[English] 日本語
Yorodumi
- PDB-8r56: Crystal structure of GH31 family Sulfoquinovosidase BmSQase in co... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8r56
TitleCrystal structure of GH31 family Sulfoquinovosidase BmSQase in covalent complex with SQ-aziridine (SQZ)
ComponentsGlycosyl hydrolase, family 31Glycoside hydrolase
KeywordsHYDROLASE / Glycoside hydrolase / CAZy family 31 / sulfoquinovose / activity-based probe
Function / homology
Function and homology information


Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, hydrolyzing O-glycosyl compounds / carbohydrate binding / carbohydrate metabolic process
Similarity search - Function
Sulfoquinovosidase YihQ-like / : / Glycosyl hydrolase family 31 C-terminal domain / Glycoside hydrolase family 31 / Glycosyl hydrolases family 31 TIM-barrel domain / Galactose mutarotase-like domain superfamily / Glycosyl hydrolase, all-beta / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / : / Glycosyl hydrolase, family 31
Similarity search - Component
Biological speciesPriestia megaterium DSM 319 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsSharma, M. / Davies, G.J.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Biotechnology and Biological Sciences Research Council (BBSRC)BB/W003805/1 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2024
Title: Detection of Sulfoquinovosidase Activity in Cell Lysates Using Activity-Based Probes.
Authors: Li, Z. / Pickles, I. / Sharma, M. / Melling, B. / Codee, J. / Pallasdies, L. / Williams, S. / Overkleeft, H. / Davies, G.J.
History
DepositionNov 16, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 8, 2024Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glycosyl hydrolase, family 31
B: Glycosyl hydrolase, family 31
C: Glycosyl hydrolase, family 31
D: Glycosyl hydrolase, family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)323,08812
Polymers321,9664
Non-polymers1,1218
Water10,575587
1
A: Glycosyl hydrolase, family 31
C: Glycosyl hydrolase, family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,5446
Polymers160,9832
Non-polymers5614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glycosyl hydrolase, family 31
D: Glycosyl hydrolase, family 31
hetero molecules


Theoretical massNumber of molelcules
Total (without water)161,5446
Polymers160,9832
Non-polymers5614
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.524, 194.726, 117.654
Angle α, β, γ (deg.)90.00, 92.29, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein
Glycosyl hydrolase, family 31 / Glycoside hydrolase


Mass: 80491.523 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Priestia megaterium DSM 319 (bacteria) / Gene: BMQ_3646 / Plasmid: pEt28a(+) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: D5E1T0
#2: Chemical
ChemComp-Y2W / [(1~{S},2~{R},3~{R},4~{S},6~{R})-6-azanyl-2,3,4-tris(oxidanyl)cyclohexyl]methanesulfonic acid


Mass: 241.262 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C7H15NO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 587 / 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: 2.22 Å3/Da / Density % sol: 44.68 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: A crystal of BmSQase was grown using a 30 mg mL-1 protein solution in buffer C, 0.15 uL protein. 0.15 uL mother liquor, the latter comprising 0.2 M KSCN and 20% w/v PEG (polyethylene glycol) ...Details: A crystal of BmSQase was grown using a 30 mg mL-1 protein solution in buffer C, 0.15 uL protein. 0.15 uL mother liquor, the latter comprising 0.2 M KSCN and 20% w/v PEG (polyethylene glycol) 3350 in 0.1 M Bis-TRIS propane buffer pH 7.5. A stock solution of 1 was prepared at 10 mM in mother liquor. Crystals were soaked for 5 min with 0.3 ul of 1 to a final concentration of 3 mM.

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.97624 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Sep 15, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97624 Å / Relative weight: 1
ReflectionResolution: 2.45→74.99 Å / Num. obs: 102876 / % possible obs: 99.9 % / Redundancy: 7.2 % / CC1/2: 0.986 / Rmerge(I) obs: 0.197 / Rpim(I) all: 0.08 / Rrim(I) all: 0.212 / Χ2: 1.11 / Net I/σ(I): 9.3 / Num. measured all: 737059
Reflection shellResolution: 2.45→2.49 Å / % possible obs: 100 % / Redundancy: 7 % / Rmerge(I) obs: 1.174 / Num. measured all: 36181 / Num. unique obs: 5135 / CC1/2: 0.637 / Rpim(I) all: 0.474 / Rrim(I) all: 1.267 / Χ2: 1.09 / Net I/σ(I) obs: 2.2

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
Aimlessdata scaling
xia2data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.45→62.55 Å / Cor.coef. Fo:Fc: 0.899 / Cor.coef. Fo:Fc free: 0.865 / SU B: 10.849 / SU ML: 0.237 / Cross valid method: THROUGHOUT / ESU R: 0.792 / ESU R Free: 0.289 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24405 4989 4.9 %RANDOM
Rwork0.21188 ---
obs0.21347 97274 99.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.234 Å2
Baniso -1Baniso -2Baniso -3
1--0.28 Å20 Å2-1.62 Å2
2--0.99 Å20 Å2
3----0.58 Å2
Refinement stepCycle: 1 / Resolution: 2.45→62.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21281 0 4 587 21872
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.01221886
X-RAY DIFFRACTIONr_bond_other_d0.0010.01619424
X-RAY DIFFRACTIONr_angle_refined_deg1.5251.81529805
X-RAY DIFFRACTIONr_angle_other_deg0.5681.74144587
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.95152683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.528590
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.226103271
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1780.23154
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0226251
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025273
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.8823.06910741
X-RAY DIFFRACTIONr_mcbond_other2.8813.06910741
X-RAY DIFFRACTIONr_mcangle_it4.3235.51213421
X-RAY DIFFRACTIONr_mcangle_other4.3235.51213422
X-RAY DIFFRACTIONr_scbond_it3.0633.18511145
X-RAY DIFFRACTIONr_scbond_other3.0633.18511143
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.7275.77316385
X-RAY DIFFRACTIONr_long_range_B_refined6.20628.4424078
X-RAY DIFFRACTIONr_long_range_B_other6.19528.4624040
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.45→2.514 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.329 380 -
Rwork0.28 7228 -
obs--99.92 %

+
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