[English] 日本語
Yorodumi
- PDB-9cu3: Allosteric mechanism of DriD transcription activator -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9cu3
TitleAllosteric mechanism of DriD transcription activator
ComponentsWYL domain-containing protein
KeywordsDNA BINDING PROTEIN / Transcription / activation
Function / homologyProtein PafC / : / WYL domain / WYL domain / WYL domain-containing protein
Function and homology information
Biological speciesCaulobacter vibrioides CB15 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsCannistraci, E.G. / Schumacher, M.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35GM130290 United States
CitationJournal: To Be Published
Title: Molecular mechanism of ssDNA-mediated allosteric activation of the C. crescentus WYL-domain containing transcription regulator, DriD
Authors: Cannistraci, E.G. / Srinivasu, B.Y. / Chavez Orozco Jr, J.C. / Gozzi, K. / Wales, T.E. / Schumacher, M.A.
History
DepositionJul 25, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 23, 2025Provider: repository / Type: Initial release

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
B: WYL domain-containing protein
A: WYL domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,9528
Polymers59,3832
Non-polymers5686
Water9,944552
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7810 Å2
ΔGint-111 kcal/mol
Surface area18450 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.796, 88.796, 141.523
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein WYL domain-containing protein


Mass: 29691.650 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Caulobacter vibrioides CB15 (bacteria) / Gene: CC_1095 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9A999
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 552 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.71 Å3/Da / Density % sol: 54.65 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: Ammonium sulfate dibasic, sodium cacodylate trihydrate

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.02 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.02 Å / Relative weight: 1
ReflectionResolution: 1.9→46.73 Å / Num. obs: 46532 / % possible obs: 95.1 % / Redundancy: 7.9 % / Biso Wilson estimate: 47.1 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.032 / Rrim(I) all: 0.092 / Net I/σ(I): 10.4
Reflection shellResolution: 2.19→2.31 Å / % possible obs: 73.9 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.574 / Num. measured all: 12020 / Num. unique obs: 3557 / CC1/2: 0.911 / Rpim(I) all: 0.347 / Rrim(I) all: 0.676 / Net I/σ(I) obs: -0.4

-
Processing

Software
NameVersionClassification
PHENIX1.21-5207refinement
Aimless8.0.012data scaling
XDS8.0.012data reduction
PHASER1.21-5207phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→44.4 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2309 1966 4.23 %
Rwork0.2021 --
obs0.2033 46531 90.33 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→44.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3125 0 32 552 3709
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075
X-RAY DIFFRACTIONf_angle_d0.845
X-RAY DIFFRACTIONf_dihedral_angle_d17.2081186
X-RAY DIFFRACTIONf_chiral_restr0.049463
X-RAY DIFFRACTIONf_plane_restr0.008575
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.950.7906730.77741624X-RAY DIFFRACTION47
1.95-20.52251060.4562500X-RAY DIFFRACTION72
2-2.060.30561420.27163165X-RAY DIFFRACTION91
2.06-2.130.22931500.22843404X-RAY DIFFRACTION98
2.13-2.20.25261530.21323480X-RAY DIFFRACTION100
2.2-2.290.4953920.43292113X-RAY DIFFRACTION61
2.29-2.390.28841500.22613412X-RAY DIFFRACTION97
2.39-2.520.24071550.21063504X-RAY DIFFRACTION100
2.52-2.680.2271570.19863490X-RAY DIFFRACTION100
2.68-2.880.21811520.20213524X-RAY DIFFRACTION100
2.89-3.170.25771550.19223543X-RAY DIFFRACTION100
3.18-3.630.20971550.15463531X-RAY DIFFRACTION100
3.63-4.580.17691570.1483547X-RAY DIFFRACTION99
4.58-100.16361690.15913728X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 42.2629 Å / Origin y: -33.2382 Å / Origin z: -11.1163 Å
111213212223313233
T0.1734 Å20.0865 Å20.0082 Å2-0.435 Å20.0359 Å2--0.2953 Å2
L1.4175 °2-0.1543 °20.6798 °2-0.3919 °2-0.166 °2--1.6619 °2
S-0.1052 Å °-0.0245 Å °0.1351 Å °0.1272 Å °0.094 Å °0.0257 Å °-0.1997 Å °-0.2439 Å °0.0079 Å °
Refinement TLS groupSelection details: all

+
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