[English] 日本語
Yorodumi
- PDB-1tuv: Crystal structure of YgiN in complex with menadione -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1tuv
TitleCrystal structure of YgiN in complex with menadione
ComponentsProtein ygiN
KeywordsUNKNOWN FUNCTION / menadione oxidase / monooxygenase / co-crystal with natural product / ferredoxin fold
Function / homology
Function and homology information


response to acidic pH / Oxidoreductases / catalytic activity / oxidoreductase activity / protein homodimerization activity / cytosol
Similarity search - Function
: / ABM domain profile. / Antibiotic biosynthesis monooxygenase / Antibiotic biosynthesis monooxygenase domain / Alpha-Beta Plaits - #100 / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
MENADIONE / Probable quinol monooxygenase YgiN / Probable quinol monooxygenase YgiN
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / direct input of native model / Resolution: 1.7 Å
AuthorsAdams, M.A. / Jia, Z.
CitationJournal: J.Biol.Chem. / Year: 2005
Title: Structural and Biochemical Evidence for an Enzymatic Quinone Redox Cycle in Escherichia coli: IDENTIFICATION OF A NOVEL QUINOL MONOOXYGENASE
Authors: Adams, M.A. / Jia, Z.
History
DepositionJun 25, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Protein ygiN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,9482
Polymers12,7761
Non-polymers1721
Water3,261181
1
A: Protein ygiN
hetero molecules

A: Protein ygiN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8964
Polymers25,5512
Non-polymers3442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_454-z-1/2,-x,y-1/21
2
A: Protein ygiN
hetero molecules

A: Protein ygiN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,8964
Polymers25,5512
Non-polymers3442
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation22_554z+1/4,-y+1/4,x-1/41
Buried area3800 Å2
ΔGint-32 kcal/mol
Surface area10270 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)102.562, 102.562, 102.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number213
Space group name H-MP4132
Components on special symmetry positions
IDModelComponents
11A-4610-

HOH

-
Components

#1: Protein Protein ygiN


Mass: 12775.716 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ygiN / Plasmid: pET21b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P40718, UniProt: P0ADU2*PLUS
#2: Chemical ChemComp-VK3 / MENADIONE / VITAMIN K3 / 2-METHYL-1,4-NAPHTHALENEDIONE


Mass: 172.180 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C11H8O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 181 / 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: 3.24 Å3/Da / Density % sol: 61.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: sodium citrate, ammonium sulfate, sodium/potassium tartrate, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 0.9788 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 25, 2004
RadiationMonochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9788 Å / Relative weight: 1
ReflectionResolution: 1.69→50 Å / Num. all: 19783 / Num. obs: 19783 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 8 % / Rmerge(I) obs: 0.07 / Rsym value: 0.07 / Net I/σ(I): 50
Reflection shellResolution: 1.69→1.77 Å / % possible all: 99

-
Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: direct input of native model / Resolution: 1.7→25.65 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.928 / SU B: 1.913 / SU ML: 0.062 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24904 1056 5.1 %RANDOM
Rwork0.20756 ---
all0.20949 19783 --
obs0.20949 19783 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.765 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms797 0 13 181 991
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.021829
X-RAY DIFFRACTIONr_bond_other_d0.0030.02756
X-RAY DIFFRACTIONr_angle_refined_deg21.9621124
X-RAY DIFFRACTIONr_angle_other_deg1.0231761
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1025102
X-RAY DIFFRACTIONr_chiral_restr0.130.2125
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.02913
X-RAY DIFFRACTIONr_gen_planes_other0.0160.02152
X-RAY DIFFRACTIONr_nbd_refined0.2430.2194
X-RAY DIFFRACTIONr_nbd_other0.2610.2909
X-RAY DIFFRACTIONr_nbtor_other0.0920.2506
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2350.2137
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2840.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.40.248
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2230.220
X-RAY DIFFRACTIONr_mcbond_it1.3371.5515
X-RAY DIFFRACTIONr_mcangle_it2.3792832
X-RAY DIFFRACTIONr_scbond_it4.1373314
X-RAY DIFFRACTIONr_scangle_it6.4284.5292
LS refinement shellResolution: 1.701→1.745 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.362 82
Rwork0.315 1411

+
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://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