[English] 日本語
Yorodumi
- PDB-2zcu: Crystal structure of a new type of NADPH-dependent quinone oxidor... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2zcu
TitleCrystal structure of a new type of NADPH-dependent quinone oxidoreductase (QOR2) from escherichia coli
ComponentsUncharacterized oxidoreductase ytfG
KeywordsOXIDOREDUCTASE / ALPHA-BETA SANDWICH
Function / homology
Function and homology information


NADPH dehydrogenase (quinone) activity / NAD(P)H dehydrogenase (quinone) / NADH:ubiquinone reductase (non-electrogenic) activity / oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor / cytosol
Similarity search - Function
NmrA-like domain / NmrA-like family / UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COPPER (II) ION / Quinone oxidoreductase 2
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsKim, I.K. / Yim, H.S. / Kim, M.K. / Kim, D.W. / Kim, Y.M. / Cha, S.S. / Kang, S.O.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Crystal structure of a new type of NADPH-dependent quinone oxidoreductase (QOR2) from Escherichia coli
Authors: Kim, I.K. / Yim, H.S. / Kim, M.K. / Kim, D.W. / Kim, Y.M. / Cha, S.S. / Kang, S.O.
History
DepositionNov 13, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Uncharacterized oxidoreductase ytfG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,8262
Polymers29,7621
Non-polymers641
Water7,548419
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Uncharacterized oxidoreductase ytfG
hetero molecules

A: Uncharacterized oxidoreductase ytfG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6524
Polymers59,5252
Non-polymers1272
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_555-x,-x+y,-z+2/31
Buried area1450 Å2
ΔGint-27 kcal/mol
Surface area22130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.685, 81.685, 76.801
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

-
Components

#1: Protein Uncharacterized oxidoreductase ytfG / hypothetical protein YTFG / YTFG gene product / NADPH-dependent quinone oxidoreductase


Mass: 29762.406 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: strain K12 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P39315, NADPH:quinone reductase
#2: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.39 Å3/Da / Density % sol: 48.8 %
Crystal growTemperature: 285 K / Method: evaporation / pH: 7.5
Details: PEG 4000, COPPER CHLRORIDE, AMMONIUM SULFATE, HEPES, pH 7.50, EVAPORATION, temperature 285K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 6B / Wavelength: 0.97934, 0.97947, 0.97167, 1.12714
DetectorType: BRUKER PROTEUM 300 / Detector: CCD / Date: May 10, 2003
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979341
20.979471
30.971671
41.127141
ReflectionResolution: 1.8→20 Å / Num. obs: 28204 / % possible obs: 97.9 % / Observed criterion σ(I): 0 / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.062
Reflection shellResolution: 1.8→1.9 Å / Rsym value: 0.294 / % possible all: 92

-
Processing

Software
NameVersionClassification
SOLVEphasing
CNS1.1refinement
SMARTdata reduction
SAINT& PROSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 1.8→19.74 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 435259.26 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.278 2618 9.9 %RANDOM
Rwork0.236 ---
obs0.236 26439 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 98.99 Å2 / ksol: 0.35 e/Å3
Displacement parametersBiso mean: 23.8 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å22.71 Å20 Å2
2---0.12 Å20 Å2
3---0.23 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.28 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.15 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 1.8→19.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1958 0 1 419 2378
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.67
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.8→1.91 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.294 432 9.7 %
Rwork0.261 4038 -
obs--97.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4NADP9.PARAMNADP9.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