[English] 日本語
Yorodumi
- PDB-2xn2: Structure of alpha-galactosidase from Lactobacillus acidophilus N... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2xn2
TitleStructure of alpha-galactosidase from Lactobacillus acidophilus NCFM with galactose
ComponentsALPHA-GALACTOSIDASE
KeywordsHYDROLASE / GLYCOSIDASE
Function / homology
Function and homology information


response to raffinose / alpha-galactosidase / alpha-galactosidase activity / carbohydrate catabolic process / protein homotetramerization
Similarity search - Function
alpha-galactosidase from lactobacil brevis / Glycosyl hydrolase family 36, N-terminal / Glycosyl hydrolase family 36, C-terminal / Alpha-galactosidase, N-terminal domain superfamily / Glycosyl hydrolase family 36 C-terminal domain / Glycosyl hydrolase family 36 N-terminal domain / Glycoside hydrolase family 36 / Melibiase / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. ...alpha-galactosidase from lactobacil brevis / Glycosyl hydrolase family 36, N-terminal / Glycosyl hydrolase family 36, C-terminal / Alpha-galactosidase, N-terminal domain superfamily / Glycosyl hydrolase family 36 C-terminal domain / Glycosyl hydrolase family 36 N-terminal domain / Glycoside hydrolase family 36 / Melibiase / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Beta-galactosidase; Chain A, domain 5 / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Distorted Sandwich / 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-D-galactopyranose / IMIDAZOLE / Alpha-galactosidase Mel36A / Alpha-galactosidase Mel36A
Similarity search - Component
Biological speciesLACTOBACILLUS ACIDOPHILUS NCFM (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsFredslund, F. / Abou Hachem, M. / Larsen, R.J. / Sorensen, P.G. / Lo Leggio, L. / Svensson, B.
CitationJournal: J.Mol.Biol. / Year: 2011
Title: Crystal Structure of Alpha-Galactosidase from Lactobacillus Acidophilus Ncfm: Insight Into Tetramer Formation and Substrate Binding.
Authors: Fredslund, F. / Abou Hachem, M. / Jonsgaard Larsen, R. / Gerd Sorensen, P. / Coutinho, P.M. / Lo Leggio, L. / Svensson, B.
History
DepositionJul 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 10, 2011Provider: repository / Type: Initial release
Revision 1.1Aug 31, 2011Group: Database references / Structure summary
Revision 1.2Sep 14, 2011Group: Database references
Revision 1.3Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_leaving_atom_flag
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 700 SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AI" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: ALPHA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,17228
Polymers84,6201
Non-polymers2,55227
Water11,241624
1
A: ALPHA-GALACTOSIDASE
hetero molecules

A: ALPHA-GALACTOSIDASE
hetero molecules

A: ALPHA-GALACTOSIDASE
hetero molecules

A: ALPHA-GALACTOSIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)348,686112
Polymers338,4804
Non-polymers10,206108
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z1
crystal symmetry operation2_565-x,-y+1,z1
crystal symmetry operation4_565x,-y+1,-z1
Buried area53500 Å2
ΔGint-83.2 kcal/mol
Surface area81450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.610, 126.700, 148.360
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2094-

HOH

21A-2236-

HOH

31A-2501-

HOH

-
Components

#1: Protein ALPHA-GALACTOSIDASE


Mass: 84619.977 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOBACILLUS ACIDOPHILUS NCFM (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q7WWP9, UniProt: G1UB44*PLUS, alpha-galactosidase
#2: Sugar ChemComp-GLA / alpha-D-galactopyranose / alpha-D-galactose / D-galactose / galactose / ALPHA D-GALACTOSE


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-galactopyranoseCOMMON NAMEGMML 1.0
a-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#4: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 624 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsALPHA D-GALACTOSE (GLA): PRESENT IN THE ACTIVE SITE IMIDAZOLE (IMD): BOUND NEAR THE ACTIVE SITE

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.53 Å3/Da / Density % sol: 51.4 % / Description: NONE
Crystal growpH: 7.5
Details: 8-12% PEG8000, 0.1M IMIDAZOLE, 10% GLYCEROL, pH 7.5

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03908
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 4, 2009 / Details: MIRRORS
RadiationMonochromator: BENT SI (111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03908 Å / Relative weight: 1
ReflectionResolution: 1.58→19.63 Å / Num. obs: 117007 / % possible obs: 92 % / Observed criterion σ(I): 2 / Redundancy: 4.1 % / Biso Wilson estimate: 11.62 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 13.7
Reflection shellResolution: 1.58→1.62 Å / Redundancy: 4 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 2.53 / % possible all: 80.6

-
Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2XN0

2xn0


Resolution: 1.58→19.632 Å / SU ML: 0.15 / σ(F): 1.99 / Phase error: 13.48 / Stereochemistry target values: ML / Details: RESIDUES 1-3 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.1554 2000 1.7 %
Rwork0.131 --
obs0.1315 117007 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 55.183 Å2 / ksol: 0.473 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-2.2323 Å20 Å20 Å2
2---1.1441 Å20 Å2
3----1.0882 Å2
Refinement stepCycle: LAST / Resolution: 1.58→19.632 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5938 0 167 624 6729
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136315
X-RAY DIFFRACTIONf_angle_d1.58512
X-RAY DIFFRACTIONf_dihedral_angle_d20.352363
X-RAY DIFFRACTIONf_chiral_restr0.104874
X-RAY DIFFRACTIONf_plane_restr0.0081097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5803-1.63680.22721970.214811288X-RAY DIFFRACTION98
1.6368-1.70230.24161970.188711398X-RAY DIFFRACTION100
1.7023-1.77970.20522000.167111435X-RAY DIFFRACTION100
1.7797-1.87350.17931990.142211488X-RAY DIFFRACTION100
1.8735-1.99070.15352000.121211484X-RAY DIFFRACTION100
1.9907-2.14430.14371990.109111481X-RAY DIFFRACTION100
2.1443-2.35970.12282010.105311532X-RAY DIFFRACTION100
2.3597-2.70040.14252020.107511570X-RAY DIFFRACTION100
2.7004-3.39940.12962010.107411613X-RAY DIFFRACTION100
3.3994-19.63380.14262040.137111718X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.196-0.0110.0250.15190.01940.05980.00720.0224-0.0272-0.0260.00640.00370.00680.0003-0.01140.033-0.0059-0.0010.0311-0.00690.0318-2.219745.8062-26.3967
20.1207-0.02950.03550.1708-0.02650.2525-0.00250.01610.0002-0.0090.0054-0.0427-0.01330.055-0.00950.073-0.00380.01090.0844-0.01480.085631.451450.9258-27.7261
30.06930.0333-0.05020.0387-0.04310.0825-0.0176-0.0368-0.01390.0082-0.0007-0.0320.03060.02120.01740.09470.0039-0.00160.0741-0.0040.098121.724141.11832.865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A AND RESID 4:332
2X-RAY DIFFRACTION2CHAIN A AND RESID 333:630
3X-RAY DIFFRACTION3CHAIN A AND RESID 631:732

+
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://pdbjlvh1.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