[English] 日本語
Yorodumi
- PDB-6ubl: Structure of DynF from the Dynemicin Biosynthesis Pathway of Micr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6ubl
TitleStructure of DynF from the Dynemicin Biosynthesis Pathway of Micromonospora chersina
ComponentsDynF
KeywordsUNKNOWN FUNCTION / Beta Barrel / Enediyne biosynthetic pathway / Dynemicin Biosynthesis
Function / homologyPALMITIC ACID / Unkown protein
Function and homology information
Biological speciesMicromonospora chersina (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.499 Å
AuthorsKosgei, A.J. / Miller, M.D. / Xu, W. / Bhardwaj, M. / Van Lanen, S.G. / Thorson, J.S. / Phillips Jr., G.N.
Funding support United States, 3items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01-GM115261 United States
National Institutes of Health/National Cancer Institute (NIH/NCI)R01-CA217255 United States
National Science Foundation (NSF, United States)STC-1231306 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2022
Title: The crystal structure of DynF from the dynemicin-biosynthesis pathway of Micromonospora chersina.
Authors: Kosgei, A.J. / Miller, M.D. / Bhardwaj, M. / Xu, W. / Thorson, J.S. / Van Lanen, S.G. / Phillips Jr., G.N.
History
DepositionSep 12, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 12, 2022Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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 / _citation_author.identifier_ORCID / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2May 22, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: DynF
B: DynF
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,9314
Polymers45,4182
Non-polymers5132
Water7,530418
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, gel filtration supports the assignment of a dimer for the oligomerization state
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5160 Å2
ΔGint-7 kcal/mol
Surface area17480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.830, 116.126, 129.877
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-583-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resid 0 through 4 or resid 6...
21(chain B and (resid 0 through 4 or resid 6...

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYS(chain A and (resid 0 through 4 or resid 6...AA0 - 41 - 5
12VALVALVALVAL(chain A and (resid 0 through 4 or resid 6...AA6 - 127 - 13
13THRTHRPROPRO(chain A and (resid 0 through 4 or resid 6...AA14 - 3215 - 33
14PROPROGLYGLY(chain A and (resid 0 through 4 or resid 6...AA34 - 5335 - 54
15SERSERMETMET(chain A and (resid 0 through 4 or resid 6...AA0 - 2101 - 211
16SERSERMETMET(chain A and (resid 0 through 4 or resid 6...AA0 - 2101 - 211
17PROPROVALVAL(chain A and (resid 0 through 4 or resid 6...AA179 - 183180 - 184
18ASPASPMETMET(chain A and (resid 0 through 4 or resid 6...AA185 - 210186 - 211
19PLMPLMPLMPLM(chain A and (resid 0 through 4 or resid 6...AC301
21SERSERLYSLYS(chain B and (resid 0 through 4 or resid 6...BB0 - 41 - 5
22VALVALVALVAL(chain B and (resid 0 through 4 or resid 6...BB6 - 127 - 13
23THRTHRPROPRO(chain B and (resid 0 through 4 or resid 6...BB14 - 3215 - 33
24VALVALVALVAL(chain B and (resid 0 through 4 or resid 6...BB67
25SERSERMETMET(chain B and (resid 0 through 4 or resid 6...BB0 - 2101 - 211
26SERSERMETMET(chain B and (resid 0 through 4 or resid 6...BB0 - 2101 - 211
27GLYGLYMETMET(chain B and (resid 0 through 4 or resid 6...BB172 - 177173 - 178
28ASPASPMETMET(chain B and (resid 0 through 4 or resid 6...BB185 - 210186 - 211
29PLMPLMPLMPLM(chain B and (resid 0 through 4 or resid 6...BD301

-
Components

#1: Protein DynF


Mass: 22709.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Micromonospora chersina (bacteria) / Gene: GA0070603_4197 / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: B2BM43
#2: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H32O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 418 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 25% (w/v) PEG 1500, 0.1 M PCB buffer, pH 7.0

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jun 12, 2018
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.499→34.716 Å / Num. obs: 70922 / % possible obs: 97.6 % / Redundancy: 6.204 % / Biso Wilson estimate: 32.428 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.056 / Rrim(I) all: 0.061 / Χ2: 1.14 / Net I/σ(I): 14.13
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.499-1.593.881.6610.63101320.3731.90487.1
1.59-1.75.9310.8611.61106970.7490.94398.1
1.7-1.846.9070.483.31101710.9280.51899.8
1.84-2.016.6390.2356.7794050.980.255100
2.01-2.256.7880.12513.2785410.9930.135100
2.25-2.596.8160.0821.1275590.9970.087100
2.59-3.176.4820.0532.2564390.9980.054100
3.17-4.466.8730.03549.1650460.9990.038100
4.46-34.7166.3550.02952.0629320.9990.03199.6

-
Phasing

PhasingMethod: SIRAS
Phasing MIRResolution: 2.7→34.7 Å
Details: The structure was phased using SIRAS with data from a potassium iodide soaked crystal and the native data from an unsoaked crystal. Prior to cryocooling, a crystal was soaked in 0.5 M KI for ~60 s.

-
Processing

Software
NameVersionClassification
XDSVERSION Jan 26, 2018 BUILT=20180409data reduction
XSCALEdata scaling
SHELX2013/2phasing
PHENIX1.16refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: SIRAS / Resolution: 1.499→34.716 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 22.21
Details: 1. Hydrogens have been added in their riding positions. 2. Automatic NCS torsion restraints have been included. 3. Mass spectrometry supports the assignment of palmitic acid as the most ...Details: 1. Hydrogens have been added in their riding positions. 2. Automatic NCS torsion restraints have been included. 3. Mass spectrometry supports the assignment of palmitic acid as the most likely species to have co-purified with the DynF protein and it was modeled into the density in the beta-barrel.
RfactorNum. reflection% reflection
Rfree0.1851 3518 4.97 %
Rwork0.1614 --
obs0.1625 70715 97.32 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 151.79 Å2 / Biso mean: 35.5675 Å2 / Biso min: 15.78 Å2
Refinement stepCycle: final / Resolution: 1.499→34.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3180 0 100 422 3702
Biso mean--53.79 40.69 -
Num. residues----422
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A1832X-RAY DIFFRACTION9.264TORSIONAL
12B1832X-RAY DIFFRACTION9.264TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.4994-1.51990.36191170.4045200074
1.5199-1.54160.39821080.3972222582
1.5416-1.56460.36061130.3711248690
1.5646-1.58910.36691410.3433262795
1.5891-1.61510.30061390.2931261896
1.6151-1.6430.28571340.275268998
1.643-1.67290.26471570.2481268398
1.6729-1.7050.24071250.23032749100
1.705-1.73980.25461520.22432681100
1.7398-1.77770.21811280.20572763100
1.7777-1.8190.22541570.18192734100
1.819-1.86450.20981380.18052757100
1.8645-1.91490.18641610.16052736100
1.9149-1.97130.18331460.15632735100
1.9713-2.03490.18041480.14842753100
2.0349-2.10760.14881480.15412757100
2.1076-2.1920.17931450.14632738100
2.192-2.29170.15881390.14472768100
2.2917-2.41250.18151300.14522789100
2.4125-2.56360.1771490.15082755100
2.5636-2.76150.20451230.16112808100
2.7615-3.03920.17581590.15742775100
3.0392-3.47860.19441560.14842803100
3.4786-4.38140.15661480.12952833100
4.3814-34.7160.16121570.15342935100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.3374-0.169-0.35530.79660.04461.1062-0.071-0.0485-0.0878-0.07730.04170.02020.14830.00830.0350.2428-0.00970.00720.19520.00540.193637.021315.111712.5694
20.7227-0.1667-0.25070.7407-0.06161.43920.0174-0.040.0989-0.06260.0541-0.0123-0.1515-0.075-0.08650.21310.0101-0.00640.2025-0.00490.20525.704837.353617.8597
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1(chain 'A' and resid 0 through 210)A0 - 210
2X-RAY DIFFRACTION2(chain 'B' and resid 0 through 210)B0 - 210

+
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