[English] 日本語
Yorodumi
- PDB-1flg: CRYSTAL STRUCTURE OF THE QUINOPROTEIN ETHANOL DEHYDROGENASE FROM ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1flg
TitleCRYSTAL STRUCTURE OF THE QUINOPROTEIN ETHANOL DEHYDROGENASE FROM PSEUDOMONAS AERUGINOSA
ComponentsPROTEIN (QUINOPROTEIN ETHANOL DEHYDROGENASE)
KeywordsOXIDOREDUCTASE / QUINOPROTEIN / SUPERBARREL / DEHYDROGENASE
Function / homology
Function and homology information


alcohol dehydrogenase (cytochrome c) activity => GO:0052934 / alcohol dehydrogenase (cytochrome c) activity => GO:0052934 / alcohol dehydrogenase (cytochrome c) / ethanol catabolic process / : / outer membrane-bounded periplasmic space / calcium ion binding / membrane
Similarity search - Function
PQQ-dependent type I alcohol dehydrogenase / Bacterial quinoprotein dehydrogenases signature 1. / Quinoprotein alcohol dehydrogenase-like superfamily / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / PQQ enzyme repeat / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Pyrrolo-quinoline quinone beta-propeller repeat ...PQQ-dependent type I alcohol dehydrogenase / Bacterial quinoprotein dehydrogenases signature 1. / Quinoprotein alcohol dehydrogenase-like superfamily / Quinoprotein dehydrogenase, conserved site / Bacterial quinoprotein dehydrogenases signature 2. / PQQ-dependent dehydrogenase, methanol/ethanol family / PQQ enzyme repeat / Pyrrolo-quinoline quinone repeat / PQQ-like domain / Pyrrolo-quinoline quinone beta-propeller repeat / beta-propeller repeat / 8 Propeller / Methanol Dehydrogenase; Chain A / Quinoprotein alcohol dehydrogenase-like superfamily / Mainly Beta
Similarity search - Domain/homology
PYRROLOQUINOLINE QUINONE / Quinoprotein ethanol dehydrogenase
Similarity search - Component
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.6 Å
AuthorsKeitel, T. / Diehl, A. / Knaute, T. / Stezowski, J.J. / Hohne, W. / Gorisch, H.
CitationJournal: J.Mol.Biol. / Year: 2000
Title: X-ray structure of the quinoprotein ethanol dehydrogenase from Pseudomonas aeruginosa: basis of substrate specificity.
Authors: Keitel, T. / Diehl, A. / Knaute, T. / Stezowski, J.J. / Hohne, W. / Gorisch, H.
History
DepositionAug 14, 2000Deposition site: RCSB / Processing site: RCSB
SupersessionAug 30, 2000ID: 1EEE
Revision 1.0Aug 30, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: PROTEIN (QUINOPROTEIN ETHANOL DEHYDROGENASE)
B: PROTEIN (QUINOPROTEIN ETHANOL DEHYDROGENASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)129,0678
Polymers128,2472
Non-polymers8216
Water1,910106
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3940 Å2
ΔGint-75 kcal/mol
Surface area38710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)159.400, 159.400, 130.950
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

#1: Protein PROTEIN (QUINOPROTEIN ETHANOL DEHYDROGENASE)


Mass: 64123.270 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Pseudomonas aeruginosa (bacteria) / References: UniProt: Q9Z4J7
#2: Chemical
ChemComp-CA / CALCIUM ION


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


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


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.5 Å3/Da / Density % sol: 50.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG1500, 50 MM CALCIUM CHLORIDE, 4.5 MM GLYCINE/NAOH PH 8, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
pH: 8 / Details: Stezowski, J.J., (1989) J. Mol. Biol., 205, 617.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
22 mg/mlprotein1drop
34.5 mMglycine-NaOH1drop
41.5 mM1dropCaCl2
50.02 %(w/v)1dropNaCN
622.5 %(v/v)PEG15501reservoir
70.01 %1reservoirNaCN
83 mM1reservoirCaCl2
950 mMglycine-NaOH1reservoir
1ethanol dehydrogenase1drop0.005ml

-
Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X31 / Wavelength: 0.97
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 29, 1989
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 2.52→25.7 Å / Num. obs: 41300 / % possible obs: 94.2 % / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Biso Wilson estimate: 28.2 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 15
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.33 / % possible all: 98.8
Reflection
*PLUS
Highest resolution: 2.52 Å / Lowest resolution: 25.7 Å / Observed criterion σ(I): 1 / Redundancy: 2.7 % / Num. measured all: 109117 / Rmerge(I) obs: 0.126 / Biso Wilson estimate: 28.2 Å2
Reflection shell
*PLUS
Highest resolution: 2.6 Å / Lowest resolution: 2.7 Å / Rmerge(I) obs: 0.36

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
ROTAVATAdata reduction
AMoREphasing
REFMACrefinement
CCP4(AGROVATAdata scaling
ROTAVATAdata scaling
RefinementResolution: 2.6→12.5 Å / σ(F): 1 / σ(I): 1 / Details: MAXIMUM LIKELIHOOD
RfactorNum. reflectionSelection details
Rfree0.274 1476 RANDOM
Rwork0.192 --
obs0.142 28304 -
Refinement stepCycle: LAST / Resolution: 2.6→12.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9074 0 52 106 9232
Refine LS restraintsType: p_bond_d / Dev ideal: 0.013
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.192
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 28.2 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg5

+
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