[English] 日本語
Yorodumi- PDB-6wnz: Structure of a dimer of the Sulfolobus solfataricus MCM N-termina... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6wnz | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of a dimer of the Sulfolobus solfataricus MCM N-terminal domain reveals potential role in MCM ring opening | ||||||
Components | Minichromosome maintenance protein MCM | ||||||
Keywords | REPLICATION / HYDROLASE / DNA Helicase | ||||||
Function / homology | Function and homology information MCM complex / DNA duplex unwinding / helicase activity / single-stranded DNA binding / DNA helicase / DNA replication / ATP hydrolysis activity / ATP binding / identical protein binding Similarity search - Function | ||||||
Biological species | Saccharolobus solfataricus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Meagher, M. / Spence, M.N. / Enemark, E.J. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2021 Title: Structure of a dimer of the Sulfolobus solfataricus MCM N-terminal domain reveals a potential role in MCM ring opening Authors: Meagher, M. / Spence, M.N. / Enemark, E.J. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6wnz.cif.gz | 119.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6wnz.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 6wnz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wn/6wnz ftp://data.pdbj.org/pub/pdb/validation_reports/wn/6wnz | HTTPS FTP |
---|
-Related structure data
Related structure data | 2vl6S S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||||
Unit cell |
| ||||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ILE / Beg label comp-ID: ILE / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: 0 / Auth seq-ID: 8 - 264 / Label seq-ID: 9 - 265
|
-Components
#1: Protein | Mass: 31343.357 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Saccharolobus solfataricus (strain ATCC 35092 / DSM 1617 / JCM 11322 / P2) (archaea) Strain: ATCC 35092 / DSM 1617 / JCM 11322 / P2 / Gene: MCM, SSO0774 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) (RIPL) / References: UniProt: Q9UXG1, DNA helicase #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.47 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 100 mM Tris, pH 8, 8% PEG8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Dec 12, 2017 |
Radiation | Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. obs: 49591 / % possible obs: 99.9 % / Redundancy: 7 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 30.4 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 6.3 % / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2454 / CC1/2: 0.776 / % possible all: 99.1 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2VL6 Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.937 / SU B: 4.838 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / ESU R Free: 0.158 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 192.63 Å2 / Biso mean: 57.006 Å2 / Biso min: 27.41 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2→50 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints NCS | Ens-ID: 1 / Number: 14967 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2→2.051 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|