[English] 日本語
Yorodumi
- PDB-6lck: TtGalA, alpha-galactosidase from Thermus thermophilus in complex ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6lck
TitleTtGalA, alpha-galactosidase from Thermus thermophilus in complex with p-nitrophenyl alpha-D-galactopyranoside (alpha-NPG)
ComponentsAlpha-galactosidase
KeywordsHYDROLASE / alpha-galactosidase / hexamer assembly / substrate specificity / thermostable / stachyose
Function / homology
Function and homology information


alpha-galactosidase activity / carbohydrate catabolic process
Similarity search - Function
Glycoside hydrolase family 36 / Melibiase / : / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
4-nitrophenyl alpha-D-galactopyranoside / Alpha-galactosidase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.85 Å
AuthorsChen, S.C. / Hsu, C.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology (Taiwan)108-2628-B-002-013 Taiwan
Ministry of Science and Technology (Taiwan)108-2113-M-002-011 Taiwan
CitationJournal: J.Agric.Food Chem. / Year: 2020
Title: Crystal Structure of alpha-Galactosidase fromThermus thermophilus: Insight into Hexamer Assembly and Substrate Specificity.
Authors: Chen, S.C. / Wu, S.P. / Chang, Y.Y. / Hwang, T.S. / Lee, T.H. / Hsu, C.H.
History
DepositionNov 19, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 1, 2020Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.mon_nstd_flag / _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-galactosidase
B: Alpha-galactosidase
C: Alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)162,8636
Polymers161,9593
Non-polymers9043
Water00
1
B: Alpha-galactosidase
C: Alpha-galactosidase
hetero molecules

B: Alpha-galactosidase
C: Alpha-galactosidase
hetero molecules

A: Alpha-galactosidase
hetero molecules

A: Alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)325,72512
Polymers323,9186
Non-polymers1,8076
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
crystal symmetry operation5_445x-1/2,y-1/2,z1
crystal symmetry operation7_544-x+1/2,y-1/2,-z-1/21
Unit cell
Length a, b, c (Å)118.631, 205.288, 163.898
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2

-
Components

#1: Protein Alpha-galactosidase / GalA


Mass: 53986.309 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (bacteria)
Gene: TTHB115 / Production host: Escherichia coli (E. coli) / References: UniProt: Q53W51
#2: Sugar ChemComp-9PG / 4-nitrophenyl alpha-D-galactopyranoside / 4-nitrophenyl alpha-D-galactoside / 4-nitrophenyl D-galactoside / 4-nitrophenyl galactoside


Type: D-saccharide / Mass: 301.249 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C12H15NO8 / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.08 Å3/Da / Density % sol: 60.07 %
Crystal growTemperature: 283 K / Method: vapor diffusion, sitting drop / Details: 0.1M CAPSO pH 9.2, 0.2M Li2SO4, 10% PEG 3000

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.9762 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 14, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.85→30 Å / Num. obs: 46936 / % possible obs: 99.9 % / Redundancy: 7.4 % / Biso Wilson estimate: 47.39 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 19.9
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 0.505 / Num. unique obs: 4617

-
Processing

Software
NameVersionClassification
PHENIX1.13_2998refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: apo structure

Resolution: 2.85→28.06 Å / SU ML: 0.3067 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.4079
RfactorNum. reflection% reflection
Rfree0.2224 2010 4.29 %
Rwork0.1736 --
obs0.1757 46892 99.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 43.38 Å2
Refinement stepCycle: LAST / Resolution: 2.85→28.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11487 0 63 0 11550
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009211919
X-RAY DIFFRACTIONf_angle_d1.058116224
X-RAY DIFFRACTIONf_chiral_restr0.05251626
X-RAY DIFFRACTIONf_plane_restr0.00682142
X-RAY DIFFRACTIONf_dihedral_angle_d3.74016891
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.85-2.920.29171410.2173109X-RAY DIFFRACTION99.09
2.92-30.30851380.22283168X-RAY DIFFRACTION100
3-3.090.28651390.223166X-RAY DIFFRACTION99.94
3.09-3.190.27351470.20453208X-RAY DIFFRACTION99.97
3.19-3.30.28481430.20113184X-RAY DIFFRACTION100
3.3-3.430.27371420.19943195X-RAY DIFFRACTION100
3.43-3.590.25251370.19193173X-RAY DIFFRACTION99.97
3.59-3.780.21951470.17673192X-RAY DIFFRACTION100
3.78-4.010.22711430.16563194X-RAY DIFFRACTION100
4.01-4.320.17911440.1523218X-RAY DIFFRACTION100
4.32-4.760.19081480.14193224X-RAY DIFFRACTION100
4.76-5.440.16931480.15063237X-RAY DIFFRACTION100
5.44-6.840.23551410.17773260X-RAY DIFFRACTION100
6.84-28.060.17721520.15353354X-RAY DIFFRACTION99.26

+
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