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Open data
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Basic information
Entry | Database: PDB / ID: 4r7z | ||||||
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Title | PfMCM-AAA double-octamer | ||||||
![]() | Cell division control protein 21 | ||||||
![]() | HYDROLASE / AAA+ / MCM / helicase / ATPase / DNA replication | ||||||
Function / homology | ![]() single-stranded 3'-5' DNA helicase activity / MCM complex / intein-mediated protein splicing / double-strand break repair via break-induced replication / DNA unwinding involved in DNA replication / single-stranded DNA binding / endonuclease activity / DNA helicase / cell division / ATP binding / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Miller, J.M. / Arachea, B.T. / Epling, L.B. / Enemark, E.J. | ||||||
![]() | ![]() Title: Analysis of the crystal structure of an active MCM hexamer. Authors: Miller, J.M. / Arachea, B.T. / Epling, L.B. / Enemark, E.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 867.8 KB | Display | ![]() |
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PDB format | ![]() | 732.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 4.5 MB | Display | ![]() |
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Full document | ![]() | 4.8 MB | Display | |
Data in XML | ![]() | 224.3 KB | Display | |
Data in CIF | ![]() | 290.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4r7yC ![]() 4fdgS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 37185.352 Da / Num. of mol.: 16 / Fragment: AAA+ domain of PfMCM (UNP 263-361/729-966) Source method: isolated from a genetically manipulated source Details: Constructed as Sumo fusion (Mossessova and Lima, 2000) Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-ADP / #3: Chemical | ChemComp-MG / Sequence details | The UNK region in the sequence is due to unknown registration. The missing sequence is ...The UNK region in the sequence is due to unknown registration. The missing sequence is GKSSSAAGLT | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.09 Å3/Da / Density % sol: 60.21 % |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 6 mg/mL PfMCM-AAA; 5 mM ADP; 50 mM MgCl2; 18 mM Hepes, pH 7.6; 180 mM NaCl; 4.5 mM 2-mercaptoethanol mixed 1:1 with 50 mM sodium cacodylate, pH 6.0; 50 mM magnesium acetate; 30% MPD; 5% ...Details: 6 mg/mL PfMCM-AAA; 5 mM ADP; 50 mM MgCl2; 18 mM Hepes, pH 7.6; 180 mM NaCl; 4.5 mM 2-mercaptoethanol mixed 1:1 with 50 mM sodium cacodylate, pH 6.0; 50 mM magnesium acetate; 30% MPD; 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 300K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 8, 2012 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.8→50 Å / Num. all: 70730 / Num. obs: 69970 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 3.3 % / Rsym value: 0.169 / Net I/σ(I): 8.3 |
Reflection shell | Resolution: 3.8→3.94 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.41 / Num. unique all: 7090 / Rsym value: 0.429 / % possible all: 97 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: placement of 16 copies of the ATPase domain of 4FDG (Slaymaker et al., 2013) Resolution: 3.8→48.37 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 4895965.68 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber Details: BULK SOLVENT MODEL USED. Strict NCS was used using the matrices provided and only chain A coordinates
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.0837 Å2 / ksol: 0.3 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 91.2 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 3.8→48.37 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: CONSTR | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 3.8→3.94 Å / Rfactor Rfree error: 0.019 / Total num. of bins used: 10
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Xplor file |
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