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- PDB-5w0u: Crystal structure of MBP fused activation-induced cytidine deamin... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5w0u | ||||||
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Title | Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with dCMP | ||||||
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![]() | HYDROLASE/DNA / Class switch recombination / Cytidine deaminase / HYDROLASE-DNA complex | ||||||
Function / homology | ![]() somatic diversification of immunoglobulins / regulation of nuclear cell cycle DNA replication / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / positive regulation of gene expression via chromosomal CpG island demethylation ...somatic diversification of immunoglobulins / regulation of nuclear cell cycle DNA replication / single-stranded DNA cytosine deaminase / DNA cytosine deamination / : / cytidine to uridine editing / cytidine deaminase activity / negative regulation of single stranded viral RNA replication via double stranded DNA intermediate / : / positive regulation of gene expression via chromosomal CpG island demethylation / isotype switching / carbohydrate transmembrane transporter activity / maltose binding / maltose transport / maltodextrin transmembrane transport / somatic hypermutation of immunoglobulin genes / ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing / B cell differentiation / Chromatin modifications during the maternal to zygotic transition (MZT) / P-body / mRNA processing / outer membrane-bounded periplasmic space / cellular response to lipopolysaccharide / defense response to virus / defense response to bacterium / ubiquitin protein ligase binding / protein-containing complex / RNA binding / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Qiao, Q. / Wang, L. / Wu, H. | ||||||
![]() | ![]() Title: AID Recognizes Structured DNA for Class Switch Recombination. Authors: Qiao, Q. / Wang, L. / Meng, F.L. / Hwang, J.K. / Alt, F.W. / Wu, H. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 242.4 KB | Display | ![]() |
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PDB format | ![]() | 190 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1019.5 KB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 41 KB | Display | |
Data in CIF | ![]() | 54.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w0rSC ![]() 5w0zC ![]() 5w1cC S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 61659.883 Da / Num. of mol.: 2 / Fragment: UNP residues 27-392,UNP residues 13-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() Gene: malE, Z5632, ECs5017, AICDA, AID / Production host: ![]() ![]() References: UniProt: P0AEY0, UniProt: Q9GZX7, single-stranded DNA cytosine deaminase |
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-DNA chain , 2 types, 2 molecules DG
#2: DNA chain | Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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#3: DNA chain | Mass: 3638.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 5 types, 9 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/DCM.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/DCM.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | #7: Chemical | ChemComp-GOL / | #8: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.95 Å3/Da / Density % sol: 58.26 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 0.1 M MES at pH 6.2, 3%PEG3350, 10 mM CaCl2, 20mM dCMP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 20, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9791 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→153.935 Å / Num. obs: 36653 / % possible obs: 98.3 % / Redundancy: 9.8 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.1 |
Reflection shell | Resolution: 2.94→3.07 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 3868 / CC1/2: 0.974 / Rpim(I) all: 0.313 / % possible all: 99.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5W0R Resolution: 2.9→153.935 Å / SU ML: 0.39 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 39.63 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→153.935 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10
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