Biso min: 0 Å2
Baniso -1Baniso -2Baniso -3
1-10.6682 Å2-6.6771 Å215.5774 Å2
2---4.5816 Å2-5.2056 Å2
3---3.6649 Å2
Refinement stepCycle: LAST / Resolution: 2.5→19.768 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7007 0 69 326 7402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0067251
X-RAY DIFFRACTIONf_angle_d1.3829874
X-RAY DIFFRACTIONf_dihedral_angle_d14.3842574
X-RAY DIFFRACTIONf_chiral_restr0.1151110
X-RAY DIFFRACTIONf_plane_restr0.0051289
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.5-2.58920.31931710.23532765293697
2.5892-2.69260.29161510.21862746289798
2.6926-2.81480.2561390.21932811295098
2.8148-2.96280.25741310.20292811294298
2.9628-3.14770.25041360.20282780291698
3.1477-3.38960.25391480.19212780292898
3.3896-3.72870.20731520.18282786293898
3.7287-4.26350.20121430.16472775291897
4.2635-5.35380.19611210.15482763288497
5.3538-19.76820.20281600.1942678283895
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)
10.0242-0.00040.02330.0986-0.06780.0863-0.02070.01340.0029-0.0261-0.07190.01190.0057-0.0623-0.02810.1114-0.01250.03680.05030.0030.064226.0382115.036187.1395
20.1118-0.0528-0.06430.13750.07150.05940.06190.03090.01570.0236-0.0378-0.1285-0.0089-0.0640.01860.0861-0.0297-0.04390.0341-0.00220.040623.4548106.193884.445
30.0335-0.0345-0.04030.04480.03030.05720.03250.0369-0.0023-0.0077-0.0288-0.0585-0.07320.01890.00560.0595-0.00190.00160.0301-0.00320.028229.874198.744374.053
40.04210.03860.01010.03780.01170.0125-0.0459-0.01130.0048-0.05120.01510.03780.00730.0179-0.03880.11660.0184-0.02770.0149-0.00160.06225.082178.488661.5101
50.1115-0.02440.00470.06520.00150.0829-0.05090.07430.1580.1043-0.0173-0.0891-0.0070.0112-0.02730.0922-0.00130.04770.0143-0.026-0.081823.274484.692571.4366
60.001-0.001200.00130.00010.0001-0.0113-0.0151-0.00170.017-0.0135-0.02910.01090.04070.00010.2488-0.09150.04690.1714-0.01840.172531.699292.727493.6211
70.06470.015-0.01830.0237-0.04770.1265-0.02330.048-0.0792-0.0295-0.02320.01290.07920.0279-0.01170.0824-0.02310.03120.0524-0.00910.060239.749235.039828.0505
80.1990.0049-0.08630.0377-0.01020.0537-0.00730.11110.044-0.06350.0381-0.0327-0.0108-0.02650.02460.0312-0.00940.00420.0666-0.01850.04939.1244.515629.2298
90.0506-0.04180.01180.06560.02840.01380.0061-0.0627-0.058-0.05280.00050.00920.0115-0.04920.0318-0.04060.0342-0.00250.03930.02820.063135.898151.511440.9122
100.0184-0.0261-0.02420.05820.03170.0355-0.0049-0.02350.062-0.02210.0369-0.0279-0.00190.01940.0138-0.0108-0.00340.03870.0799-0.02840.130628.440671.407845.0298
110.1585-0.0291-0.00420.1350.00460.0563-0.01460.05250.0469-0.09770.0871-0.0406-0.0358-0.00630.0335-0.2961-0.09450.21620.01930.0456-0.064235.320466.588640.3832
120.0054-0.00130.00230.002-0.00070.00110.0125-0.0005-0.00110.0029-0.0046-0.02250.00420.02170.00010.11290.00370.02250.14420.05520.122454.743453.38432.2418
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 248:282)A248 - 282
5X-RAY DIFFRACTION5(chain A and resid 283:461)A283 - 461
6X-RAY DIFFRACTION6(chain A and resid 462:469)A462 - 470
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 128:234)B128 - 234
10X-RAY DIFFRACTION10(chain B and resid 242:282)B242 - 282
11X-RAY DIFFRACTION11(chain B and resid 283:461)B283 - 461
12X-RAY DIFFRACTION12(chain B and resid 462:469)B462 - 470

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more