[English] 日本語
![](img/lk-miru.gif)
- PDB-5w1c: Crystal structure of MBP fused activation-induced cytidine deamin... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 5w1c | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with cytidine | ||||||
![]() |
| ||||||
![]() | DNA BINDING PROTEIN/DNA / Class switch recombination / Cytidine deaminase / DNA BINDING PROTEIN-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. | ||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 244.3 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 190.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 474.3 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 495 KB | Display | |
Data in XML | ![]() | 41.3 KB | Display | |
Data in CIF | ![]() | 55.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5w0rSC ![]() 5w0uC ![]() 5w0zC S: Starting model for refinement C: citing same article ( |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-
Components
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 62081.289 Da / Num. of mol.: 2 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 |
---|
-DNA chain , 2 types, 2 molecules DG
#2: DNA chain | Mass: 3687.417 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
---|---|
#3: DNA chain | Mass: 3638.379 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
-Non-polymers , 4 types, 8 molecules ![](data/chem/img/ZN.gif)
![](data/chem/img/CTN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CTN.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.92 % |
---|---|
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 and 20mM Cytidine |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Mar 18, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 3.18→155.3 Å / Num. obs: 28767 / % possible obs: 99.3 % / Redundancy: 6.5 % / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 3.18→3.36 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.543 / Mean I/σ(I) obs: 2.5 / Num. unique obs: 4138 / CC1/2: 0.974 / Rpim(I) all: 0.335 / % possible all: 99.7 |
-
Processing
Software |
| ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting model: 5W0R Resolution: 3.18→125.455 Å / SU ML: 0.38 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 38.1 / Stereochemistry target values: ML
| ||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.18→125.455 Å
| ||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||
LS refinement shell | Resolution: 3.1801→3.2937 Å
|