[English] 日本語
Yorodumi
- PDB-7dva: Structure of wild type Bt4394, a GH20 family sulfoglycosidase, in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dva
TitleStructure of wild type Bt4394, a GH20 family sulfoglycosidase, in complex with 6S-GlcNAc
ComponentsBeta-N-acetylhexosaminidaseHexosaminidase
KeywordsHYDROLASE / GH20 / Complex
Function / homology
Function and homology information


beta-N-acetylhexosaminidase / beta-N-acetylhexosaminidase activity / N-acetyl-beta-D-galactosaminidase activity / carbohydrate metabolic process
Similarity search - Function
Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Beta-hexosaminidase-like, domain 2 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-NGS / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsZhang, Z. / He, Y. / Jin, Y.
Funding support United Kingdom, China, 2items
OrganizationGrant numberCountry
Wellcome Trust209057/Z/17/Z United Kingdom
National Natural Science Foundation of China (NSFC)31400663 China
CitationJournal: Acs Catalysis / Year: 2023
Title: Mechanistic and Structural Insights into the Specificity and Biological Functions of Bacterial Sulfoglycosidases
Authors: Zhang, Z. / Dong, M. / Zallot, R. / Blackburn, G.M. / Wang, N. / Wang, C. / Chen, L. / Baumann, P. / Wu, Z. / Wang, Z. / Fan, H. / Roth, C. / Jin, Y. / He, Y.
History
DepositionJan 13, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Derived calculations / Structure summary
Category: atom_type / citation ...atom_type / citation / citation_author / struct
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _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.title / _citation.year / _struct.title
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: Beta-N-acetylhexosaminidase
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,5669
Polymers123,5032
Non-polymers1,0637
Water10,196566
1
B: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,2374
Polymers61,7511
Non-polymers4853
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-0 kcal/mol
Surface area20800 Å2
MethodPISA
2
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3295
Polymers61,7511
Non-polymers5784
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-0 kcal/mol
Surface area20850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.500, 125.596, 84.640
Angle α, β, γ (deg.)90.000, 90.631, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Beta-N-acetylhexosaminidase / Hexosaminidase


Mass: 61751.281 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Production host: Escherichia coli (E. coli)
References: UniProt: A0A0P0FIE8, beta-N-acetylhexosaminidase
#2: Sugar ChemComp-NGS / 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucopyranose / 2-(acetylamino)-2-deoxy-6-O-sulfo-beta-D-glucopyranose / N-ACETYL-D-GLUCOSAMINE-6-SULFATE / N-acetyl-6-O-sulfo-beta-D-glucosamine / 2-acetamido-2-deoxy-6-O-sulfo-beta-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-D-glucose / 2-acetamido-2-deoxy-6-O-sulfo-glucose


Type: D-saccharide, beta linking / Mass: 301.271 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H15NO9S / Feature type: SUBJECT OF INVESTIGATION
IdentifierTypeProgram
DGlcpNAc[6S]bCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-6-sulfo-b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpNAc6SO3IUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 566 / 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: 2.13 Å3/Da / Density % sol: 42.26 %
Crystal growTemperature: 282 K / Method: vapor diffusion, sitting drop
Details: 10 mM of 4MU-6S-GlcNAc with 10 mg/mL protein in the buffer of 25 mM PH 8.0, =300 mM NaCl was mixed with 0.1 M BICINE, pH 8.5, 20 % (w/v) PEG 10000 at 1:1 to carry on co-crystallization.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979191 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 28, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979191 Å / Relative weight: 1
ReflectionResolution: 1.55→70.19 Å / Num. obs: 145268 / % possible obs: 97.4 % / Redundancy: 6.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.097 / Net I/σ(I): 11.5
Reflection shellResolution: 1.55→1.58 Å / Rmerge(I) obs: 1.005 / Mean I/σ(I) obs: 2 / Num. unique obs: 7086 / CC1/2: 0.584

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rcn

3rcn


Resolution: 1.55→50.483 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.965 / WRfactor Rfree: 0.195 / WRfactor Rwork: 0.147 / SU B: 3.681 / SU ML: 0.057 / Average fsc free: 0.9221 / Average fsc work: 0.9352 / Cross valid method: FREE R-VALUE / ESU R: 0.092 / ESU R Free: 0.076
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1844 7467 5.142 %
Rwork0.1417 137760 -
all0.144 --
obs-145227 97.224 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.979 Å2
Baniso -1Baniso -2Baniso -3
1--0.449 Å2-0 Å20.328 Å2
2--1.723 Å20 Å2
3----1.281 Å2
Refinement stepCycle: LAST / Resolution: 1.55→50.483 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8495 0 68 566 9129
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0128856
X-RAY DIFFRACTIONr_angle_refined_deg1.2171.64711997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.46651061
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.20723.172476
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.863151561
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.4141546
X-RAY DIFFRACTIONr_chiral_restr0.0920.21129
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026808
X-RAY DIFFRACTIONr_nbd_refined0.2020.24175
X-RAY DIFFRACTIONr_nbtor_refined0.3150.25983
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1130.2560
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.240.275
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.221
X-RAY DIFFRACTIONr_mcbond_it1.7621.9634221
X-RAY DIFFRACTIONr_mcangle_it2.2842.9595283
X-RAY DIFFRACTIONr_scbond_it2.6252.3444635
X-RAY DIFFRACTIONr_scangle_it3.0693.3626712
X-RAY DIFFRACTIONr_lrange_it3.4428.0413768
X-RAY DIFFRACTIONr_rigid_bond_restr1.46738856
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.590.3225120.28110063X-RAY DIFFRACTION95.8662
1.59-1.6340.3235280.2569744X-RAY DIFFRACTION95.9193
1.634-1.6810.2535420.1889467X-RAY DIFFRACTION95.8349
1.681-1.7330.2354920.1599287X-RAY DIFFRACTION96.4303
1.733-1.790.2044750.1329060X-RAY DIFFRACTION96.7529
1.79-1.8520.2034690.1218764X-RAY DIFFRACTION97.0465
1.852-1.9220.2094460.1478454X-RAY DIFFRACTION96.8971
1.922-2.0010.184360.1268149X-RAY DIFFRACTION97.1484
2.001-2.090.1934090.1257854X-RAY DIFFRACTION97.487
2.09-2.1920.174110.1197541X-RAY DIFFRACTION97.9672
2.192-2.310.1813940.1237121X-RAY DIFFRACTION97.6228
2.31-2.450.1773860.1236802X-RAY DIFFRACTION98.1297
2.45-2.620.1793300.1286411X-RAY DIFFRACTION98.0224
2.62-2.8290.1873610.1435943X-RAY DIFFRACTION99.0261
2.829-3.0990.1872940.1425513X-RAY DIFFRACTION98.2905
3.099-3.4650.1672690.1345008X-RAY DIFFRACTION99.0428
3.465-40.1622410.1294351X-RAY DIFFRACTION97.5776
4-4.8980.1592080.143751X-RAY DIFFRACTION99.0245

+
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