[English] 日本語
Yorodumi
- PDB-1wvl: Crystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1wvl
TitleCrystal Structure of Multimeric DNA-binding Protein Sac7d-GCN4 with DNA decamer
Components
  • 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3'
  • DNA-binding proteins 7a/7b/7d, GCN4
KeywordsSTRUCTURAL PROTEIN/DNA / leucine zipper / protein engineering / synchrotron radiation / thermophile / STRUCTURAL PROTEIN-DNA COMPLEX
Function / homology
Function and homology information


RNA endonuclease activity / DNA binding / cytoplasm
Similarity search - Function
DNA-binding 7kDa protein / 7kD DNA-binding domain / OB fold (Dihydrolipoamide Acetyltransferase, E2P) - #40 / Chromo-like domain superfamily / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
DNA / DNA-binding protein 7d
Similarity search - Component
Biological speciesSulfolobus acidocaldarius (acidophilic)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsWu, S.W. / Wang, A.H.
CitationJournal: Proteins / Year: 2005
Title: Design and characterization of a multimeric DNA binding protein using Sac7d and GCN4 as templates
Authors: Wu, S.W. / Ko, T.P. / Chou, C.C. / Wang, A.H.
History
DepositionDec 16, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
C: 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3'
D: 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3'
A: DNA-binding proteins 7a/7b/7d, GCN4
B: DNA-binding proteins 7a/7b/7d, GCN4


Theoretical massNumber of molelcules
Total (without water)24,5264
Polymers24,5264
Non-polymers00
Water2,630146
1
C: 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3'
D: 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3'
A: DNA-binding proteins 7a/7b/7d, GCN4
B: DNA-binding proteins 7a/7b/7d, GCN4

C: 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3'
D: 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3'
A: DNA-binding proteins 7a/7b/7d, GCN4
B: DNA-binding proteins 7a/7b/7d, GCN4


Theoretical massNumber of molelcules
Total (without water)49,0518
Polymers49,0518
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_465y-1,x+1,-z+3/41
Unit cell
Length a, b, c (Å)58.650, 58.650, 186.680
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number91
Space group name H-MP4122
Components on special symmetry positions
IDModelComponents
11A-214-

HOH

DetailsThe biological assembly is a tetramer generated from the dimer in the asymmetric unit by the operations: -1+y, 1+x, 3/4-z.

-
Components

#1: DNA chain 5'-D(*CP*CP*TP*AP*TP*AP*TP*AP*GP*G)-3'


Mass: 3044.016 Da / Num. of mol.: 2 / Source method: obtained synthetically
#2: Protein DNA-binding proteins 7a/7b/7d, GCN4 / Sac7d-GCN4 fusion protein


Mass: 9218.810 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus acidocaldarius (acidophilic)
Plasmid: pET-11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P13123
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

-
Sample preparation

CrystalDensity Matthews: 3.27 Å3/Da / Density % sol: 62.35 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1.6M Tri-Sodium Citrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Components of the solutions
IDNameCrystal-IDSol-ID
1Tri-Sodium Citrate11
2H2O11
3Tri-Sodium Citrate12
4H2O12

-
Data collection

DiffractionMean temperature: 116 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Apr 30, 2003
RadiationMonochromator: MSC confocal optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.6→20 Å / Num. all: 11603 / Num. obs: 10690 / % possible obs: 99.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 1
Reflection shellResolution: 2.6→2.7 Å / % possible all: 100

-
Processing

Software
NameClassification
CrystalCleardata collection
XDSdata reduction
CNSrefinement
CrystalCleardata reduction
XDSdata scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1azp

1azp


Resolution: 2.6→20 Å / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.269 526 RANDOM
Rwork0.23 --
all0.237 10702 -
obs0.276 10550 -
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.85 Å0.79 Å
Refinement stepCycle: LAST / Resolution: 2.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1286 389 0 146 1821
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.02874
X-RAY DIFFRACTIONc_angle_deg2.50755
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.046
RfactorNum. reflection% reflection
Rfree0.428 86 -
Rwork0.388 --
obs--100 %

+
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