[English] 日本語
Yorodumi
- PDB-5m16: Structure of GH36 alpha-galactosidase from Thermotoga maritima in... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5m16
TitleStructure of GH36 alpha-galactosidase from Thermotoga maritima in complex with a hydrolysed cyclopropyl carbasugar.
ComponentsAlpha-galactosidase
KeywordsHYDROLASE / Alpha-galactosidase / glycoside hydrolase
Function / homology
Function and homology information


alpha-galactosidase / alpha-galactosidase activity / glycoside catabolic process / carbohydrate binding / carbohydrate metabolic process / protein homodimerization activity
Similarity search - Function
Immunoglobulin-like - #2760 / Alpha-galactosidase, N-terminal / Melibiase / : / Galactose mutarotase-like domain superfamily / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel ...Immunoglobulin-like - #2760 / Alpha-galactosidase, N-terminal / Melibiase / : / Galactose mutarotase-like domain superfamily / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-7D2 / Alpha-galactosidase / Alpha-galactosidase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsPengelly, R. / Gloster, T.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2016
Title: Structural Snapshots for Mechanism-Based Inactivation of a Glycoside Hydrolase by Cyclopropyl Carbasugars.
Authors: Adamson, C. / Pengelly, R.J. / Shamsi Kazem Abadi, S. / Chakladar, S. / Draper, J. / Britton, R. / Gloster, T.M. / Bennet, A.J.
History
DepositionOct 7, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 9, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2016Group: Database references
Revision 1.2Jan 17, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,6055
Polymers66,1981
Non-polymers4074
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area500 Å2
ΔGint-37 kcal/mol
Surface area20230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.300, 96.020, 98.050
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Alpha-galactosidase


Mass: 66198.094 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: galA / Production host: Escherichia coli (E. coli)
References: UniProt: O33835, UniProt: G4FEF4*PLUS, alpha-galactosidase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-7D2 / (1~{R},2~{S},3~{S},4~{S},5~{S},6~{S})-1-(hydroxymethyl)bicyclo[4.1.0]heptane-2,3,4,5-tetrol


Mass: 190.194 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H14O5
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.43 Å3/Da / Density % sol: 49.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M magnesium sulfate, 20% (w/v) PEG 3350 Crystals were soaked for 7 days in 1 mM inhibitor, 30% (w/v) PEG 3350 before freezing.
Temp details: Room temperature

-
Data collection

DiffractionMean temperature: 80 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Oct 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 1.62→55.66 Å / Num. obs: 82206 / % possible obs: 99.6 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.055 / Net I/σ(I): 15.8
Reflection shellResolution: 1.62→1.66 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.4 / % possible all: 99.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5M0X

5m0x


Resolution: 1.62→55.66 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.069 / SU ML: 0.067 / Cross valid method: THROUGHOUT / ESU R: 0.081 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19788 4059 4.9 %RANDOM
Rwork0.1722 ---
obs0.17351 78077 99.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.183 Å2
Baniso -1Baniso -2Baniso -3
1-3.26 Å20 Å20 Å2
2---1.45 Å20 Å2
3----1.81 Å2
Refinement stepCycle: 1 / Resolution: 1.62→55.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4316 0 24 355 4695
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0194570
X-RAY DIFFRACTIONr_bond_other_d0.0010.024247
X-RAY DIFFRACTIONr_angle_refined_deg1.6071.9586222
X-RAY DIFFRACTIONr_angle_other_deg0.8473.0019809
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9755556
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.61124225
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.16315769
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.641530
X-RAY DIFFRACTIONr_chiral_restr0.110.2658
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0215193
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021073
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_it2.3332.1552191
X-RAY DIFFRACTIONr_mcbond_other2.3312.1542190
X-RAY DIFFRACTIONr_mcangle_it3.0163.222758
X-RAY DIFFRACTIONr_mcangle_other3.0163.2222759
X-RAY DIFFRACTIONr_scbond_it3.6682.5022379
X-RAY DIFFRACTIONr_scbond_other3.6682.5022380
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.1953.6073462
X-RAY DIFFRACTIONr_long_range_B_refined5.98925.2225072
X-RAY DIFFRACTIONr_long_range_B_other5.98825.2225073
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 276 -
Rwork0.273 5763 -
obs--99.65 %

+
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