[English] 日本語
Yorodumi- PDB-5w0r: Crystal structure of MBP fused activation-induced cytidine deamin... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w0r | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of MBP fused activation-induced cytidine deaminase (AID) in complex with cacodylic acid | ||||||
Components | MBP fused activation-induced cytidine deaminase | ||||||
Keywords | HYDROLASE / Class switch recombination / Cytidine deaminase | ||||||
Function / homology | Function and homology information 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 | Escherichia coli O157:H7 (bacteria) Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å | ||||||
Authors | Qiao, Q. / Wang, L. / Wu, H. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Mol. Cell / Year: 2017 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: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5w0r.cif.gz | 444.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5w0r.ent.gz | 365.7 KB | Display | PDB format |
PDBx/mmJSON format | 5w0r.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5w0r_validation.pdf.gz | 454.3 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 5w0r_full_validation.pdf.gz | 464.6 KB | Display | |
Data in XML | 5w0r_validation.xml.gz | 39.8 KB | Display | |
Data in CIF | 5w0r_validation.cif.gz | 54.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w0/5w0r ftp://data.pdbj.org/pub/pdb/validation_reports/w0/5w0r | HTTPS FTP |
-Related structure data
Related structure data | 5w0uC 5w0zC 5w1cC 3vd8S 3vowS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 61659.883 Da / Num. of mol.: 2 Fragment: UNP P0AEY0 residues 27-392, UNP Q9GZX7 residues 13-181 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli O157:H7 (bacteria), (gene. exp.) Homo sapiens (human) Gene: malE, Z5632, ECs5017, AICDA, AID / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P0AEY0, UniProt: Q9GZX7, single-stranded DNA cytosine deaminase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.52 % |
---|---|
Crystal grow | Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.05 M sodium cacodylate at pH 5.5, 20 mM MgCl2, 10 mM CaCl2, 10 mM spermidine, 5% PEG3350 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9793 Å |
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: 2.4→188.1 Å / Num. obs: 48976 / % possible obs: 99.3 % / Redundancy: 11.9 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 2.42→2.5 Å / Redundancy: 5.6 % / Rmerge(I) obs: 1.354 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 53182 / CC1/2: 0.883 / Rpim(I) all: 0.577 / % possible all: 84.3 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3VD8, 3VOW Resolution: 2.4→24.809 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 24.75 / 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: 2.4→24.809 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement TLS group |
|