[English] 日本語
Yorodumi
- PDB-1zy9: Crystal structure of Alpha-galactosidase (EC 3.2.1.22) (Melibiase... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1zy9
TitleCrystal structure of Alpha-galactosidase (EC 3.2.1.22) (Melibiase) (tm1192) from Thermotoga maritima at 2.34 A resolution
Componentsalpha-galactosidase
KeywordsHYDROLASE / tm1192 / Alpha-galactosidase (EC 3.2.1.22) (Melibiase) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
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 ...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
Alpha-galactosidase / Alpha-galactosidase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.34 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: to be published
Title: Crystal structure of alpha-galactosidase (ec 3.2.1.22) (melibiase) (tm1192) from Thermotoga maritima at 2.34 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionJun 9, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 12, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / struct_conn ...database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,0086
Polymers65,6681
Non-polymers3405
Water4,396244
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)121.729, 160.533, 88.258
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221

-
Components

#1: Protein alpha-galactosidase


Mass: 65667.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: tm1192 / Production host: Escherichia coli (E. coli)
References: UniProt: O33835, UniProt: G4FEF4*PLUS, alpha-galactosidase
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 244 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.4 Å3/Da / Density % sol: 63.58 %
Crystal growTemperature: 273 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.3
Details: 0.2M K3Cirtrate, 20.0% PEG-3350, No Buffer, pH 8.3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 273K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.979413, 0.918370, 0.979170
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 1, 2005
Details: Flat mirror, Side-defelecting monochromator (Si 111)
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9794131
20.918371
30.979171
ReflectionResolution: 2.34→42.88 Å / Num. obs: 35967 / % possible obs: 98 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.129 / Rsym value: 0.129 / Net I/σ(I): 5.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsRsym value
2.34-2.4799.43.70.6031.352880.603
2.47-2.6299.13.70.4721.649660.472
2.62-2.898.93.70.3562.147080.356
2.8-3.0298.63.70.2383.243270.238
3.02-3.3198.23.70.151539910.151
3.31-3.797.73.70.0977.836210.097
3.7-4.2796.63.70.0729.831530.072
4.27-5.23963.70.05812.226700.058
5.23-7.495.53.70.06211.520740.062
7.4-42.8893.93.60.04213.611690.042

-
Phasing

PhasingMethod: MAD

-
Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
SCALAdata scaling
PDB_EXTRACT1.601data extraction
XDSdata reduction
CCP4(SCALA)data scaling
SHELXDphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.34→42.504 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.837 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.207 / ESU R Free: 0.187
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE DENSITY BLOB BETWEEN SIDE CHAINS OF A220,A387 IS TENATIVELY MODELED AS A GLYCEROL.
RfactorNum. reflection% reflectionSelection details
Rfree0.213 1792 5 %RANDOM
Rwork0.162 ---
all0.165 ---
obs-34093 97.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.38 Å20 Å20 Å2
2--1.61 Å20 Å2
3----1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.34→42.504 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4232 0 22 244 4498
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0224397
X-RAY DIFFRACTIONr_bond_other_d0.0010.023954
X-RAY DIFFRACTIONr_angle_refined_deg1.551.9555970
X-RAY DIFFRACTIONr_angle_other_deg0.81239198
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.1025535
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.94824.258209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.63315732
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7581524
X-RAY DIFFRACTIONr_chiral_restr0.0890.2638
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024881
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02919
X-RAY DIFFRACTIONr_nbd_refined0.1930.2839
X-RAY DIFFRACTIONr_nbd_other0.1840.24137
X-RAY DIFFRACTIONr_nbtor_refined0.1830.22130
X-RAY DIFFRACTIONr_nbtor_other0.0890.22672
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2214
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1080.26
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1750.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1370.25
X-RAY DIFFRACTIONr_mcbond_it2.58832841
X-RAY DIFFRACTIONr_mcbond_other0.50831066
X-RAY DIFFRACTIONr_mcangle_it3.32454284
X-RAY DIFFRACTIONr_scbond_it5.91781997
X-RAY DIFFRACTIONr_scangle_it7.69111682
LS refinement shellResolution: 2.34→2.401 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 123 -
Rwork0.236 2559 -
obs--99.3 %

+
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