[English] 日本語
Yorodumi
- PDB-8bal: Niako3494, a bacterial protein structure in glycoside hydrolase f... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8bal
TitleNiako3494, a bacterial protein structure in glycoside hydrolase family 20
ComponentsBeta-N-acetylhexosaminidase
KeywordsHYDROLASE / GH20 apo protein
Function / homology
Function and homology information


: / beta-N-acetylhexosaminidase activity / carbohydrate metabolic process / metal ion binding
Similarity search - Function
Glycoside hydrolase family 20, catalytic domain / Glycosyl hydrolase family 20, catalytic domain / Glycosidases / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Glycoside hydrolase, family 20, catalytic core
Similarity search - Component
Biological speciesNiastella koreensis GR20-10 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsDong, M.D. / Roth, C.R. / Jin, Y.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust218568/Z/19/Z United Kingdom
Royal SocietyRG170406 United Kingdom
Wellcome Trust209057/Z/17/Z United Kingdom
CitationJournal: Acs Catalysis / Year: 2022
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
DepositionOct 11, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: 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
A: Beta-N-acetylhexosaminidase
C: Beta-N-acetylhexosaminidase
D: Beta-N-acetylhexosaminidase
E: Beta-N-acetylhexosaminidase
F: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)218,04410
Polymers217,7165
Non-polymers3275
Water50428
1
A: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6092
Polymers43,5431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6092
Polymers43,5431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6092
Polymers43,5431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
E: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6092
Polymers43,5431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
F: Beta-N-acetylhexosaminidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6092
Polymers43,5431
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)146.987, 254.589, 139.580
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein
Beta-N-acetylhexosaminidase


Mass: 43543.293 Da / Num. of mol.: 5
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Niastella koreensis GR20-10 (bacteria) / Strain: DSM 17620 / KACC 11465 / NBRC 106392 / GR20-10 / Gene: Niako_3494 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: G8TKW6, beta-N-acetylhexosaminidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 28 / 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: 3 Å3/Da / Density % sol: 58.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: Protein stock at 18mg/mL, in the precipitant: 0.1 M MMT buffer (DL-Malic acid, MES monohydrate, Tris base [ratio 1:2:2]), pH 6.0, 25 % w/v PEG 1500, protein to precipitant ratio 1:1, 1 uL ...Details: Protein stock at 18mg/mL, in the precipitant: 0.1 M MMT buffer (DL-Malic acid, MES monohydrate, Tris base [ratio 1:2:2]), pH 6.0, 25 % w/v PEG 1500, protein to precipitant ratio 1:1, 1 uL drop size, +50 nL 1:10000 diluted seed stock. Cryoprotectant used was made up with 20% PEG400 in 80% mother liquor.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 29, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
Reflection twin
TypeCrystal-IDIDOperatorDomain-IDFraction
pseudo-merohedral11H, K, L10.3317
pseudo-merohedral221/2H+1/2K, 3/2H-1/2K, -L20.334
pseudo-merohedral331/2H-1/2K, -3/2H-1/2K, -L30.3342
ReflectionResolution: 2.27→73.49 Å / Num. obs: 120442 / % possible obs: 99.9 % / Redundancy: 13.9 % / CC1/2: 0.958 / Net I/σ(I): 6.3
Reflection shellResolution: 2.27→2.31 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 1.1 / Num. unique obs: 5852 / CC1/2: 0.336 / % possible all: 99.1

-
Processing

Software
NameVersionClassification
REFMAC5.8.0352refinement
xia2data reduction
xia2data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold

Resolution: 2.27→73.49 Å / Cor.coef. Fo:Fc: 0.878 / Cor.coef. Fo:Fc free: 0.811 / SU B: 5.491 / SU ML: 0.148 / Cross valid method: FREE R-VALUE / ESU R: 0.067 / ESU R Free: 0.06
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3561 6125 5.087 %
Rwork0.2828 114286 -
all0.287 --
obs-120411 99.939 %
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: 31.39 Å2
Baniso -1Baniso -2Baniso -3
1-6.14 Å20 Å20 Å2
2--7.703 Å20 Å2
3----13.844 Å2
Refinement stepCycle: LAST / Resolution: 2.27→73.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13710 0 5 28 13743
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01214097
X-RAY DIFFRACTIONr_bond_other_d0.0010.01612978
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.6519107
X-RAY DIFFRACTIONr_angle_other_deg0.5151.56730354
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.3945.0031696
X-RAY DIFFRACTIONr_dihedral_angle_2_deg10.329579
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.057102462
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.82910640
X-RAY DIFFRACTIONr_chiral_restr0.0710.22032
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0215756
X-RAY DIFFRACTIONr_gen_planes_other0.0020.022799
X-RAY DIFFRACTIONr_nbd_refined0.2880.24410
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2340.215711
X-RAY DIFFRACTIONr_nbtor_refined0.1980.26748
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0880.27799
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.290.2632
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1060.246
X-RAY DIFFRACTIONr_metal_ion_refined0.3420.211
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2370.257
X-RAY DIFFRACTIONr_nbd_other0.2010.2241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3470.28
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.2030.21
X-RAY DIFFRACTIONr_mcbond_it2.8023.2846801
X-RAY DIFFRACTIONr_mcbond_other2.8023.2846801
X-RAY DIFFRACTIONr_mcangle_it4.124.928489
X-RAY DIFFRACTIONr_mcangle_other4.124.9218490
X-RAY DIFFRACTIONr_scbond_it2.1763.2177296
X-RAY DIFFRACTIONr_scbond_other2.1763.2177295
X-RAY DIFFRACTIONr_scangle_it3.2024.8410618
X-RAY DIFFRACTIONr_scangle_other3.2024.8410619
X-RAY DIFFRACTIONr_lrange_it5.83642.85917551
X-RAY DIFFRACTIONr_lrange_other5.83642.8617552
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.27-2.3290.694120.6178389X-RAY DIFFRACTION99.2893
2.329-2.3930.6484720.5268110X-RAY DIFFRACTION100
2.393-2.4620.5144570.4667897X-RAY DIFFRACTION100
2.462-2.5380.5683910.3837821X-RAY DIFFRACTION100
2.538-2.6210.5223540.3547513X-RAY DIFFRACTION100
2.621-2.7130.4114040.2797226X-RAY DIFFRACTION100
2.713-2.8150.4633460.2957059X-RAY DIFFRACTION100
2.815-2.930.4093270.2526774X-RAY DIFFRACTION100
2.93-3.0610.3133400.236475X-RAY DIFFRACTION100
3.061-3.210.3522770.2616240X-RAY DIFFRACTION100
3.21-3.3830.2813450.2235890X-RAY DIFFRACTION100
3.383-3.5890.322810.2645615X-RAY DIFFRACTION100
3.589-3.8360.2882850.2395233X-RAY DIFFRACTION100
3.836-4.1430.3013120.2354877X-RAY DIFFRACTION100
4.143-4.5380.2782320.2254549X-RAY DIFFRACTION100
4.538-5.0730.2612370.2524110X-RAY DIFFRACTION100
5.073-5.8570.3392090.2533597X-RAY DIFFRACTION100
5.857-7.170.3162130.2413073X-RAY DIFFRACTION100
7.17-100.291450.2482439X-RAY DIFFRACTION100
8-73.490.307860.2981399X-RAY DIFFRACTION99.2647

+
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