[English] 日本語
Yorodumi
- PDB-5wwc: The crystal structure of Cren7 mutant L28M in complex with dsDNA -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5wwc
TitleThe crystal structure of Cren7 mutant L28M in complex with dsDNA
Components
  • Chromatin protein Cren7
  • DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')
KeywordsDNA BINDING PROTEIN/DNA / BETA-SHEET / DNA BINDING / DNA BINDING PROTEIN-DNA COMPLEX / Crenarchaeal chromatin protein
Function / homology
Function and homology information


chromosome / double-stranded DNA binding / cytoplasm
Similarity search - Function
Chromatin protein Cren7 / Double-stranded DNA-binding Cren7 / Cren7 superfamily / Chromatin protein Cren7 / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
DNA / Chromatin protein Cren7
Similarity search - Component
Biological speciesSulfolobus solfataricus (archaea)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsZhang, Z.F. / Zhao, M.H. / Wang, L. / Chen, Y.Y. / Dong, Y.H. / Gong, Y. / Huang, L.
CitationJournal: Biochem. J. / Year: 2017
Title: Roles of Leu28 side chain intercalation in the interaction between Cren7 and DNA
Authors: Zhang, Z. / Zhao, M. / Wang, L. / Chen, Y. / Dong, Y. / Gong, Y. / Huang, L.
History
DepositionDec 31, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 26, 2017Provider: repository / Type: Initial release
Revision 1.1May 24, 2017Group: Database references
Revision 1.2Nov 22, 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
A: Chromatin protein Cren7
B: Chromatin protein Cren7
C: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')
D: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')
E: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')
F: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)23,0946
Polymers23,0946
Non-polymers00
Water1,53185
1
A: Chromatin protein Cren7
C: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')
D: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)11,5473
Polymers11,5473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-14 kcal/mol
Surface area5810 Å2
MethodPISA
2
B: Chromatin protein Cren7
E: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')
F: DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')


Theoretical massNumber of molelcules
Total (without water)11,5473
Polymers11,5473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2370 Å2
ΔGint-13 kcal/mol
Surface area5730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)31.167, 52.370, 57.016
Angle α, β, γ (deg.)90.00, 94.95, 90.00
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein Chromatin protein Cren7


Mass: 6695.952 Da / Num. of mol.: 2 / Mutation: L28M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sulfolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea)
Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: creN7, SSO6901 / Plasmid: PET30A / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA 2 (DE3) / References: UniProt: Q97ZE3
#2: DNA chain
DNA (5'-D(*GP*TP*AP*AP*TP*TP*AP*C)-3')


Mass: 2425.629 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.8 / Details: 30% PEG1500

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.98 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 28, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 14394 / % possible obs: 99.2 % / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 30.5
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.8 % / Rmerge(I) obs: 0.662 / Mean I/σ(I) obs: 3.9 / % possible all: 99

-
Processing

Software
NameVersionClassification
PHENIX(1.11_2567: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3LWH

3lwh


Resolution: 1.9→50 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.45
RfactorNum. reflection% reflection
Rfree0.2347 722 5.03 %
Rwork0.1975 --
obs0.1995 14362 98.81 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms902 644 0 85 1631
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011648
X-RAY DIFFRACTIONf_angle_d1.222353
X-RAY DIFFRACTIONf_dihedral_angle_d27.798675
X-RAY DIFFRACTIONf_chiral_restr0.055252
X-RAY DIFFRACTIONf_plane_restr0.008191
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-2.04660.3271440.26282659X-RAY DIFFRACTION97
2.0466-2.25250.3231390.24492735X-RAY DIFFRACTION99
2.2525-2.57820.27191360.2362723X-RAY DIFFRACTION99
2.5782-3.24730.26111460.22852752X-RAY DIFFRACTION100
3.2473-26.31050.19491570.16342771X-RAY DIFFRACTION99

+
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