[English] 日本語
Yorodumi
- PDB-4j0d: tannin acyl hydrolase from Lactobacillus plantarum (Cadmium) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j0d
Titletannin acyl hydrolase from Lactobacillus plantarum (Cadmium)
ComponentsTannase
KeywordsHYDROLASE / tannin / hydrolase fold
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 / TRIETHYLENE GLYCOL / Tannase
Similarity search - Component
Biological speciesLactobacillus plantarum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.6 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
Revision 1.2May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Tannase
B: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,74520
Polymers106,5892
Non-polymers2,15618
Water14,178787
1
A: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,9887
Polymers53,2951
Non-polymers6936
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tannase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,75713
Polymers53,2951
Non-polymers1,46212
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.940, 62.918, 84.070
Angle α, β, γ (deg.)70.58, 85.70, 78.96
Int Tables number1
Space group name H-MP1

-
Components

-
Protein , 1 types, 2 molecules AB

#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

-
Non-polymers , 5 types, 805 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 787 / 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: 2.16 Å3/Da / Density % sol: 42.95 %
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: 1.6 Å / Num. obs: 109375 / % possible obs: 93.1 % / Biso Wilson estimate: 14.12 Å2
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.059 / Mean I/σ(I) obs: 2.9 / % possible all: 72.9

-
Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.7.1_743)refinement
XDSdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR / Resolution: 1.6→20.018 Å / Occupancy max: 1 / Occupancy min: 0.13 / FOM work R set: 0.9069 / SU ML: 0.35 / σ(F): 1.98 / Phase error: 16.75 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1747 1849 1.69 %
Rwork0.1435 --
obs0.144 109373 93.1 %
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 68.592 Å2 / ksol: 0.418 e/Å3
Displacement parametersBiso max: 144.72 Å2 / Biso mean: 21.4172 Å2 / Biso min: 4.94 Å2
Baniso -1Baniso -2Baniso -3
1-3.7855 Å20.1005 Å20.5244 Å2
2---3.9841 Å2-1.3131 Å2
3---0.1985 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20.018 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7163 0 117 787 8067
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0197583
X-RAY DIFFRACTIONf_angle_d1.59610311
X-RAY DIFFRACTIONf_dihedral_angle_d13.7712745
X-RAY DIFFRACTIONf_chiral_restr0.1121153
X-RAY DIFFRACTIONf_plane_restr0.0081346
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 13

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6-1.64320.2578960.23595707580364
1.6432-1.69150.23261130.1887451756483
1.6915-1.74610.22181500.16358476862695
1.7461-1.80850.1941420.15528476861895
1.8085-1.88080.19821540.14078519867396
1.8808-1.96640.18041470.13268510865796
1.9664-2.06990.19011490.13298525867496
2.0699-2.19950.19021460.12778593873997
2.1995-2.3690.14731490.12848620876997
2.369-2.6070.17071460.12688659880597
2.607-2.98320.15851520.13748619877197
2.9832-3.75440.17771480.13888659880798
3.7544-20.01910.15341570.15598710886798
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)
10.3674-0.36720.01541.0014-0.03571.3020.0022-0.02010.07490.170.02-0.0448-0.3990.03110.00830.33430.0088-0.01120.02230.01530.089227.4401114.857687.5528
20.5542-0.01860.24560.9107-0.15991.9464-0.02360.01430.08870.1042-0.01090.0048-0.343-0.10470.0550.17440.0234-0.01210.07850.0030.086624.668106.146784.9272
30.1832-0.0608-0.09281.11180.24111.19950.00450.04710.0512-0.0556-0.042-0.038-0.14330.07950.04120.08120.0128-0.00020.0870.01840.061130.252198.385173.8774
44.36780.72722.37821.365-1.43344.3857-0.0738-0.60610.45160.21120.0271-0.0014-0.3878-0.09730.13250.2308-0.00570.06680.8438-0.04390.78234.2283102.917275.6911
50.81160.5714-0.13411.55730.05321.8368-0.1196-0.19540.1791-0.02070.00890.1340.0499-0.24420.07260.15610.03050.00860.1558-0.0420.094722.158180.644762.8756
60.4590.1191-0.01750.7829-0.0221.154-0.02140.05220.0041-0.0110.0108-0.00740.1351-0.02940.01130.10380.011-0.00130.1041-0.00670.062923.316484.503171.4144
73.1518-0.19590.38291.6398-0.00222.524-0.1049-0.34880.06080.25870.1134-0.2541-0.13420.3040.04740.2050.0114-0.04720.1386-0.01190.102432.655892.570493.4555
81.0860.171-0.37611.0466-0.05630.9396-0.03870.067-0.1221-0.1122-0.0023-0.01440.1435-0.02060.05150.0922-0.00490.01270.067-0.01140.11239.402434.837728.1532
91.1298-0.1439-0.55021.14110.31480.97260.02180.0644-0.0631-0.1268-0.022-0.00050.0038-0.0437-0.01310.05270.00430.00220.0537-0.00390.097438.780744.349429.2714
100.2143-0.0361-0.08640.78230.31170.43980.0141-0.0287-0.04980.0094-0.0379-0.01180.0273-0.01760.02040.0289-0.0085-0.00590.07340.00860.076836.262951.239841.7136
110.3767-0.1069-0.44112.24691.09262.74110.20060.7463-0.645-0.20020.0397-0.07990.82090.0313-0.34910.7658-0.0234-0.33060.3922-0.10980.571621.542556.449721.4242
121.2588-0.30930.36421.19580.25741.68610.01940.07390.0207-0.1016-0.05890.0964-0.086-0.06870.06320.053-0.0075-0.00210.0689-0.02540.060528.179872.03745.2122
130.6935-0.0579-0.0140.89640.1260.41980.014-0.04270.04-0.0991-0.0066-0.021-0.0739-0.004-0.00780.0505-0.00140.00250.0667-0.00760.063734.719766.829340.5754
142.59670.71561.73540.5606-0.39994.45870.02950.0662-0.2886-0.07190.115-0.30440.12670.4652-0.05290.05830.00860.03750.1135-0.02210.19254.246553.444431.9711
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 230:242)A230 - 242
5X-RAY DIFFRACTION5(chain A and resid 243:282)A243 - 282
6X-RAY DIFFRACTION6(chain A and resid 283:461)A283 - 461
7X-RAY DIFFRACTION7(chain A and resid 462:469)A462 - 469
8X-RAY DIFFRACTION8(chain B and resid 1:51)B1 - 51
9X-RAY DIFFRACTION9(chain B and resid 52:127)B52 - 127
10X-RAY DIFFRACTION10(chain B and resid 128:229)B128 - 229
11X-RAY DIFFRACTION11(chain B and resid 230:242)B230 - 242
12X-RAY DIFFRACTION12(chain B and resid 243:282)B243 - 282
13X-RAY DIFFRACTION13(chain B and resid 283:461)B283 - 461
14X-RAY DIFFRACTION14(chain B and resid 462:469)B462 - 469

+
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