[English] 日本語
Yorodumi
- PDB-7omi: Bs164 in complex with mannocyclophellitol epoxide -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7omi
TitleBs164 in complex with mannocyclophellitol epoxide
ComponentsGlyco_hydro_42M domain-containing protein
KeywordsHYDROLASE / Inhibitor complex
Function / homology
Function and homology information


beta-galactosidase activity / carbohydrate metabolic process
Similarity search - Function
Glycoside hydrolase, family 42 / Beta-galactosidase trimerisation / Beta-galactosidase trimerisation domain / Class I glutamine amidotransferase-like / Glycoside hydrolase superfamily
Similarity search - Domain/homology
L(+)-TARTARIC ACID / Chem-VKN / Beta-galactosidase trimerisation domain-containing protein
Similarity search - Component
Biological speciesBacteroides salyersiae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å
AuthorsArmstrong, Z. / Mcgregor, N. / Davies, G.
CitationJournal: Org.Biomol.Chem. / Year: 2022
Title: Synthesis of broad-specificity activity-based probes for exo -beta-mannosidases.
Authors: McGregor, N.G.S. / Kuo, C.L. / Beenakker, T.J.M. / Wong, C.S. / Offen, W.A. / Armstrong, Z. / Florea, B.I. / Codee, J.D.C. / Overkleeft, H.S. / Aerts, J.M.F.G. / Davies, G.J.
History
DepositionMay 24, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 2, 2022Provider: repository / Type: Initial release
Revision 1.1Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Glyco_hydro_42M domain-containing protein
BBB: Glyco_hydro_42M domain-containing protein
CCC: Glyco_hydro_42M domain-containing protein
DDD: Glyco_hydro_42M domain-containing protein
EEE: Glyco_hydro_42M domain-containing protein
FFF: Glyco_hydro_42M domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)465,03959
Polymers460,0606
Non-polymers4,97953
Water38,4622135
1
AAA: Glyco_hydro_42M domain-containing protein
CCC: Glyco_hydro_42M domain-containing protein
DDD: Glyco_hydro_42M domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,61331
Polymers230,0303
Non-polymers2,58328
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13840 Å2
ΔGint-10 kcal/mol
Surface area67520 Å2
MethodPISA
2
BBB: Glyco_hydro_42M domain-containing protein
EEE: Glyco_hydro_42M domain-containing protein
FFF: Glyco_hydro_42M domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)232,42628
Polymers230,0303
Non-polymers2,39625
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12870 Å2
ΔGint-16 kcal/mol
Surface area67210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.452, 104.426, 170.781
Angle α, β, γ (deg.)92.292, 97.351, 106.554
Int Tables number1
Space group name H-MP1

-
Components

-
Protein / Sugars , 2 types, 12 molecules AAABBBCCCDDDEEEFFF

#1: Protein
Glyco_hydro_42M domain-containing protein


Mass: 76676.672 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides salyersiae (bacteria) / Gene: HMPREF1071_03408 / Production host: Escherichia coli (E. coli) / References: UniProt: I9SUA3
#5: Sugar
ChemComp-VKN / (1R,2S,4S,5R)-6-(hydroxymethyl)cyclohexane-1,2,3,4,5-pentol


Type: saccharide / Mass: 194.182 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C7H14O6 / Feature type: SUBJECT OF INVESTIGATION

-
Non-polymers , 4 types, 2182 molecules

#2: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 29 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-TLA / L(+)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H6O6
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2135 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.55 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Ammonium tartrate pH 6.5 , 14 % PEG 3,350

-
Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.976284 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Apr 25, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976284 Å / Relative weight: 1
ReflectionResolution: 1.76→65.87 Å / Num. obs: 438305 / % possible obs: 97.2 % / Redundancy: 3.1 % / CC1/2: 0.994 / Net I/σ(I): 7.6
Reflection shellResolution: 1.76→1.79 Å / Num. unique obs: 21409 / CC1/2: 0.302

-
Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
DIALSdata reduction
xia2data scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6T7G

6t7g


Resolution: 1.76→65.87 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.93 / Cross valid method: FREE R-VALUE / ESU R: 0.146 / ESU R Free: 0.135
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2609 22062 5.035 %
Rwork0.2314 416151 -
all0.233 --
obs-438213 97.15 %
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: 34.914 Å2
Baniso -1Baniso -2Baniso -3
1-1.461 Å21.673 Å2-0.551 Å2
2--0.165 Å20.088 Å2
3----2.376 Å2
Refinement stepCycle: LAST / Resolution: 1.76→65.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms31540 0 314 2135 33989
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.01332708
X-RAY DIFFRACTIONr_bond_other_d0.0350.01729439
X-RAY DIFFRACTIONr_angle_refined_deg1.4221.64344233
X-RAY DIFFRACTIONr_angle_other_deg2.3111.57368605
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.34753922
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.57323.9191628
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.339155522
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1881591
X-RAY DIFFRACTIONr_chiral_restr0.0710.24223
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0236252
X-RAY DIFFRACTIONr_gen_planes_other0.010.026965
X-RAY DIFFRACTIONr_nbd_refined0.20.25996
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2090.226083
X-RAY DIFFRACTIONr_nbtor_refined0.170.215642
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0670.212714
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.21880
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2210.24
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2120.215
X-RAY DIFFRACTIONr_nbd_other0.2640.280
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1940.27
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0260.21
X-RAY DIFFRACTIONr_mcbond_it2.8253.56215703
X-RAY DIFFRACTIONr_mcbond_other2.8253.56215702
X-RAY DIFFRACTIONr_mcangle_it3.7765.33519620
X-RAY DIFFRACTIONr_mcangle_other3.7775.33519621
X-RAY DIFFRACTIONr_scbond_it3.4333.85817005
X-RAY DIFFRACTIONr_scbond_other3.4333.85817006
X-RAY DIFFRACTIONr_scangle_it4.9855.65224613
X-RAY DIFFRACTIONr_scangle_other4.9855.65224614
X-RAY DIFFRACTIONr_lrange_it6.0640.97936911
X-RAY DIFFRACTIONr_lrange_other6.05740.94736863
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.76-1.8060.37217190.35930319X-RAY DIFFRACTION95.8619
1.806-1.8550.34115800.34129693X-RAY DIFFRACTION96.1211
1.855-1.9090.31914450.30228688X-RAY DIFFRACTION95.4361
1.909-1.9680.31714730.2928203X-RAY DIFFRACTION96.5324
1.968-2.0320.29514180.27827372X-RAY DIFFRACTION96.5719
2.032-2.1030.28414160.25726460X-RAY DIFFRACTION96.7782
2.103-2.1830.27913700.24725600X-RAY DIFFRACTION97.3014
2.183-2.2720.26313520.23624716X-RAY DIFFRACTION97.5124
2.272-2.3730.26512200.23123629X-RAY DIFFRACTION96.8394
2.373-2.4890.27112070.2322482X-RAY DIFFRACTION96.6031
2.489-2.6230.27611690.23821669X-RAY DIFFRACTION98.0256
2.623-2.7820.27111220.22220431X-RAY DIFFRACTION97.7638
2.782-2.9750.24210630.21419335X-RAY DIFFRACTION98.5792
2.975-3.2130.259010.22218031X-RAY DIFFRACTION98.4094
3.213-3.5190.2788840.2416640X-RAY DIFFRACTION98.6156
3.519-3.9340.2567780.23815036X-RAY DIFFRACTION98.7326
3.934-4.5430.2827020.2513177X-RAY DIFFRACTION98.0294
4.543-5.5630.1775380.15311253X-RAY DIFFRACTION98.8929
5.563-7.8630.1974560.1678702X-RAY DIFFRACTION98.9626
7.863-65.870.1982490.1684717X-RAY DIFFRACTION98.4731

+
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