[English] 日本語
Yorodumi
- PDB-7dvb: D335N variant of Bt4394 in complex with 6SO3-NAG-oxazoline interm... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7dvb
TitleD335N variant of Bt4394 in complex with 6SO3-NAG-oxazoline intermediate
ComponentsBeta-N-acetylhexosaminidase
KeywordsHYDROLASE / GH20 / Complex
Function / homology
Function and homology information


glycosaminoglycan metabolic process / beta-N-acetylhexosaminidase / beta-N-acetylglucosaminidase activity / carbohydrate metabolic process / membrane
Similarity search - Function
Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily ...Beta-hexosaminidase / Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Chitobiase/beta-hexosaminidase domain 2-like / Beta-hexosaminidase, bacterial type, N-terminal / Glycosyl hydrolase family 20, domain 2 / Chitobiase; domain 2 / Beta-hexosaminidase-like, domain 2 / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-NGS / Chem-Q4Z / beta-N-acetylhexosaminidase
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 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 / entity / 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 / _entity.pdbx_mutation / _struct.title
Revision 1.2Nov 29, 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: Beta-N-acetylhexosaminidase
B: Beta-N-acetylhexosaminidase
C: Beta-N-acetylhexosaminidase
D: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)248,4359
Polymers247,0014
Non-polymers1,4345
Water8,179454
1
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0342
Polymers61,7501
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0342
Polymers61,7501
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,0342
Polymers61,7501
Non-polymers2831
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,3353
Polymers61,7501
Non-polymers5852
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.026, 67.002, 192.803
Angle α, β, γ (deg.)90.000, 94.673, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
32A
42C
53A
63D
74B
84C
95B
105D
116C
126D

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLUMETMETAA23 - 5453 - 525
211GLUGLUMETMETBB23 - 5453 - 525
322GLUGLUMETMETAA23 - 5453 - 525
422GLUGLUMETMETCC23 - 5453 - 525
533ILEILEMETMETAA24 - 5454 - 525
633ILEILEMETMETDD24 - 5454 - 525
744GLUGLUMETMETBB23 - 5453 - 525
844GLUGLUMETMETCC23 - 5453 - 525
955ILEILEMETMETBB24 - 5454 - 525
1055ILEILEMETMETDD24 - 5454 - 525
1166ILEILEILEILECC24 - 5444 - 524
1266ILEILEILEILEDD24 - 5444 - 524

NCS ensembles :
IDDetails
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4
3Local NCS retraints between domains: 5 6
4Local NCS retraints between domains: 7 8
5Local NCS retraints between domains: 9 10
6Local NCS retraints between domains: 11 12

-
Components

#1: Protein
Beta-N-acetylhexosaminidase


Mass: 61750.297 Da / Num. of mol.: 4 / Mutation: D335N
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: Chemical
ChemComp-Q4Z / [(3~{a}~{R},5~{R},6~{S},7~{R},7~{a}~{R})-2-methyl-6,7-bis(oxidanyl)-5,6,7,7~{a}-tetrahydro-3~{a}~{H}-pyrano[3,2-d][1,3]oxazol-1-ium-5-yl]methyl sulfate


Mass: 283.256 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H13NO8S / Feature type: SUBJECT OF INVESTIGATION
#3: 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.: 1 / 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
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 454 / 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: 2.14 Å3/Da / Density % sol: 42.47 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop
Details: 10 mg/mL protein in the buffer of 25 mM PH 8.0 and 300 mM NaCl was mixed with 0.1 M MES, pH 5.5, 23 % (w/v) PEG 10000 at 1:1 to grow apo crystal. Then the apo was soaked directly with 4MU-6S- ...Details: 10 mg/mL protein in the buffer of 25 mM PH 8.0 and 300 mM NaCl was mixed with 0.1 M MES, pH 5.5, 23 % (w/v) PEG 10000 at 1:1 to grow apo crystal. Then the apo was soaked directly with 4MU-6S-GlcNAc powder for 11 min.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Nov 12, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
ReflectionResolution: 2.05→19.716 Å / Num. obs: 130228 / % possible obs: 99.2 % / Redundancy: 6.6 % / CC1/2: 0.998 / Rmerge(I) obs: 0.107 / Net I/σ(I): 9.1
Reflection shellResolution: 2.05→2.09 Å / Rmerge(I) obs: 1.024 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6345 / CC1/2: 0.53

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-3000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3rcn

3rcn


Resolution: 2.05→19.716 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.927 / WRfactor Rfree: 0.255 / WRfactor Rwork: 0.225 / SU B: 6.297 / SU ML: 0.166 / Average fsc free: 0.8736 / Average fsc work: 0.8846 / Cross valid method: FREE R-VALUE / ESU R: 0.269 / ESU R Free: 0.202 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2585 6601 5.069 %
Rwork0.2285 123624 -
all0.23 --
obs-130225 99.159 %
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: 37.394 Å2
Baniso -1Baniso -2Baniso -3
1--0.66 Å2-0 Å2-0.629 Å2
2--1.133 Å20 Å2
3----0.365 Å2
Refinement stepCycle: LAST / Resolution: 2.05→19.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16687 0 91 454 17232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.01217232
X-RAY DIFFRACTIONr_angle_refined_deg0.9441.64323329
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42252046
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92522.982929
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.38153047
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.11592
X-RAY DIFFRACTIONr_chiral_restr0.080.22205
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0213100
X-RAY DIFFRACTIONr_nbd_refined0.1910.27396
X-RAY DIFFRACTIONr_nbtor_refined0.3060.211567
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1220.2621
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2640.295
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1310.215
X-RAY DIFFRACTIONr_mcbond_it1.6183.688211
X-RAY DIFFRACTIONr_mcangle_it2.535.51210248
X-RAY DIFFRACTIONr_scbond_it1.8593.7689021
X-RAY DIFFRACTIONr_scangle_it2.9015.57713081
X-RAY DIFFRACTIONr_lrange_it4.57748.28125531
X-RAY DIFFRACTIONr_ncsr_local_group_10.0590.0517624
X-RAY DIFFRACTIONr_ncsr_local_group_20.0650.0517524
X-RAY DIFFRACTIONr_ncsr_local_group_30.0630.0517509
X-RAY DIFFRACTIONr_ncsr_local_group_40.0710.0517549
X-RAY DIFFRACTIONr_ncsr_local_group_50.0670.0517521
X-RAY DIFFRACTIONr_ncsr_local_group_60.0620.0517962
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.058970.05011
12BX-RAY DIFFRACTIONLocal ncs0.058970.05011
23AX-RAY DIFFRACTIONLocal ncs0.065110.0501
24CX-RAY DIFFRACTIONLocal ncs0.065110.0501
35AX-RAY DIFFRACTIONLocal ncs0.063180.0501
36DX-RAY DIFFRACTIONLocal ncs0.063180.0501
47BX-RAY DIFFRACTIONLocal ncs0.071370.0501
48CX-RAY DIFFRACTIONLocal ncs0.071370.0501
59BX-RAY DIFFRACTIONLocal ncs0.067340.0501
510DX-RAY DIFFRACTIONLocal ncs0.067340.0501
611CX-RAY DIFFRACTIONLocal ncs0.061920.05011
612DX-RAY DIFFRACTIONLocal ncs0.061920.05011
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.05-2.1030.3385080.3149026X-RAY DIFFRACTION98.3495
2.103-2.1610.3214390.2998847X-RAY DIFFRACTION98.4939
2.161-2.2240.2954390.2828595X-RAY DIFFRACTION99.1657
2.224-2.2920.3274210.278383X-RAY DIFFRACTION99.2
2.292-2.3670.2884330.268091X-RAY DIFFRACTION99.0587
2.367-2.450.2583940.2587857X-RAY DIFFRACTION99.0873
2.45-2.5430.34280.2567587X-RAY DIFFRACTION99.1833
2.543-2.6460.33880.2567384X-RAY DIFFRACTION99.3227
2.646-2.7640.2843670.2466983X-RAY DIFFRACTION99.3646
2.764-2.8990.3133690.2536712X-RAY DIFFRACTION99.4243
2.899-3.0560.2693510.2456408X-RAY DIFFRACTION99.3824
3.056-3.2410.3043240.2496038X-RAY DIFFRACTION99.7335
3.241-3.4650.2863090.2385722X-RAY DIFFRACTION99.7519
3.742-4.0990.2162440.1974940X-RAY DIFFRACTION99.8844
4.099-4.5830.2172430.1734457X-RAY DIFFRACTION99.8513
4.583-5.2910.1872070.163950X-RAY DIFFRACTION99.8319
5.291-6.4790.222020.1963334X-RAY DIFFRACTION99.9152
6.479-9.1580.2371550.1992626X-RAY DIFFRACTION99.9281

+
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