[English] 日本語
Yorodumi
- PDB-4j5t: Crystal structure of Processing alpha-Glucosidase I -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4j5t
TitleCrystal structure of Processing alpha-Glucosidase I
ComponentsMannosyl-oligosaccharide glucosidase
KeywordsHYDROLASE / Super-beta sandwich linked to (alpha/alpha)6 toroid / Glycoside Hydrolase / Glycosylation / ER membrane / N-glycoprotein
Function / homology
Function and homology information


fungal-type cell wall beta-glucan biosynthetic process / fungal-type cell wall biogenesis / mannosyl-oligosaccharide glucosidase / Glc3Man9GlcNAc2 oligosaccharide glucosidase activity / oligosaccharide metabolic process / fungal-type vacuole / protein N-linked glycosylation / membrane => GO:0016020 / endoplasmic reticulum membrane
Similarity search - Function
Glycosyl hydrolase family 63, N-terminal domain / Glycosyl hydrolase family 63, C-terminal / Glycosyl hydrolase family 63, N-terminal / Glycosyl hydrolase family 63, N-terminal domain superfamily / Glycosyl hydrolase family 63 C-terminal domain / Glycosyl hydrolase family 63 N-terminal domain / Glycoside hydrolase family 63 / Glycosyltransferase - #10 / Beta-galactosidase; Chain A, domain 5 / Six-hairpin glycosidase-like superfamily ...Glycosyl hydrolase family 63, N-terminal domain / Glycosyl hydrolase family 63, C-terminal / Glycosyl hydrolase family 63, N-terminal / Glycosyl hydrolase family 63, N-terminal domain superfamily / Glycosyl hydrolase family 63 C-terminal domain / Glycosyl hydrolase family 63 N-terminal domain / Glycoside hydrolase family 63 / Glycosyltransferase - #10 / Beta-galactosidase; Chain A, domain 5 / Six-hairpin glycosidase-like superfamily / Six-hairpin glycosidase superfamily / Glycosyltransferase / Alpha/alpha barrel / Distorted Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Mannosyl-oligosaccharide glucosidase
Similarity search - Component
Biological speciesSaccharomyces cerevisiae (brewer's yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.04 Å
AuthorsBarker, M.K. / Rose, D.R.
CitationJournal: J.Biol.Chem. / Year: 2013
Title: Specificity of processing alpha-glucosidase I is guided by the substrate conformation: crystallographic and in silico studies.
Authors: Barker, M.K. / Rose, D.R.
History
DepositionFeb 9, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Database references / 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_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_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_2 / _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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_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 / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mannosyl-oligosaccharide glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,1323
Polymers94,2841
Non-polymers8492
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.800, 101.800, 103.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein Mannosyl-oligosaccharide glucosidase / / Processing A-glucosidase I / Glucosidase I


Mass: 94283.641 Da / Num. of mol.: 1 / Fragment: UNP residues 31-833
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Saccharomyces cerevisiae (brewer's yeast)
Strain: ATCC 204508 / S288c / Gene: CWH41, GLS1, YGL027C / Plasmid: pPICZ-alphaA / Production host: Komagataella pastoris (fungus) / Strain (production host): X-33
References: UniProt: P53008, mannosyl-oligosaccharide glucosidase
#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: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.65 Å3/Da / Density % sol: 53.51 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 4mg/mL protein in 20mM potassium phosphate pH 6.8 100mM NaCl; Crystallized in 1:1 drops with reservoir solution (15% PEG 4000 0.1M MES pH 6.5, 0.1M sodium phosphate, pH 6.5, 0.1M potassium ...Details: 4mg/mL protein in 20mM potassium phosphate pH 6.8 100mM NaCl; Crystallized in 1:1 drops with reservoir solution (15% PEG 4000 0.1M MES pH 6.5, 0.1M sodium phosphate, pH 6.5, 0.1M potassium phosphate pH 6.5, 0.6M NaCl) , VAPOR DIFFUSION, SITTING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CHESS / Beamline: F1 / Wavelength: 0.997 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 18, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.04→28 Å / Num. all: 64056 / Num. obs: 63223 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.3 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 9.3
Reflection shellResolution: 2.04→2.11 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.477 / Mean I/σ(I) obs: 3.4 / % possible all: 98.9

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIXmodel building
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.04→28 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.947 / SU B: 0.004 / SU ML: 0 / Cross valid method: THROUGHOUT / ESU R: 0.16 / ESU R Free: 0.167 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.23467 3135 5 %RANDOM
Rwork0.22583 ---
obs0.22626 59503 97.75 %-
all-64056 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 46.064 Å2
Baniso -1Baniso -2Baniso -3
1--1.29 Å20 Å20 Å2
2--2.44 Å20 Å2
3----1.15 Å2
Refinement stepCycle: LAST / Resolution: 2.04→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6448 0 56 285 6789
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.026739
X-RAY DIFFRACTIONr_bond_other_d0.0010.024572
X-RAY DIFFRACTIONr_angle_refined_deg0.891.9529146
X-RAY DIFFRACTIONr_angle_other_deg0.766311093
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2185799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.42724.587351
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.211151122
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3411532
X-RAY DIFFRACTIONr_chiral_restr0.0530.2954
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0217535
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021433
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: 2.042→2.095 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.309 231 -
Rwork0.305 4060 -
obs--97.48 %

+
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