[English] 日本語
Yorodumi
- PDB-6tef: Crystal structure of monooxygenase RutA complexed with dioxygen u... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6tef
TitleCrystal structure of monooxygenase RutA complexed with dioxygen under 0.5 MPa / 5 bars of oxygen pressure.
ComponentsPyrimidine monooxygenase RutA
KeywordsFLAVOPROTEIN / monooxygenase / RutA / FMN / flavin-N5-oxide / bioengineering
Function / homology
Function and homology information


pyrimidine oxygenase / uracil oxygenase activity / alkanesulfonate monooxygenase activity / pyrimidine nucleobase catabolic process / uracil catabolic process / thymine catabolic process / alkanesulfonate catabolic process / nitrogen utilization / monooxygenase activity
Similarity search - Function
Pyrimidine monooxygenase RutA / : / Luciferase-like domain / Luciferase-like monooxygenase / Luciferase-like domain superfamily
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / OXYGEN MOLECULE / Pyrimidine monooxygenase RutA
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsSaleem-Batcha, R. / Matthews, A. / Teufel, R.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research FoundationTE 931/2-1 Germany
German Research Foundation235777276/GRK1976 Germany
CitationJournal: Nat.Chem.Biol. / Year: 2020
Title: Aminoperoxide adducts expand the catalytic repertoire of flavin monooxygenases.
Authors: Matthews, A. / Saleem-Batcha, R. / Sanders, J.N. / Stull, F. / Houk, K.N. / Teufel, R.
History
DepositionNov 11, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 5, 2020Provider: repository / Type: Initial release
Revision 1.1May 6, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z ..._atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: Pyrimidine monooxygenase RutA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,9807
Polymers40,1111
Non-polymers8696
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-31 kcal/mol
Surface area13850 Å2
MethodPISA
Unit cell
Length a, b, c (Å)87.673, 87.673, 96.571
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

-
Components

-
Protein , 1 types, 1 molecules AAA

#1: Protein Pyrimidine monooxygenase RutA


Mass: 40111.336 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: rutA, ycdM, b1012, JW0997 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P75898, pyrimidine oxygenase

-
Non-polymers , 5 types, 207 molecules

#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H21N4O9P / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-OXY / OXYGEN MOLECULE


Mass: 31.999 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has ligand of interestY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.67 Å3/Da / Density % sol: 53.95 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: 100 mM Bis-Tris pH 6.5, 1900 mM Ammonium Sulphate, 2-5% MPD (v/v), 1 mM FMN

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 27, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→48.29 Å / Num. obs: 40277 / % possible obs: 100 % / Redundancy: 9.9 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 17.2
Reflection shellResolution: 1.8→1.9 Å / Num. unique obs: 5809 / CC1/2: 0.84

-
Processing

Software
NameVersionClassification
REFMAC5.8.0257refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5WAN

5wan


Resolution: 1.8→43.875 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.956 / SU B: 2.032 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.097 / ESU R Free: 0.099
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1963 2088 5.189 %
Rwork0.1598 --
all0.162 --
obs-40237 99.963 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 27.675 Å2
Baniso -1Baniso -2Baniso -3
1-0.105 Å20.053 Å20 Å2
2--0.105 Å20 Å2
3----0.342 Å2
Refinement stepCycle: LAST / Resolution: 1.8→43.875 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2618 0 54 201 2873
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132755
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172477
X-RAY DIFFRACTIONr_angle_refined_deg1.811.6583745
X-RAY DIFFRACTIONr_angle_other_deg1.5381.5815733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9045342
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.25721.971137
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.95815428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.7371516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2354
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023089
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02613
X-RAY DIFFRACTIONr_nbd_refined0.2140.2520
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1840.22293
X-RAY DIFFRACTIONr_nbtor_refined0.1770.21375
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0850.21163
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2168
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1690.28
X-RAY DIFFRACTIONr_nbd_other0.1840.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2520.29
X-RAY DIFFRACTIONr_mcbond_it2.4792.6171356
X-RAY DIFFRACTIONr_mcbond_other2.4782.6131355
X-RAY DIFFRACTIONr_mcangle_it3.2153.9071693
X-RAY DIFFRACTIONr_mcangle_other3.2143.9121694
X-RAY DIFFRACTIONr_scbond_it4.2673.1681399
X-RAY DIFFRACTIONr_scbond_other4.2653.1681397
X-RAY DIFFRACTIONr_scangle_it6.0454.5852049
X-RAY DIFFRACTIONr_scangle_other6.0444.5862050
X-RAY DIFFRACTIONr_lrange_it7.46632.1873234
X-RAY DIFFRACTIONr_lrange_other7.42431.7193190
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.2511400.242783X-RAY DIFFRACTION100
1.847-1.8970.2481650.2252715X-RAY DIFFRACTION100
1.897-1.9520.2211560.1962621X-RAY DIFFRACTION100
1.952-2.0120.2281160.1652599X-RAY DIFFRACTION99.9264
2.012-2.0780.211120.172519X-RAY DIFFRACTION99.924
2.078-2.1510.2111170.1672421X-RAY DIFFRACTION99.9606
2.151-2.2320.21260.1652338X-RAY DIFFRACTION100
2.232-2.3230.191260.1522240X-RAY DIFFRACTION99.8312
2.323-2.4270.202900.1522171X-RAY DIFFRACTION100
2.427-2.5450.1951140.1582076X-RAY DIFFRACTION100
2.545-2.6820.1881090.1531963X-RAY DIFFRACTION99.9518
2.682-2.8450.2141000.1551868X-RAY DIFFRACTION100
2.845-3.0410.211100.1591747X-RAY DIFFRACTION100
3.041-3.2840.1991140.1561614X-RAY DIFFRACTION100
3.284-3.5970.1811010.1521518X-RAY DIFFRACTION100
3.597-4.020.168770.141367X-RAY DIFFRACTION100
4.02-4.640.141710.131232X-RAY DIFFRACTION99.8467
4.64-5.6780.198660.1491035X-RAY DIFFRACTION100
5.678-8.0070.242530.186825X-RAY DIFFRACTION100
8.007-43.8750.211250.199497X-RAY DIFFRACTION99.4286

+
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