[English] 日本語
Yorodumi
- PDB-1cq1: Soluble Quinoprotein Glucose Dehydrogenase from Acinetobacter Cal... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1cq1
TitleSoluble Quinoprotein Glucose Dehydrogenase from Acinetobacter Calcoaceticus in Complex with PQQH2 and Glucose
ComponentsSOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE
KeywordsOXIDOREDUCTASE / BETA-PROPELLER / SUPERBARREL / COMPLEX WITH COFACTOR AND SUBSTRATE
Function / homology
Function and homology information


glucose 1-dehydrogenase (PQQ, quinone) / quinoprotein glucose dehydrogenase activity / metal ion binding
Similarity search - Function
PQQ-dependent dehydrogenase, s-GDH family / Glucose/Sorbosone dehydrogenase / Glucose / Sorbosone dehydrogenase / Soluble quinoprotein glucose/sorbosone dehydrogenase / TolB, C-terminal domain / Six-bladed beta-propeller, TolB-like / 6 Propeller / Neuraminidase / Mainly Beta
Similarity search - Domain/homology
beta-D-glucopyranose / PYRROLOQUINOLINE QUINONE / Quinoprotein glucose dehydrogenase B
Similarity search - Component
Biological speciesAcinetobacter calcoaceticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsOubrie, A. / Rozeboom, H.J. / Dijkstra, B.W.
Citation
Journal: EMBO J. / Year: 1999
Title: Structure and mechanism of soluble quinoprotein glucose dehydrogenase.
Authors: Oubrie, A. / Rozeboom, H.J. / Kalk, K.H. / Olsthoorn, A.J. / Duine, J.A. / Dijkstra, B.W.
#1: Journal: J.Mol.Biol. / Year: 1999
Title: The 1.7 Angstrom crystal structure of the apo form of the soluble quinoprotein glucose dehydrogenase from Acinetobacter calcoaceticus reveals a novel internal sequence repeat
Authors: Oubrie, A. / Rozeboom, H.J. / Kalk, K.H. / Duine, J.A. / Dijkstra, B.W.
History
DepositionAug 4, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 4, 2000Provider: repository / Type: Initial release
Revision 1.1Oct 21, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Jul 24, 2019Group: Data collection / Refinement description / Category: diffrn_source / software
Item: _diffrn_source.pdbx_synchrotron_site / _software.classification / _software.name
Revision 1.5Aug 14, 2019Group: Data collection / Category: computing
Revision 1.6Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_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_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_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_comp_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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE
B: SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)101,84812
Polymers100,5862
Non-polymers1,26110
Water10,629590
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)60.899, 91.972, 85.747
Angle α, β, γ (deg.)90.00, 104.62, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein SOLUBLE QUINOPROTEIN GLUCOSE DEHYDROGENASE


Mass: 50293.207 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Acinetobacter calcoaceticus (bacteria) / Cellular location: PERIPLASM / Production host: Escherichia coli (E. coli) / References: UniProt: P13650, EC: 1.1.99.17
#2: Sugar ChemComp-BGC / beta-D-glucopyranose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O6
IdentifierTypeProgram
DGlcpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-glucopyranoseCOMMON NAMEGMML 1.0
b-D-GlcpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#4: Chemical ChemComp-PQQ / PYRROLOQUINOLINE QUINONE


Mass: 330.206 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H6N2O8
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.31 Å3/Da / Density % sol: 46.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: PEG 6000, SODIUM CHLORIDE, CALCIUM CHLORIDE, TRIS, GLYCINE, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-23 %(w/v)PEG60001reservoir
2120 mM1reservoirNaCl
33 mM1reservoirCaCl2
450 mMTris-Gly1reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7A / Wavelength: 1.0736
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 23, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0736 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 92216 / Num. obs: 92032 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.5 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.064 / Net I/σ(I): 18.6
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.814 / % possible all: 98.1
Reflection shell
*PLUS
% possible obs: 98.1 %

-
Processing

Software
NameVersionClassification
X-PLORrefinement
SCALEPACKdata scaling
REFMACrefinement
X-PLORmodel building
DENZOdata reduction
X-PLOR3.843phasing
RefinementResolution: 1.9→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.226 3442 -RANDOM
Rwork0.19 ---
all0.19 68659 --
obs0.19 68659 95.4 %-
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6961 0 78 590 7629
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.008
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.009
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: 'REFMAC, X-PLOR 3.843' / Classification: refinement
Refine LS restraints
*PLUS
Type: x_angle_deg / Dev ideal: 3

+
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