[English] 日本語
Yorodumi
- PDB-2g8s: Crystal structure of the soluble Aldose sugar dehydrogenase (Asd)... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2g8s
TitleCrystal structure of the soluble Aldose sugar dehydrogenase (Asd) from Escherichia coli in the apo-form
ComponentsGlucose/sorbosone dehydrogenases
KeywordsSUGAR BINDING PROTEIN / 6 bladed beta-propellor / pyrolloquinoline quinone (PQQ) / quinoprotein
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-OH group of donors; With a quinone or similar compound as acceptor / oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor / pyrroloquinoline quinone binding / cell outer membrane / outer membrane-bounded periplasmic space / calcium ion binding
Similarity search - Function
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
PHOSPHATE ION / Aldose sugar dehydrogenase YliI
Similarity search - Component
Biological speciesEscherichia coli K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.5 Å
AuthorsSouthall, S.M. / Doel, J.J. / Richardson, D.J. / Oubrie, A.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Soluble Aldose Sugar Dehydrogenase from Escherichia coli: A HIGHLY EXPOSED ACTIVE SITE CONFERRING BROAD SUBSTRATE SPECIFICITY.
Authors: Southall, S.M. / Doel, J.J. / Richardson, D.J. / Oubrie, A.
History
DepositionMar 3, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 8, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Glucose/sorbosone dehydrogenases
B: Glucose/sorbosone dehydrogenases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,23130
Polymers78,5042
Non-polymers1,72728
Water18,0151000
1
A: Glucose/sorbosone dehydrogenases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,19416
Polymers39,2521
Non-polymers94215
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Glucose/sorbosone dehydrogenases
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,03714
Polymers39,2521
Non-polymers78513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)40.829, 113.475, 75.372
Angle α, β, γ (deg.)90.00, 90.03, 90.00
Int Tables number4
Space group name H-MP1211
DetailsThe biological unit is a monomer of which there are two in the asymmetric unit.

-
Components

#1: Protein Glucose/sorbosone dehydrogenases


Mass: 39252.191 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Species: Escherichia coli / Strain: K-12 / Gene: yliI / Plasmid: pET M-11 / Production host: Escherichia coli (E. coli) / Strain (production host): B843 (DE3) / References: UniProt: P75804
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#4: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1000 / 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: 2.22 Å3/Da / Density % sol: 44.67 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 9.2
Details: 18 % PEG 6000, 100 mM CHES, 100 mM sodium chloride, 1 mM calcium chloride, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97935 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 11, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.315→75.378 Å / Num. all: 162184 / Num. obs: 162184 / % possible obs: 72.2 % / Observed criterion σ(F): 0.2 / Observed criterion σ(I): 5 / Redundancy: 3.3 % / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 6.9
Reflection shellResolution: 1.31→1.38 Å / % possible obs: 10.9 % / Redundancy: 1.7 % / Rmerge(I) obs: 0.386 / Mean I/σ(I) obs: 1.9 / Num. measured all: 4343 / Num. unique obs: 2572 / Rsym value: 0.386 / % possible all: 10.9

-
Phasing

PhasingMethod: SAD
Phasing MADD res high: 1.35 Å / D res low: 75.38 Å / FOM : 0.207 / FOM acentric: 0.211 / FOM centric: 0 / Reflection: 116796 / Reflection acentric: 114663 / Reflection centric: 2133
Phasing MAD setR cullis acentric: 1.42 / R cullis centric: 1 / Highest resolution: 1.35 Å / Lowest resolution: 75.38 Å / Loc acentric: 0.2 / Loc centric: 0.2 / Power acentric: 0 / Power centric: 0 / Reflection acentric: 114663 / Reflection centric: 2133
Phasing MAD set shell

ID: 1 / R cullis centric: 1 / Power acentric: 0 / Power centric: 0

Resolution (Å)R cullis acentricLoc acentricLoc centricReflection acentricReflection centric
9.6-75.381.370.80.637840
5.12-9.61.460.70.42231130
3.5-5.1210.60.55756215
2.65-3.51.150.40.310890293
2.14-2.651.310.20.217680372
1.79-2.141.760.10.126128447
1.54-1.796.790.1032852458
1.35-1.541.860.1018748178
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se17.3280.2460.4530.9580
2Se17.6110.7460.2790.5420
3Se17.3790.8490.2160.3010
4Se17.2010.6520.0140.8010
5Se18.6230.5720.2870.5920
6Se19.4620.4090.4070.7830
7Se19.0250.9090.3230.7160
8Se22.390.3280.4410.850
9Se24.8830.8280.290.6490
10Se19.1650.0710.4440.9080
11Se28.5840.7480.10.2040
12Se27.6220.7560.130.7010
Phasing MAD shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
9.6-75.380.2770.307041837840
5.12-9.60.4310.456023612231130
3.5-5.120.3320.344059715756215
2.65-3.50.3210.32901118310890293
2.14-2.650.3350.34201805217680372
1.79-2.140.2420.24602657526128447
1.54-1.790.1280.1303331032852458
1.35-1.540.0390.03901892618748178
Phasing dmMethod: Solvent flattening and Histogram matching / Reflection: 116796
Phasing dm shell
Resolution (Å)Delta phi finalFOM Reflection
7.32-10061.10.509967
5.17-7.3259.20.7961749
4.22-5.1759.30.8062258
3.66-4.2259.60.7852648
3.27-3.6660.90.7653018
2.99-3.2759.60.7493329
2.77-2.99610.7583600
2.59-2.7759.90.7673891
2.44-2.5959.40.784126
2.31-2.44600.7764357
2.21-2.3159.60.7794586
2.11-2.2159.60.7724806
2.03-2.1162.40.7654938
1.96-2.0363.40.7585193
1.89-1.9664.60.7545397
1.83-1.8965.70.7315579
1.77-1.8366.20.7285685
1.72-1.7769.80.7225961
1.68-1.7270.50.6896026
1.64-1.6874.10.6836028
1.6-1.6477.70.6745672
1.56-1.678.10.6685135
1.53-1.5680.40.6424685
1.49-1.5381.30.6494216
1.46-1.4981.70.633646
1.44-1.46840.5813082
1.41-1.4486.30.592517
1.38-1.4185.90.61939
1.35-1.3885.90.5471762

-
Processing

Software
NameVersionClassificationNB
SCALAdata scaling
MLPHAREphasing
DM5phasing
REFMACrefinement
PDB_EXTRACT1.701data extraction
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.5→7.96 Å / Cor.coef. Fo:Fc: 0.967 / SU B: 1.833 / SU ML: 0.032 / σ(F): 0 / ESU R: 0.098 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflection
Rfree0.183 97142 -
Rwork0.149 --
all0.149 117547 -
obs0.148 117547 94.15 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 12.384 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.5→7.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5963 0 115 1024 7102
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226276
X-RAY DIFFRACTIONr_angle_refined_deg1.2151.9628559
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1845852
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.27324.135312
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.659151098
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.9921550
X-RAY DIFFRACTIONr_chiral_restr0.0860.2876
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024938
X-RAY DIFFRACTIONr_nbd_refined0.2120.23056
X-RAY DIFFRACTIONr_nbtor_refined0.320.24234
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1260.2974
X-RAY DIFFRACTIONr_metal_ion_refined0.0470.28
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1490.293
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1630.278
X-RAY DIFFRACTIONr_mcbond_it0.7821.53844
X-RAY DIFFRACTIONr_mcangle_it1.12526068
X-RAY DIFFRACTIONr_scbond_it1.62432788
X-RAY DIFFRACTIONr_scangle_it2.3124.52415
X-RAY DIFFRACTIONr_rigid_bond_restr0.92736632
X-RAY DIFFRACTIONr_sphericity_free2.59931026
X-RAY DIFFRACTIONr_sphericity_bonded1.59536076
LS refinement shellResolution: 1.5→1.538 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rwork0.168 4944 -
obs--63.74 %

+
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