[English] 日本語
Yorodumi
- PDB-3thd: Crystal structure of human beta-galactosidase in complex with 1-d... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3thd
TitleCrystal structure of human beta-galactosidase in complex with 1-deoxygalactonojirimycin
ComponentsBeta-galactosidase
KeywordsHYDROLASE / BETA-GALACTOSIDASE / TIM-BARREL DOMAIN / GLYCOSYL HYDROLASE / Glycosylation
Function / homology
Function and homology information


MPS IV - Morquio syndrome B / keratan sulfate proteoglycan catabolic process / response to cortisone / response to Thyroglobulin triiodothyronine / Defective NEU1 causes sialidosis / Keratan sulfate degradation / galactose catabolic process / Sialic acid metabolism / heparan sulfate proteoglycan catabolic process / glycosphingolipid catabolic process ...MPS IV - Morquio syndrome B / keratan sulfate proteoglycan catabolic process / response to cortisone / response to Thyroglobulin triiodothyronine / Defective NEU1 causes sialidosis / Keratan sulfate degradation / galactose catabolic process / Sialic acid metabolism / heparan sulfate proteoglycan catabolic process / glycosphingolipid catabolic process / HS-GAG degradation / glycoprotein catabolic process / galactoside binding / Glycosphingolipid catabolism / beta-galactosidase / ganglioside catabolic process / vacuole / beta-galactosidase activity / lysosomal lumen / azurophil granule lumen / carbohydrate metabolic process / ficolin-1-rich granule lumen / lysosome / intracellular membrane-bounded organelle / Neutrophil degranulation / perinuclear region of cytoplasm / Golgi apparatus / protein homodimerization activity / extracellular exosome / extracellular region / membrane / cytoplasm
Similarity search - Function
Beta-galactosidase 1-like / : / Beta-galactosidase, first all-beta domain / : / Beta-galactosidase second all-beta domain / Beta-galactosidase, galactose-binding domain / Glycoside hydrolase, family 35, conserved site / Glycosyl hydrolases family 35 putative active site. / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 ...Beta-galactosidase 1-like / : / Beta-galactosidase, first all-beta domain / : / Beta-galactosidase second all-beta domain / Beta-galactosidase, galactose-binding domain / Glycoside hydrolase, family 35, conserved site / Glycosyl hydrolases family 35 putative active site. / Glycoside hydrolase 35, catalytic domain / Glycosyl hydrolases family 35 / Glycoside hydrolase, family 35 / Galactose-binding domain-like / Galactose-binding-like domain superfamily / Glycosidases / Glycoside hydrolase superfamily / Jelly Rolls / TIM Barrel / Alpha-Beta Barrel / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-DGJ / Beta-galactosidase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.79 Å
AuthorsOhto, U. / Shimizu, T.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal structure of human beta-galactosidase: structural basis of Gm1 gangliosidosis and morquio B diseases
Authors: Ohto, U. / Usui, K. / Ochi, T. / Yuki, K. / Satow, Y. / Shimizu, T.
History
DepositionAug 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / 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_entity_nonpoly.name / _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_seq_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 1.3Nov 1, 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 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-galactosidase
B: Beta-galactosidase
C: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)300,26044
Polymers294,6614
Non-polymers5,59940
Water39,3452184
1
A: Beta-galactosidase
D: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,13022
Polymers147,3312
Non-polymers2,79920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6170 Å2
ΔGint-39 kcal/mol
Surface area44370 Å2
MethodPISA
2
B: Beta-galactosidase
C: Beta-galactosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)150,13022
Polymers147,3312
Non-polymers2,79920
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6160 Å2
ΔGint-38 kcal/mol
Surface area44440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)94.792, 115.996, 140.327
Angle α, β, γ (deg.)90.00, 92.22, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

-
Protein / Sugars , 2 types, 20 molecules ABCD

#1: Protein
Beta-galactosidase


Mass: 73665.336 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GLB1, ELNR1 / Production host: Pichia pastoris (fungus) / References: UniProt: P16278, beta-galactosidase
#2: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 16
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

-
Non-polymers , 5 types, 2208 molecules

#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-DGJ / (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol / 1-deoxygalactonojirimycin


Mass: 163.172 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H13NO4 / Comment: medication, Galafold*YM
#5: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: SO4
#6: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2184 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% (w/v) PEG3350 0.2M ammonium sulfate 100mM Tris HCl pH 8.0 , VAPOR DIFFUSION, SITTING DROP, temperature 293K

-
Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Oct 24, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.79→29.29 Å / Num. obs: 249160

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3D3A

3d3a


Resolution: 1.79→29.29 Å / Cor.coef. Fo:Fc: 0.933 / Cor.coef. Fo:Fc free: 0.914 / SU B: 5.008 / SU ML: 0.087 / Cross valid method: THROUGHOUT / ESU R Free: 0.127 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22796 13274 5.1 %RANDOM
Rwork0.19752 ---
obs0.19906 249160 92.84 %-
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: 20.053 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å2-0.02 Å2
2--0.01 Å2-0 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.79→29.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19198 0 344 2184 21726
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0220421
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5111.97327915
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.43252468
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.96223.835910
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.836153094
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4441594
X-RAY DIFFRACTIONr_chiral_restr0.180.23016
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02115859
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.794→1.841 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 826 -
Rwork0.261 15403 -
obs--78.93 %
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)
10.3670.0177-0.00150.18420.01670.2169-0.0150.0351-0.004-0.01620.010.01320.00240.00540.0050.05440.0006-0.02410.0477-0.00390.02230.1540.58113.732
21.9145-2.26710.25144.47171.9172.9187-0.2069-0.2613-0.19790.31570.04120.35680.0641-0.25340.16570.04810.01190.00910.15150.04110.0572-3.676-2.63139.671
30.3628-0.05270.11310.3426-0.0650.3731-0.01910.06680.0508-0.03930.0209-0.0058-0.0078-0.0091-0.00180.0638-0.00460.0060.05740.01670.024537.06421.5524.504
40.5496-0.237-0.07710.24780.17780.246-0.0219-0.0389-0.02080.05020.038-0.02390.0370.0104-0.01620.06290.0103-0.00260.0467-0.00570.030547.6714.7727.645
50.4159-0.0654-0.05460.12980.0920.5884-0.0032-0.06550.00330.0288-0.0079-0.01870.0199-0.01720.0110.05520.0034-0.00450.1013-0.03080.0169.55928.91261.966
60.4498-0.2614-0.25480.2611-0.10050.79330.06920.09960.02780.01140.0022-0.0069-0.1769-0.1637-0.07140.08660.06210.01310.08760.00040.01860.07846.53739.097
70.447-0.10920.07770.1731-0.10320.5652-0.0167-0.0742-0.01280.03160.01510.0384-0.02070.0280.00160.04990-0.0040.10350.03330.022632.444-15.761.046
80.8158-0.4350.31480.2691-0.0260.8040.10220.1349-0.0981-0.0277-0.03030.05870.18250.1859-0.07190.08440.0596-0.03690.0837-0.00570.04142.051-32.78337.716
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A29 - 625
2X-RAY DIFFRACTION2A626 - 647
3X-RAY DIFFRACTION3B29 - 357
4X-RAY DIFFRACTION4B358 - 647
5X-RAY DIFFRACTION5C29 - 357
6X-RAY DIFFRACTION6C358 - 647
7X-RAY DIFFRACTION7D29 - 357
8X-RAY DIFFRACTION8D358 - 647

+
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