[English] 日本語
Yorodumi
- PDB-1jmx: crystal structure of a quinohemoprotein amine dehydrogenase from ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1jmx
Titlecrystal structure of a quinohemoprotein amine dehydrogenase from pseudomonas putida
Components(Amine Dehydrogenase) x 3
KeywordsOXIDOREDUCTASE / Amine Dehydrogenase
Function / homology
Function and homology information


Oxidoreductases; Acting on the CH-NH2 group of donors; With a copper protein as acceptor / oxidoreductase activity, acting on the CH-NH2 group of donors / periplasmic space / electron transfer activity / heme binding / metal ion binding
Similarity search - Function
Quinohemoprotein amine dehydrogenase, alpha subunit, domain 2 / Quinohemoprotein amine dehydrogenase, alpha subunit domain III / Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding / Quinohemoprotein amine dehydrogenase, gamma subunit / Quinohemoprotein amine dehydrogenase alpha subunit, domain 2 superfamily / Quinohemoprotein amine dehydrogenase, gamma subunit structural domain superfamily / Quinohemoprotein amine dehydrogenase, alpha subunit / Quinohemoprotein amine dehydrogenase, beta subunit / Quinohemoprotein amine dehydrogenase, alpha subunit domain IV / Quinohemoprotein amine dehydrogenase, alpha subunit domain III ...Quinohemoprotein amine dehydrogenase, alpha subunit, domain 2 / Quinohemoprotein amine dehydrogenase, alpha subunit domain III / Quinohemoprotein amine dehydrogenase A, alpha subunit, haem binding / Quinohemoprotein amine dehydrogenase, gamma subunit / Quinohemoprotein amine dehydrogenase alpha subunit, domain 2 superfamily / Quinohemoprotein amine dehydrogenase, gamma subunit structural domain superfamily / Quinohemoprotein amine dehydrogenase, alpha subunit / Quinohemoprotein amine dehydrogenase, beta subunit / Quinohemoprotein amine dehydrogenase, alpha subunit domain IV / Quinohemoprotein amine dehydrogenase, alpha subunit domain III / Quinohemoprotein amine dehydrogenase, alpha subunit, haem binding domain / Quinohemoprotein amine dehydrogenase, gamma subunit, structural domain / Quinohemoprotein amine dehydrogenase, alpha subunit domain II / Quinohemoprotein amine dehydrogenase, alpha subunit domain IV / Quinohemoprotein amine dehydrogenase / Quinohemoprotein amine dehydrogenase, gamma subunit structural domain / Quinohemoprotein amine dehydrogenase alpha subunit, domain 2 / Quinoprotein amine dehydrogenase, beta chain-like / YVTN repeat-like/Quinoprotein amine dehydrogenase / Cytochrome c-like domain superfamily / 7 Propeller / Methylamine Dehydrogenase; Chain H / Lipocalin / Irregular / Few Secondary Structures / Immunoglobulin E-set / WD40/YVTN repeat-like-containing domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Beta Barrel / Sandwich / Mainly Beta
Similarity search - Domain/homology
Quinohemoprotein amine dehydrogenase 40 kDa subunit / HEME C / Quinohemoprotein amine dehydrogenase subunit gamma / NICKEL (II) ION / Quinohemoprotein amine dehydrogenase 60 kDa subunit
Similarity search - Component
Biological speciesPseudomonas putida (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.9 Å
AuthorsSatoh, A. / Miyahara, I. / Hirotsu, K.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Crystal structure of quinohemoprotein amine dehydrogenase from Pseudomonas putida. Identification of a novel quinone cofactor encaged by multiple thioether cross-bridges.
Authors: Satoh, A. / Kim, J.K. / Miyahara, I. / Devreese, B. / Vandenberghe, I. / Hacisalihoglu, A. / Okajima, T. / Kuroda, S. / Adachi, O. / Duine, J.A. / Van Beeumen, J. / Tanizawa, K. / Hirotsu, K.
History
DepositionJul 20, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 16, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Amine Dehydrogenase
B: Amine Dehydrogenase
G: Amine Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,1986
Polymers101,9023
Non-polymers1,2963
Water8,233457
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11250 Å2
ΔGint-95 kcal/mol
Surface area32390 Å2
MethodPISA
2
A: Amine Dehydrogenase
B: Amine Dehydrogenase
G: Amine Dehydrogenase
hetero molecules

A: Amine Dehydrogenase
B: Amine Dehydrogenase
G: Amine Dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)206,39512
Polymers203,8046
Non-polymers2,5916
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area25070 Å2
ΔGint-203 kcal/mol
Surface area62200 Å2
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)167.21, 92.37, 79.30
Angle α, β, γ (deg.)90.00, 112.00, 90.00
Int Tables number5
Space group name H-MC121

-
Components

-
Protein , 3 types, 3 molecules ABG

#1: Protein Amine Dehydrogenase /


Mass: 53986.910 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: Q8VW85
#2: Protein Amine Dehydrogenase /


Mass: 39284.551 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: Q8VW82
#3: Protein Amine Dehydrogenase /


Mass: 8630.408 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Pseudomonas putida (bacteria) / References: UniProt: P0A182

-
Non-polymers , 3 types, 460 molecules

#4: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ni
#5: Chemical ChemComp-HEC / HEME C / Heme C


Mass: 618.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H34FeN4O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 457 / 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: 2.78 Å3/Da / Density % sol: 55.83 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: PEG MME2000, nickel chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
112 mg/mlprotein1drop
218 %(w/v)PEG2000 MME1reservoir
350 mM1reservoirNiCl2

-
Data collection

DiffractionMean temperature: 90 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-18B / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 20, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 89255 / % possible obs: 99.9 % / Observed criterion σ(F): 2
Reflection
*PLUS
Rmerge(I) obs: 0.051
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 2.8

-
Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
SHARPphasing
X-PLOR3.851refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 1.9→10 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.267 3292 RANDOM
Rwork0.209 --
obs-64940 -
Refinement stepCycle: LAST / Resolution: 1.9→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7067 0 87 457 7611
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.609
Refinement
*PLUS
σ(F): 2 / Rfactor obs: 0.211 / Rfactor Rfree: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Rfactor Rfree: 0.296 / Rfactor obs: 0.237

+
About Yorodumi

-
News

-
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

+
Jun 16, 2017. Omokage search with filter

Omokage search with filter

Result of Omokage search can be filtered by keywords and the database types

Related info.:Omokage search

-
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