[English] 日本語
Yorodumi- PDB-4bzc: Crystal structure of the tetrameric dGTP-bound wild type SAMHD1 c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bzc | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of the tetrameric dGTP-bound wild type SAMHD1 catalytic core | ||||||
Components | DEOXYNUCLEOSIDE TRIPHOSPHATE TRIPHOSPHOHYDROLASE SAMHD1 | ||||||
Keywords | HYDROLASE / HIV RESTRICTION FACTOR / DNTPASE | ||||||
Function / homology | Function and homology information Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / deoxyribonucleotide catabolic process / dGTP catabolic process ...Nucleotide catabolism / Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases / deoxynucleoside triphosphate hydrolase activity / triphosphoric monoester hydrolase activity / dGTP binding / dATP catabolic process / dGTPase activity / tetraspanin-enriched microdomain / deoxyribonucleotide catabolic process / dGTP catabolic process / DNA strand resection involved in replication fork processing / negative regulation of type I interferon-mediated signaling pathway / regulation of innate immune response / somatic hypermutation of immunoglobulin genes / RNA nuclease activity / double-strand break repair via homologous recombination / Interferon alpha/beta signaling / site of double-strand break / single-stranded DNA binding / protein homotetramerization / defense response to virus / nucleic acid binding / immune response / innate immune response / DNA damage response / GTP binding / RNA binding / zinc ion binding / nucleoplasm / identical protein binding / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å | ||||||
Authors | Ji, X. / Yang, H. / Wu, Y. / Yan, J. / Mehrens, J. / DeLucia, M. / Hao, C. / Gronenborn, A.M. / Skowronski, J. / Ahn, J. / Xiong, Y. | ||||||
Citation | Journal: Nat.Struct.Mol.Biol. / Year: 2013 Title: Mechanism of Allosteric Activation of Samhd1 by Dgtp Authors: Ji, X. / Wu, Y. / Yan, J. / Mehrens, J. / Yang, H. / Delucia, M. / Hao, C. / Gronenborn, A.M. / Skowronski, J. / Ahn, J. / Xiong, Y. | ||||||
History |
| ||||||
Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 4-STRANDED BARREL THIS IS REPRESENTED BY A 5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 4-STRANDED BARREL THIS IS REPRESENTED BY A 5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "CB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 4-STRANDED BARREL THIS IS REPRESENTED BY A 5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "DB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 4-STRANDED BARREL THIS IS REPRESENTED BY A 5-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4bzc.cif.gz | 801.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bzc.ent.gz | 665.2 KB | Display | PDB format |
PDBx/mmJSON format | 4bzc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bzc_validation.pdf.gz | 4 MB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4bzc_full_validation.pdf.gz | 4 MB | Display | |
Data in XML | 4bzc_validation.xml.gz | 70.5 KB | Display | |
Data in CIF | 4bzc_validation.cif.gz | 93.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/4bzc ftp://data.pdbj.org/pub/pdb/validation_reports/bz/4bzc | HTTPS FTP |
-Related structure data
Related structure data | 4bzbC 3u1nS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 63408.320 Da / Num. of mol.: 4 / Fragment: HD DOMAIN, RESIDUES 113-626 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA 2 References: UniProt: Q9Y3Z3, Hydrolases; Acting on ester bonds; Triphosphoric-monoester hydrolases #2: Chemical | ChemComp-T8T / #3: Chemical | ChemComp-MN / #4: Chemical | ChemComp-MG / #5: Water | ChemComp-HOH / | Nonpolymer details | 2'-DEOXYGUANO | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
---|---|
Crystal grow | pH: 6.7 / Details: 100 MM BIS-TRIS PH 6.7 AND 25% (W/V) PEG1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 2.88→50 Å / Num. obs: 40369 / % possible obs: 95.6 % / Observed criterion σ(I): 1 / Redundancy: 2.9 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 8.2 |
Reflection shell | Resolution: 2.88→2.93 Å / Redundancy: 3 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 1.2 / % possible all: 97.4 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3U1N Resolution: 2.88→49.71 Å / Cor.coef. Fo:Fc: 0.932 / Cor.coef. Fo:Fc free: 0.89 / SU B: 40.606 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.559 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 278-281, 466-471 AND 600-626 ARE DISORDERED
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 66.501 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.88→49.71 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|