[English] 日本語
Yorodumi
- PDB-1t0o: The structure of alpha-galactosidase from Trichoderma reesei comp... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1t0o
TitleThe structure of alpha-galactosidase from Trichoderma reesei complexed with beta-D-galactose
Componentsalpha-galactosidase
KeywordsHYDROLASE / (beta/alpha)8 barrel / two domains / glycoprotein / complex / beta-D-galactose
Function / homology
Function and homology information


alpha-galactosidase / alpha-galactosidase activity / carbohydrate metabolic process / extracellular region
Similarity search - Function
Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / Aldolase class I / Aldolase-type TIM barrel ...Alpha galactosidase, C-terminal beta sandwich domain / Alpha galactosidase C-terminal beta sandwich domain / Alpha galactosidase A / Glycoside hydrolase, family 27 / Glycoside hydrolase family 27/36, conserved site / Alpha-galactosidase signature. / Golgi alpha-mannosidase II / Glycosyl hydrolase, all-beta / 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
beta-D-galactopyranose / : / Alpha-galactosidase
Similarity search - Component
Biological speciesHypocrea jecorina (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å
AuthorsGolubev, A.M. / Nagem, R.A.P. / Brandao Neto, J.R. / Neustroev, K.N. / Eneyskaya, E.V. / Kulminskaya, A.A. / Shabalin, K.A. / Savel'ev, A.N. / Polikarpov, I.
Citation
Journal: J.Mol.Biol. / Year: 2004
Title: Crystal structure of alpha-galactosidase from Trichoderma reesei and its complex with galactose: implications for catalytic mechanism
Authors: Golubev, A.M. / Nagem, R.A.P. / Brandao Neto, J.R. / Neustroev, K.N. / Eneyskaya, E.V. / Kulminskaya, A.A. / Shabalin, K.A. / Savel'ev, A.N. / Polikarpov, I.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of alpha-galactosidase from Trichoderma reesei.
Authors: Golubev, A.M. / Neustroev, K.N.
History
DepositionApr 12, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 23, 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
Revision 2.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE Leu37, Pro70, Ala72, Ala88, Asn148, Phe151, Lys153, Thr161, Asp165, Thr167, Gly185, ...SEQUENCE Leu37, Pro70, Ala72, Ala88, Asn148, Phe151, Lys153, Thr161, Asp165, Thr167, Gly185, His196, Met202, Gln207, Ser216, Asp225, Asn230, Arg236, Leu238, Leu240, Leu245, Asp249, Met258, Asn297, Asn300, Ile327, Val335, Tyr337, Phe341, Val355, Ile360, Ala362, Thr363, Asn369, His378, Ser386, Asp389, Ala398, Gln415, Arg416 differ from the sequence database. These residues were used on the basis of the electron density map. The difference may be due to the use of different strains of Trichoderma reesei for sequencing and for the X-ray structure.

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: alpha-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6246
Polymers45,6111
Non-polymers3,0135
Water6,918384
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)57.834, 58.313, 153.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe biological assembly is a monomer

-
Components

-
Protein / Non-polymers , 2 types, 385 molecules A

#1: Protein alpha-galactosidase


Mass: 45610.863 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Hypocrea jecorina (fungus)
References: GenBank: 1580816, UniProt: Q92456*PLUS, alpha-galactosidase
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 384 / Source method: isolated from a natural source / Formula: H2O

-
Sugars , 4 types, 5 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 1235.105 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpa1-6[DManpa1-3]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,7,6/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3-3-3/a4-b1_b4-c1_c3-d1_c6-e1_e3-f1_e6-g1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#5: Sugar ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: EG 6000, potassium phosphate, sodium phosphate, D-galactose, VAPOR DIFFUSION, HANGING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: D03B-MX1 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 25, 1998
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→9.9 Å / Num. obs: 28741 / % possible obs: 63.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Biso Wilson estimate: 25.2 Å2 / Rsym value: 0.07 / Net I/σ(I): 10.1
Reflection shellResolution: 2→2.05 Å / Rsym value: 0.364 / % possible all: 64

-
Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1SZN

1szn


Resolution: 1.96→9 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.944 / SU B: 4.034 / SU ML: 0.115 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.225 / ESU R Free: 0.184 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.20491 2659 10 %RANDOM
Rwork0.15141 ---
all0.169 26738 --
obs0.15686 24004 72.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.205 Å2
Baniso -1Baniso -2Baniso -3
1-1.78 Å20 Å20 Å2
2---0.5 Å20 Å2
3----1.29 Å2
Refinement stepCycle: LAST / Resolution: 1.96→9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3213 0 201 384 3798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0213524
X-RAY DIFFRACTIONr_angle_refined_deg1.5941.9924836
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5563416
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.97515533
X-RAY DIFFRACTIONr_chiral_restr0.1390.2562
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022599
X-RAY DIFFRACTIONr_nbd_refined0.2170.32006
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.5543
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.334
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.210.520
X-RAY DIFFRACTIONr_mcbond_it0.6631.52069
X-RAY DIFFRACTIONr_mcangle_it1.23723312
X-RAY DIFFRACTIONr_scbond_it1.93831455
X-RAY DIFFRACTIONr_scangle_it3.1184.51524
LS refinement shellResolution: 1.96→2.025 Å / Total num. of bins used: 15 /
RfactorNum. reflection
Rfree0.253 224
Rwork0.198 2111

+
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