[English] 日本語
Yorodumi- PDB-1epa: STRUCTURE OF THE EPIDIDYMAL RETINOIC ACID-BINDING PROTEIN AT 2.1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1epa | ||||||
---|---|---|---|---|---|---|---|
Title | STRUCTURE OF THE EPIDIDYMAL RETINOIC ACID-BINDING PROTEIN AT 2.1 ANGSTROMS RESOLUTION | ||||||
Components | EPIDIDYMAL RETINOIC ACID-BINDING PROTEIN | ||||||
Keywords | RETINOIC ACID-BINDING PROTEIN | ||||||
Function / homology | Function and homology information | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.1 Å | ||||||
Authors | Newcomer, M.E. | ||||||
Citation | Journal: Structure / Year: 1993 Title: Structure of the epididymal retinoic acid binding protein at 2.1 A resolution. Authors: Newcomer, M.E. #1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1993 Title: X-Ray Crystallographic Identification of a Protein Binding Site for Both All-Trans-and 9-Cis-Retinoic Acid Authors: Newcomer, M.E. / Pappas, R.S. / Ong, D.E. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1epa.cif.gz | 70.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1epa.ent.gz | 56.2 KB | Display | PDB format |
PDBx/mmJSON format | 1epa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ep/1epa ftp://data.pdbj.org/pub/pdb/validation_reports/ep/1epa | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Atom site foot note | 1: ONLY CA'S ARE GIVEN FOR RESIDUES 24 - 32 IN BOTH COPIES OF THE MOLECULE. ELECTRON DENSITY IN THIS REGION IS POOR. 2: GLY A 72 - PRO A 73 OMEGA = 219.16 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION | ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.9949, 0.0386, 0.0928), Vector: |
-Components
#1: Protein | Mass: 18249.795 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / References: UniProt: P06911 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.76 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | *PLUS Method: other | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Radiation | Scattering type: x-ray |
---|---|
Radiation wavelength | Relative weight: 1 |
Reflection | *PLUS Highest resolution: 2.1 Å / Num. obs: 16724 / % possible obs: 99.8 % / Num. measured all: 63562 / Rmerge(I) obs: 0.0548 |
Reflection shell | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 2.26 Å / Mean I/σ(I) obs: 4.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.1→6 Å / Rfactor Rwork: 0.196 / Rfactor obs: 0.196 / σ(F): 2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→6 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.196 / Rfactor Rwork: 0.196 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_d / Dev ideal: 3.73 |