[English] 日本語
Yorodumi
- PDB-8a90: Crystal structure of FrsH -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 8a90
TitleCrystal structure of FrsH
ComponentsNon-heme diiron monooxygenase
KeywordsOXIDOREDUCTASE / NRPS
Function / homologyDiiron non-heme beta-hydroxylase, N-terminal domain / Diiron non-heme beta-hydroxylase N-terminal domain / Beta-lactamase superfamily domain / monooxygenase activity / Ribonuclease Z/Hydroxyacylglutathione hydrolase-like / ACETATE ION / : / OXYGEN ATOM / Non-heme diiron monooxygenase
Function and homology information
Biological speciesChromobacterium vaccinii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.574 Å
AuthorsSchneberger, N. / Wirtz, D.A. / Cruesemann, M. / Hagelueken, G.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Acs Chem.Biol. / Year: 2023
Title: Adenylation Domain-Guided Recruitment of Trans- Acting Nonheme Monooxygenases in Nonribosomal Peptide Biosynthesis.
Authors: Wirtz, D.A. / Schneberger, N. / Kloppel, S. / Richarz, R. / Geyer, M. / Konig, G.M. / Hagelueken, G. / Crusemann, M.
History
DepositionJun 27, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 30, 2023Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Feb 7, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Non-heme diiron monooxygenase
B: Non-heme diiron monooxygenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)121,19613
Polymers120,5462
Non-polymers65011
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-66 kcal/mol
Surface area35520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)117.715, 117.715, 234.261
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212
Space group name HallP4abw2nw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+1/4
#3: y+1/2,-x+1/2,z+3/4
#4: x+1/2,-y+1/2,-z+3/4
#5: -x+1/2,y+1/2,-z+1/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-725-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 4 through 531)
d_2ens_1(chain "B" and resid 4 through 531)

NCS domain segments:

Component-ID: 1 / Ens-ID: ens_1 / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Auth seq-ID: 4 - 531 / Label seq-ID: 4 - 531

Dom-IDAuth asym-IDLabel asym-ID
d_1AA
d_2BB

NCS oper: (Code: givenMatrix: (-0.346109814363, -0.82662189853, 0.443738924676), (-0.835612433918, 0.0565613263848, -0.546399740702), (0.426567528867, -0.559908075695, -0.710311966735)Vector: 74. ...NCS oper: (Code: given
Matrix: (-0.346109814363, -0.82662189853, 0.443738924676), (-0.835612433918, 0.0565613263848, -0.546399740702), (0.426567528867, -0.559908075695, -0.710311966735)
Vector: 74.4404423509, 176.781717289, 226.281231967)

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Non-heme diiron monooxygenase


Mass: 60273.219 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chromobacterium vaccinii (bacteria) / Gene: frsH / Production host: Escherichia coli (E. coli) / References: UniProt: A0A7S9SWM2

-
Non-polymers , 5 types, 66 molecules

#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-O / OXYGEN ATOM


Mass: 15.999 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: O
#5: Chemical
ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Fe / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / 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: 3.37 Å3/Da / Density % sol: 63.46 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, sitting drop
Details: 0.10 M HEPES pH 7.8, 10.89% (w/v) PEG 20000, 0.08 M KAc, 1.36% glycerol

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.999987 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 6, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.999987 Å / Relative weight: 1
ReflectionResolution: 2.574→48.02 Å / Num. obs: 87244 / % possible obs: 93.03 % / Redundancy: 4.2 % / Biso Wilson estimate: 54.27 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.151 / Net I/σ(I): 7.22
Reflection shellResolution: 2.574→2.665 Å / Mean I/σ(I) obs: 1.01 / Num. unique obs: 4482 / CC1/2: 0.458

-
Processing

Software
NameVersionClassification
XDS1.20_4444data reduction
PHENIX1.20_4444refinement
PHENIX1.20_4444phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4jo0

4jo0


Resolution: 2.574→48.02 Å / SU ML: 0.4679 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.2121
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2639 3459 3.96 %
Rwork0.2166 83785 -
obs0.2185 87244 87.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.68 Å2
Refinement stepCycle: LAST / Resolution: 2.574→48.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8448 0 32 55 8535
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00418675
X-RAY DIFFRACTIONf_angle_d0.881611756
X-RAY DIFFRACTIONf_chiral_restr0.0471263
X-RAY DIFFRACTIONf_plane_restr0.00671550
X-RAY DIFFRACTIONf_dihedral_angle_d5.4191168
Refine LS restraints NCSType: Torsion NCS / Rms dev position: 0.878145075047 Å
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.574-2.610.4293890.42021901X-RAY DIFFRACTION49.68
2.61-2.650.40471280.38823132X-RAY DIFFRACTION82.45
2.65-2.690.38551330.35663288X-RAY DIFFRACTION84.85
2.69-2.730.41641290.33843292X-RAY DIFFRACTION86.24
2.73-2.770.30311420.32643286X-RAY DIFFRACTION86.52
2.77-2.820.3471410.30823382X-RAY DIFFRACTION87.62
2.82-2.870.3071370.29563363X-RAY DIFFRACTION87.37
2.87-2.930.39571360.29193323X-RAY DIFFRACTION87.33
2.93-2.990.33311310.29733328X-RAY DIFFRACTION86.63
2.99-3.050.32711350.3053296X-RAY DIFFRACTION86.05
3.05-3.120.31891400.27053279X-RAY DIFFRACTION86.06
3.12-3.20.34531350.25773288X-RAY DIFFRACTION85.68
3.2-3.290.30081270.25163291X-RAY DIFFRACTION85.69
3.29-3.380.33481390.24093476X-RAY DIFFRACTION90.53
3.38-3.490.30861460.23443550X-RAY DIFFRACTION92.86
3.49-3.620.26261440.21943528X-RAY DIFFRACTION92.47
3.62-3.760.26531500.22133580X-RAY DIFFRACTION93.34
3.76-3.930.31531450.2043544X-RAY DIFFRACTION92.39
3.93-4.140.24661470.18943480X-RAY DIFFRACTION91.11
4.14-4.40.19591450.17233403X-RAY DIFFRACTION88.83
4.4-4.740.24191450.16173443X-RAY DIFFRACTION90.13
4.74-5.220.2241520.17343601X-RAY DIFFRACTION94.15
5.22-5.970.24461570.18773696X-RAY DIFFRACTION95.77
5.97-7.510.2451450.19223522X-RAY DIFFRACTION92.34
7.52-48.020.14521410.1483513X-RAY DIFFRACTION91.56

+
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