[English] 日本語
Yorodumi
- PDB-6ld0: Structure of Bifidobacterium dentium beta-glucuronidase complexed... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ld0
TitleStructure of Bifidobacterium dentium beta-glucuronidase complexed with C6-hexyl uronic isofagomine
ComponentsLacZ1 Beta-galactosidase
KeywordsCARBOHYDRATE / inhibitor / complex / glycosidase
Function / homology
Function and homology information


glucuronoside catabolic process / beta-glucuronidase / beta-glucuronidase activity / beta-galactosidase activity / carbohydrate binding / carbohydrate metabolic process / signaling receptor binding / extracellular space
Similarity search - Function
Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 ...Glycoside hydrolase, family 2, active site / Glycosyl hydrolases family 2 acid/base catalyst. / Glycoside hydrolase, family 2, conserved site / Glycosyl hydrolases family 2 signature 1. / Glycoside hydrolase, family 2 / Glycoside hydrolase family 2, catalytic domain / Glycosyl hydrolases family 2, TIM barrel domain / Glycoside hydrolase, family 2, immunoglobulin-like beta-sandwich / Glycosyl hydrolases family 2, sugar binding domain / Glycosyl hydrolases family 2 / Glycosyl hydrolases family 2, sugar binding domain / Beta-Galactosidase/glucuronidase domain superfamily / Galactose-binding-like domain superfamily / Glycoside hydrolase superfamily / Immunoglobulin-like fold
Similarity search - Domain/homology
Chem-E8X / Beta-glucuronidase
Similarity search - Component
Biological speciesBifidobacterium dentium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.901 Å
AuthorsLin, H.-Y. / Hsieh, T.-J. / Lin, C.-H.
Funding support Taiwan, 1items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)108-2113-M-001 -001 Taiwan
CitationJournal: Commun Biol / Year: 2021
Title: Entropy-driven binding of gut bacterial beta-glucuronidase inhibitors ameliorates irinotecan-induced toxicity.
Authors: Lin, H.Y. / Chen, C.Y. / Lin, T.C. / Yeh, L.F. / Hsieh, W.C. / Gao, S. / Burnouf, P.A. / Chen, B.M. / Hsieh, T.J. / Dashnyam, P. / Kuo, Y.H. / Tu, Z. / Roffler, S.R. / Lin, C.H.
History
DepositionNov 20, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2021Provider: repository / Type: Initial release
Revision 1.1Aug 11, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 22, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: LacZ1 Beta-galactosidase
B: LacZ1 Beta-galactosidase
C: LacZ1 Beta-galactosidase
D: LacZ1 Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)299,3368
Polymers298,3554
Non-polymers9814
Water28,9681608
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20100 Å2
ΔGint-123 kcal/mol
Surface area75860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.914, 105.395, 162.293
Angle α, β, γ (deg.)90.000, 91.160, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11chain A
21chain B
31chain C
41chain D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ASN / Beg label comp-ID: ASN / End auth comp-ID: LYS / End label comp-ID: LYS / Auth seq-ID: -1 - 667 / Label seq-ID: 1 - 669

Dom-IDSelection detailsAuth asym-IDLabel asym-ID
1chain AAA
2chain BBB
3chain CCC
4chain DDD

-
Components

#1: Protein
LacZ1 Beta-galactosidase


Mass: 74588.648 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bifidobacterium dentium (strain ATCC 27534 / DSM 20436 / JCM 1195 / Bd1) (bacteria)
Strain: ATCC 27534 / DSM 20436 / JCM 1195 / Bd1 / Gene: lacZ1, BDP_2112 / Production host: Escherichia coli (E. coli) / References: UniProt: D2Q7B1, beta-galactosidase
#2: Chemical
ChemComp-E8X / (2~{S},3~{S},4~{R},5~{R})-2-hexyl-4,5-bis(oxidanyl)piperidine-3-carboxylic acid


Mass: 245.315 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H23NO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1608 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 0.1 M sodium cacodylate, pH 6.5, 8% w/v PEG 20K

-
Data collection

DiffractionMean temperature: 110 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL15A1 / Wavelength: 1 Å
DetectorType: RAYONIX MX300HE / Detector: CCD / Date: Oct 5, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 241740 / % possible obs: 98.7 % / Redundancy: 4.1 % / Biso Wilson estimate: 17.25 Å2 / Rmerge(I) obs: 0.077 / Rpim(I) all: 0.044 / Rrim(I) all: 0.089 / Χ2: 0.854 / Net I/σ(I): 9.5 / Num. measured all: 980607
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.9-1.974.10.446243430.8810.250.5131.26899.8
1.97-2.054.20.44243470.8790.2460.5050.61199.9
2.05-2.144.20.287243780.930.160.3290.63999.9
2.14-2.2540.278244050.9550.1590.3211.37299.8
2.25-2.3940.252243690.9610.1440.2911.00399.8
2.39-2.584.20.108244520.9860.060.1240.65499.9
2.58-2.844.10.069244090.9920.0390.080.63499.9
2.84-3.254.10.042244420.9960.0240.0480.64399.8
3.25-4.093.80.038220250.9960.0220.0441.22489.6
4.09-303.80.018245700.9990.0110.0210.5698.8

-
Processing

Software
NameVersionClassification
HKL-2000data scaling
PHENIX1.8.2_1309refinement
PDB_EXTRACT3.25data extraction
Blu-Icedata collection
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3k46

3k46


Resolution: 1.901→20.194 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 24
RfactorNum. reflection% reflection
Rfree0.2349 1776 1 %
Rwork0.2009 --
obs0.2012 216169 88.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 158.16 Å2 / Biso mean: 29.82 Å2 / Biso min: 4.28 Å2
Refinement stepCycle: final / Resolution: 1.901→20.194 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19636 0 68 1608 21312
Biso mean--25.82 35.46 -
Num. residues----2480
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00420228
X-RAY DIFFRACTIONf_angle_d1.00327516
X-RAY DIFFRACTIONf_chiral_restr0.0412896
X-RAY DIFFRACTIONf_plane_restr0.0063644
X-RAY DIFFRACTIONf_dihedral_angle_d13.4237228
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A11680X-RAY DIFFRACTION7.632TORSIONAL
12B11680X-RAY DIFFRACTION7.632TORSIONAL
13C11680X-RAY DIFFRACTION7.632TORSIONAL
14D11680X-RAY DIFFRACTION7.632TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9011-1.95240.51741030.52071312870
1.9524-2.00980.30891060.31881309671
2.0098-2.07460.25191440.21481722092
2.0746-2.14870.22681470.20661750094
2.1487-2.23460.37291120.28871291669
2.2346-2.33620.3841090.34461389174
2.3362-2.45920.21411440.18111798896
2.4592-2.61290.20071600.17831825398
2.6129-2.81420.19741550.17811848899
2.8142-3.09650.23891550.17711852999
3.0965-3.54250.18441560.16131848099
3.5425-4.45520.20031280.15041601085
4.4552-20.1940.18761570.15461889499
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)
10.051-0.03440.00230.0424-0.01810.0130.00030.02660.0583-0.0305-0.0245-0.01490.00090.008-0.00310.14010.0173-0.01850.0670.0260.1704-26.68733.1308-78.2212
20.0531-0.0163-0.02850.00270.00650.0117-0.0197-0.05480.090.0617-0.00110.037-0.063-0.0215-0.01490.16660.0616-0.03460.0365-0.03340.2185-37.180339.1751-55.3744
30.03990.0170.01740.00380.00660.0083-0.01650.115-0.0613-0.116-0.00310.07920.0109-0.0291-0.01130.2215-0.0297-0.07740.1056-0.04120.1764-47.33079.2993-87.7477
40.17110.0531-0.00080.1572-0.06870.1024-0.0034-0.0647-0.0114-0.01150.00730.0838-0.0081-0.06290.00080.06330.0073-0.00960.091-0.0050.1318-46.582117.0622-59.8053
50.0532-0.01560.00940.03710.00650.05050.04750.0615-0.0763-0.0755-0.0334-0.01590.082-0.00460.03740.18960.0298-0.00210.0695-0.02730.1585-18.39265.0426-79.9232
60.0383-0.01670.01350.0106-0.00350.0038-0.0256-0.0498-0.07320.0230.0143-0.01630.04370.0241-0.01180.16330.0457-0.01930.03610.02580.2138-8.355-3.9344-57.8067
70.04530.0136-0.02560.02310.00460.0358-0.02570.14040.083-0.0907-0.0608-0.0864-0.04190.0374-0.01670.2654-0.02370.07160.18650.07180.27062.437129.8445-85.9247
80.19770.06620.02540.11590.02270.10560.0014-0.04880.0032-0.0237-0.0139-0.09430.00610.03290.0010.10620.01520.00850.10220.02040.16981.206218.5276-59.3138
90.0165-0.0256-0.00160.03050.00240.0155-0.0325-0.14390.01750.0919-0.00140.0086-0.02190.028100.2505-0.0136-0.02210.44590.03520.153-8.614112.878-4.736
100.01840.004-0.00510.01040.00310.01540.0341-0.0809-0.03160.037-0.0488-0.0285-0.00670.0187-0.00030.21710.0245-0.03690.41060.06020.17430.8541.603-24.193
110.0104-0.00560.00930.0019-0.0050.00780.0061-0.03410.00820.0108-0.0523-0.06840.0241-0.013200.22240.015-0.01930.34650.06640.20561.22518.1325-27.9725
120.00190.0065-0.00550.0067-0.01130.0125-0.0063-0.0878-0.05530.05620.04480.04810.0375-0.00910.04630.3409-0.08570.04880.51560.23140.222-28.5951-12.20572.3491
130.0560.0153-0.00380.0734-0.0260.11740.0072-0.2174-0.16520.0205-0.04390.0310.11590.0059-0.01590.1993-0.00020.01540.23420.16870.1654-18.9964-7.9181-24.7344
140.0352-0.0006-0.01190.02980.01340.016-0.0193-0.1008-0.0240.13130.01160.0258-0.0021-0.04510.01860.24420.00110.06050.44630.00130.1196-37.411816.1808-4.7125
150.0161-0.0002-0.00780.01040.00610.0062-0.0137-0.04040.01980.0531-0.07130.05530.0165-0.03440.00010.26620.00160.07270.4421-0.02630.1696-43.320821.9381-10.6608
160.0094-0.0044-0.00730.00140.0050.0074-0.024-0.01730.007-0.0059-0.01830.0374-0.0014-0.01470.00010.19990.03130.01360.3456-0.05090.177-47.040823.5502-27.4026
170.00280.00050.00330.00170.00180.0051-0.0317-0.08250.05540.09440.0402-0.0219-0.0157-0.01110.00260.4067-0.0259-0.03990.5109-0.17280.2309-17.828140.66175.4753
180.07490.0307-0.01620.1294-0.00170.1041-0.0645-0.20920.14470.0654-0.0631-0.0116-0.1496-0.0835-0.17120.21690.058-0.030.2856-0.19020.118-26.981539.1864-21.9915
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid -1 through 134 )A-1 - 134
2X-RAY DIFFRACTION2chain 'A' and (resid 135 through 189 )A135 - 189
3X-RAY DIFFRACTION3chain 'A' and (resid 190 through 325 )A190 - 325
4X-RAY DIFFRACTION4chain 'A' and (resid 326 through 667 )A326 - 667
5X-RAY DIFFRACTION5chain 'B' and (resid -1 through 134 )B-1 - 134
6X-RAY DIFFRACTION6chain 'B' and (resid 135 through 189 )B135 - 189
7X-RAY DIFFRACTION7chain 'B' and (resid 190 through 325 )B190 - 325
8X-RAY DIFFRACTION8chain 'B' and (resid 326 through 667 )B326 - 667
9X-RAY DIFFRACTION9chain 'C' and (resid -1 through 134 )C-1 - 117
10X-RAY DIFFRACTION10chain 'C' and (resid 135 through 154 )C118 - 154
11X-RAY DIFFRACTION11chain 'C' and (resid 155 through 189 )C155 - 189
12X-RAY DIFFRACTION12chain 'C' and (resid 190 through 325 )C190 - 325
13X-RAY DIFFRACTION13chain 'C' and (resid 326 through 667 )C326 - 667
14X-RAY DIFFRACTION14chain 'D' and (resid -1 through 117 )D-1 - 117
15X-RAY DIFFRACTION15chain 'D' and (resid 118 through 154 )D118 - 154
16X-RAY DIFFRACTION16chain 'D' and (resid 155 through 189 )D155 - 189
17X-RAY DIFFRACTION17chain 'D' and (resid 190 through 325 )D190 - 325
18X-RAY DIFFRACTION18chain 'D' and (resid 326 through 667 )D326 - 667

+
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://pdbjlvh1.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