[English] 日本語
Yorodumi
- PDB-3wfa: Catalytic role of the calcium ion in GH97 inverting glycoside hyd... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 3wfa
TitleCatalytic role of the calcium ion in GH97 inverting glycoside hydrolase
ComponentsAlpha-glucosidase
KeywordsHYDROLASE / TIM BARREL / inverting glycoside hydrolase / Calcium binding
Function / homology
Function and homology information


glucan 1,4-alpha-glucosidase / alpha-1,4-glucosidase activity / glucan 1,4-alpha-glucosidase activity / starch catabolic process / carbohydrate binding / periplasmic space / calcium ion binding / plasma membrane
Similarity search - Function
Glycosyl-hydrolase 97, catalytic domain / Glycosyl-hydrolase 97, C-terminal oligomerisation domain / Glycosyl-hydrolase 97, N-terminal domain / Glycoside hydrolase 97 / Glycosyl-hydrolase 97 N-terminal / Glycosyl-hydrolase 97 C-terminal, oligomerisation / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Distorted Sandwich ...Glycosyl-hydrolase 97, catalytic domain / Glycosyl-hydrolase 97, C-terminal oligomerisation domain / Glycosyl-hydrolase 97, N-terminal domain / Glycoside hydrolase 97 / Glycosyl-hydrolase 97 N-terminal / Glycosyl-hydrolase 97 C-terminal, oligomerisation / Beta-galactosidase; Chain A, domain 5 - #10 / Glycoside hydrolase-type carbohydrate-binding / Beta-galactosidase; Chain A, domain 5 / Distorted Sandwich / Aldolase class I / Aldolase-type TIM barrel / Glycoside hydrolase superfamily / TIM Barrel / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-EDT / Glucan 1,4-alpha-glucosidase SusB / Glucan 1,4-alpha-glucosidase SusB
Similarity search - Component
Biological speciesBacteroides thetaiotaomicron (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOkuyama, M. / Yoshida, T. / Hondoh, H. / Mori, H. / Yao, M. / Kimura, A.
CitationJournal: To be Published
Title: Catalytic role of the calcium ion in GH97 inverting glycoside hydrolase
Authors: Okuyama, M. / Yoshida, T. / Hondoh, H. / Mori, H. / Yao, M. / Kimura, A.
History
DepositionJul 18, 2013Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 16, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Alpha-glucosidase
B: Alpha-glucosidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,2676
Polymers166,6372
Non-polymers6304
Water21,9421218
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4310 Å2
ΔGint-25 kcal/mol
Surface area48170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.520, 111.960, 102.360
Angle α, β, γ (deg.)90.00, 100.49, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Alpha-glucosidase / BtGH97a


Mass: 83318.359 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 22-738
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteroides thetaiotaomicron (bacteria)
Gene: susB / Plasmid: pET23d / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: P71094, UniProt: G8JZS4*PLUS
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-EDT / {[-(BIS-CARBOXYMETHYL-AMINO)-ETHYL]-CARBOXYMETHYL-AMINO}-ACETIC ACID


Mass: 292.243 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1218 / 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: 2.55 Å3/Da / Density % sol: 51.83 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 12% (w/v) polyethylene glycol 6000, 0.1mM imidazole-HCl (pH 7.8), VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Aug 6, 2009
RadiationMonochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 107958 / % possible obs: 95.8 % / Observed criterion σ(F): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.059 / Rsym value: 0.034 / Net I/σ(I): 14.9
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.147 / Mean I/σ(I) obs: 7.8 / Num. unique all: 15018 / Rsym value: 0.087 / % possible all: 91.5

-
Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
CNS1.2refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 2d73

2d73


Resolution: 2→19.81 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1600323.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.2 5440 5 %RANDOM
Rwork0.171 ---
obs0.171 107892 95.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.3116 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 14.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.67 Å20 Å2-1.02 Å2
2--0.33 Å20 Å2
3----3 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.19 Å
Luzzati d res low-20 Å
Luzzati sigma a0.14 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2→19.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11288 0 42 1218 12548
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d24.5
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it0.871.5
X-RAY DIFFRACTIONc_mcangle_it1.262
X-RAY DIFFRACTIONc_scbond_it1.482
X-RAY DIFFRACTIONc_scangle_it2.122.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.229 861 5 %
Rwork0.185 16261 -
obs--91.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4water.paramwater.top
X-RAY DIFFRACTION5edt.paramedt.top

+
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