+Open data
-Basic information
Entry | Database: PDB / ID: 1xca | ||||||
---|---|---|---|---|---|---|---|
Title | APO-CELLULAR RETINOIC ACID BINDING PROTEIN II | ||||||
Components | CELLULAR RETINOIC ACID BINDING PROTEIN TYPE II | ||||||
Keywords | RETINOIC ACID TRANSPORT / CRABPII / RETINOIC ACID / LIGAND ENTRY / VITAMIN A | ||||||
Function / homology | Function and homology information positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport ...positive regulation of collateral sprouting / retinoid binding / retinal binding / retinoic acid binding / embryonic forelimb morphogenesis / retinoic acid metabolic process / retinol binding / Signaling by Retinoic Acid / epidermis development / fatty acid transport / cyclin binding / fatty acid binding / regulation of DNA-templated transcription / endoplasmic reticulum / signal transduction / extracellular exosome / nucleoplasm / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Chen, X. / Ji, X. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1998 Title: Crystal structure of apo-cellular retinoic acid-binding protein type II (R111M) suggests a mechanism of ligand entry. Authors: Chen, X. / Tordova, M. / Gilliland, G.L. / Wang, L. / Li, Y. / Yan, H. / Ji, X. #1: Journal: J.Mol.Biol. / Year: 1995 Title: Crystal Structure of Cellular Retinoic Acid Binding Protein I Shows Increased Access to the Binding Cavity due to Formation of an Intermolecular Beta-Sheet Authors: Thompson, J.R. / Bratt, J.M. / Banaszak, L.J. #2: Journal: Structure / Year: 1994 Title: Crystal Structures of Cellular Retinoic Acid Binding Proteins I and II in Complex with All-Trans-Retinoic Acid and a Synthetic Retinoid Authors: Kleywegt, G.J. / Bergfors, T. / Senn, H. / Le Motte, P. / Gsell, B. / Shudo, K. / Jones, T.A. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1xca.cif.gz | 72.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1xca.ent.gz | 54.1 KB | Display | PDB format |
PDBx/mmJSON format | 1xca.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/xc/1xca ftp://data.pdbj.org/pub/pdb/validation_reports/xc/1xca | HTTPS FTP |
---|
-Related structure data
Related structure data | 1cbsS S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 15555.804 Da / Num. of mol.: 2 / Mutation: R111M Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: BL21 / Cellular location: CYTOPLASM / Plasmid: BL21 / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) PLYSS / References: UniProt: P29373 #2: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.35 Å3/Da / Density % sol: 48.6 % | ||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | pH: 8 Details: PROTEIN CONC, 30MG/ML BUFFER 0.1M TRIS, PH 8.0 SALT 0.2M SODIUM ACETATE PRECIPITANT 30% PEG 8000 | ||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Apr 15, 1995 / Details: COLLIMATOR |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→20 Å / Num. obs: 13213 / % possible obs: 81.9 % / Observed criterion σ(I): 0 / Redundancy: 2.75 % / Biso Wilson estimate: 57.5 Å2 / Rmerge(I) obs: 0.08 / Rsym value: 0.059 / Net I/σ(I): 10.4 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 1.64 % / Mean I/σ(I) obs: 1.5 / Rsym value: 0.279 / % possible all: 55.9 |
Reflection | *PLUS Num. measured all: 32588 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1CBS WITH LIGAND AND SOLVENT MOLECULES REMOVED Resolution: 2.3→8 Å / Rfactor Rfree error: 0.0086 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: UNRESTRAINED / Cross valid method: THROUGHOUT UNTIL LAST FEW CYCLES / σ(F): 2 Details: RESIDUES 24 - 37 OF CHAIN A WERE NOT OBSERVED AND NOT INCLUDED IN THE REFINEMENT; RESTRAINTS BETWEEN THE TWO COPIES OF MOLECULES WERE APPLIED DURING THE INITIAL STAGE OF THE REFINEMENT THE ...Details: RESIDUES 24 - 37 OF CHAIN A WERE NOT OBSERVED AND NOT INCLUDED IN THE REFINEMENT; RESTRAINTS BETWEEN THE TWO COPIES OF MOLECULES WERE APPLIED DURING THE INITIAL STAGE OF THE REFINEMENT THE DISORDERED REGION (RESIDUES 24 - 37 OF CHAIN A) WAS MODELED STEREOCHEMICALLY.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.6 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→8 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.4 Å / Rfactor Rfree error: 0.039 / Total num. of bins used: 8
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.18 / Rfactor Rwork: 0.18 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|