+Open data
-Basic information
Entry | Database: PDB / ID: 4c9z | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of Siah1 at 1.95 A resolution | ||||||
Components | E3 UBIQUITIN-PROTEIN LIGASE SIAH1 | ||||||
Keywords | LIGASE | ||||||
Function / homology | Function and homology information Netrin-1 signaling / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / anatomical structure morphogenesis / canonical Wnt signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / axon guidance / RING-type E3 ubiquitin transferase / protein catabolic process / ubiquitin-protein transferase activity ...Netrin-1 signaling / beta-catenin destruction complex / ubiquitin conjugating enzyme binding / anatomical structure morphogenesis / canonical Wnt signaling pathway / positive regulation of intrinsic apoptotic signaling pathway / axon guidance / RING-type E3 ubiquitin transferase / protein catabolic process / ubiquitin-protein transferase activity / ubiquitin protein ligase activity / Antigen processing: Ubiquitination & Proteasome degradation / nervous system development / ubiquitin-dependent protein catabolic process / spermatogenesis / proteasome-mediated ubiquitin-dependent protein catabolic process / neuron apoptotic process / amyloid fibril formation / protein ubiquitination / positive regulation of apoptotic process / Amyloid fiber formation / apoptotic process / zinc ion binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Rimsa, V. / Eadsforth, T.C. / Hunter, W.N. | ||||||
Citation | Journal: Acta Crystallogr.,Sect.F / Year: 2013 Title: Two High-Resolution Structures of the Human E3 Ubiquitin Ligase Siah1. Authors: Rimsa, V. / Eadsforth, T.C. / Hunter, W.N. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4c9z.cif.gz | 174.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4c9z.ent.gz | 139.3 KB | Display | PDB format |
PDBx/mmJSON format | 4c9z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c9z_validation.pdf.gz | 477.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4c9z_full_validation.pdf.gz | 487.8 KB | Display | |
Data in XML | 4c9z_validation.xml.gz | 19.7 KB | Display | |
Data in CIF | 4c9z_validation.cif.gz | 27.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/4c9z ftp://data.pdbj.org/pub/pdb/validation_reports/c9/4c9z | HTTPS FTP |
-Related structure data
Related structure data | 4ca1C 2a25S S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||
Unit cell |
| ||||||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 21921.082 Da / Num. of mol.: 2 Fragment: TWO ZINC FINGERS AND SUBSTRATE BINDING DOMAIN, RESIDUES 91-282 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): GOLD References: UniProt: Q8IUQ4, Ligases; Forming carbon-nitrogen bonds; Acid-amino-acid ligases (peptide synthases) |
---|
-Non-polymers , 6 types, 233 molecules
#2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-CL / #4: Chemical | #5: Chemical | #6: Chemical | #7: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 59 % / Description: NONE |
---|---|
Crystal grow | Details: CRYSTALS GREW FROM EQUAL VOLUMES OF PROTEIN SOLUTION (15 MG ML-1 IN 15 MM TRIS-HCL PH7.5, 30 MM NACL AND 10 MM DTT) AND RESERVOIR SOLUTION (100 MES PH6.5, 1.5 M MGSO4). |
-Data collection
Diffraction | Mean temperature: 287 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 12, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→44.99 Å / Num. obs: 38340 / % possible obs: 99.3 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 19.3 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4.5 / % possible all: 96 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2A25 Resolution: 1.95→40 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.924 / SU B: 6.872 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.149 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN A CONTAINS METHIONINE AT THE N-TERMINAL END, WHICH WAS LEFT FROM THE HISTIDINE TAG. RESIDUES 91-94 IN CHAIN B ARE DISORDERED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.28 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|