[English] 日本語
Yorodumi
- PDB-7ouj: Crystal structure of the flavoprotein monooxygenase RubL from rub... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 7ouj
TitleCrystal structure of the flavoprotein monooxygenase RubL from rubromycin biosynthesis
ComponentsRubL
KeywordsFLAVOPROTEIN / monooxygenase / griseorhodin A biosynthesis / rubromycin biosynthesis
Function / homology
Function and homology information


oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen / FAD binding
Similarity search - Function
Aromatic-ring hydroxylase, C-terminal / : / FAD-binding domain / FAD binding domain / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
(2S)-hexane-1,2,6-triol / FLAVIN-ADENINE DINUCLEOTIDE / 4-HYDROXYPROLINE / Polyketide hydroxylase
Similarity search - Component
Biological speciesStreptomyces collinus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.573 Å
AuthorsSaleem-Batcha, R. / Toplak, M. / Teufel, R.
Funding support Germany, Austria, 3items
OrganizationGrant numberCountry
German Research Foundation (DFG)TE 931/3-1 Germany
German Research Foundation (DFG)TE 931/4-1 Germany
Austrian Science FundJ4482-B Austria
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2021
Title: Catalytic Control of Spiroketal Formation in Rubromycin Polyketide Biosynthesis.
Authors: Toplak, M. / Saleem-Batcha, R. / Piel, J. / Teufel, R.
History
DepositionJun 11, 2021Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 3, 2021Provider: repository / Type: Initial release
Revision 1.1Dec 22, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.name
Revision 1.2Jan 31, 2024Group: Data collection / Derived calculations / Refinement description
Category: atom_type / chem_comp_atom ...atom_type / chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
AAA: RubL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,3658
Polymers57,9191
Non-polymers1,4477
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1930 Å2
ΔGint-19 kcal/mol
Surface area21570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.323, 57.514, 122.379
Angle α, β, γ (deg.)90.000, 95.183, 90.000
Int Tables number5
Space group name H-MI121

-
Components

-
Protein , 1 types, 1 molecules AAA

#1: Protein RubL


Mass: 57918.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: HYP is ligand from crystallisation buffer / Source: (gene. exp.) Streptomyces collinus (bacteria) / Gene: rubL / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q8KY42

-
Non-polymers , 6 types, 201 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: FAD*YM
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1JW / (2S)-hexane-1,2,6-triol / (-)-1,2,6-Hexanetriol / 6999990


Mass: 134.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O3
#5: Chemical ChemComp-HYP / 4-HYDROXYPROLINE / HYDROXYPROLINE


Type: L-peptide linking / Mass: 131.130 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C5H9NO3
#6: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.34 Å3/Da / Density % sol: 47.43 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 20 mM DL-Arginine hydrochloride, 20 mM DL-Threonine, 20 mM DL-Histidine monohydrochloride monohydrate, 20 mM DL-5-Hydroxylysine hydrochloride, 20 mM trans-4-hydroxy-L-proline, 100 mM BES/TEA ...Details: 20 mM DL-Arginine hydrochloride, 20 mM DL-Threonine, 20 mM DL-Histidine monohydrochloride monohydrate, 20 mM DL-5-Hydroxylysine hydrochloride, 20 mM trans-4-hydroxy-L-proline, 100 mM BES/TEA pH 7.5 buffer system, 12.5% PEG 4000 and 20% 1,2,6-Hexanetriol

-
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: Jul 9, 2020
RadiationMonochromator: M / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.57→46.08 Å / Num. obs: 70014 / % possible obs: 94 % / Redundancy: 2.4 % / CC1/2: 0.99 / Rmerge(I) obs: 0.046 / Net I/σ(I): 9.4
Reflection shellResolution: 1.57→1.66 Å / Rmerge(I) obs: 0.55 / Num. unique obs: 10481 / CC1/2: 0.7

-
Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3IHG

3ihg


Resolution: 1.573→37.778 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.96 / WRfactor Rfree: 0.214 / WRfactor Rwork: 0.18 / SU B: 2.014 / SU ML: 0.066 / Average fsc free: 0.8812 / Average fsc work: 0.8859 / Cross valid method: FREE R-VALUE / ESU R: 0.088 / ESU R Free: 0.087
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2095 3673 5.247 %
Rwork0.183 66335 -
all0.184 --
obs-70008 94.034 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 27.196 Å2
Baniso -1Baniso -2Baniso -3
1-0.061 Å20 Å2-0.002 Å2
2--0.051 Å20 Å2
3----0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.573→37.778 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3974 0 96 194 4264
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0134145
X-RAY DIFFRACTIONr_bond_other_d0.0010.0173915
X-RAY DIFFRACTIONr_angle_refined_deg1.7021.655651
X-RAY DIFFRACTIONr_angle_other_deg1.5111.5878984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2895539
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.75819.539217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.7315596
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0241547
X-RAY DIFFRACTIONr_chiral_restr0.0850.2530
X-RAY DIFFRACTIONr_chiral_restr_other0.0530.21
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024748
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02931
X-RAY DIFFRACTIONr_nbd_refined0.210.2777
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1830.23778
X-RAY DIFFRACTIONr_nbtor_refined0.1650.22060
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.22066
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1270.2204
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2910.26
X-RAY DIFFRACTIONr_nbd_other0.2250.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2090.27
X-RAY DIFFRACTIONr_mcbond_it2.2752.6812162
X-RAY DIFFRACTIONr_mcbond_other2.2752.6812162
X-RAY DIFFRACTIONr_mcangle_it3.1844.0162699
X-RAY DIFFRACTIONr_mcangle_other3.1834.0182700
X-RAY DIFFRACTIONr_scbond_it3.5243.051983
X-RAY DIFFRACTIONr_scbond_other3.5233.051984
X-RAY DIFFRACTIONr_scangle_it5.2254.4112952
X-RAY DIFFRACTIONr_scangle_other5.2254.4112953
X-RAY DIFFRACTIONr_lrange_it6.22531.7574435
X-RAY DIFFRACTIONr_lrange_other6.20131.6634415
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.573-1.6140.3762500.3735023X-RAY DIFFRACTION95.4389
1.614-1.6580.3342650.3344936X-RAY DIFFRACTION98.0951
1.658-1.7060.2932610.294795X-RAY DIFFRACTION97.3806
1.706-1.7590.2622650.2584653X-RAY DIFFRACTION97.444
1.759-1.8160.262540.2314411X-RAY DIFFRACTION96.1261
1.816-1.880.2392390.2074135X-RAY DIFFRACTION91.7943
1.88-1.9510.1952320.1724127X-RAY DIFFRACTION96.2889
1.951-2.030.2062120.1564044X-RAY DIFFRACTION96.1156
2.03-2.1210.181940.1523829X-RAY DIFFRACTION95.1289
2.121-2.2240.2051930.1523617X-RAY DIFFRACTION94.5879
2.224-2.3440.1912180.1623409X-RAY DIFFRACTION94.2078
2.344-2.4860.2051880.1693190X-RAY DIFFRACTION93.4181
2.486-2.6580.1811530.1692948X-RAY DIFFRACTION89.8841
2.658-2.870.2141730.1612777X-RAY DIFFRACTION92.3896
2.87-3.1430.1871480.1582543X-RAY DIFFRACTION91.9686
3.143-3.5140.1811300.1572262X-RAY DIFFRACTION89.5545
3.514-4.0550.1921140.1711961X-RAY DIFFRACTION87.775
4.055-4.9620.21720.1741628X-RAY DIFFRACTION84.4091
4.962-6.9990.213760.2111289X-RAY DIFFRACTION87.1648
6.999-37.7780.184360.163758X-RAY DIFFRACTION87.9291

+
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