[English] 日本語
Yorodumi- PDB-1ekj: THE X-RAY CRYSTALLOGRAPHIC STRUCTURE OF BETA CARBONIC ANHYDRASE F... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ekj | ||||||
---|---|---|---|---|---|---|---|
Title | THE X-RAY CRYSTALLOGRAPHIC STRUCTURE OF BETA CARBONIC ANHYDRASE FROM THE C3 DICOT PISUM SATIVUM | ||||||
Components | BETA-CARBONIC ANHYDRASE | ||||||
Keywords | LYASE / ROSSMAN FOLD DOMAIN / STRAND EXCHANGE | ||||||
Function / homology | Function and homology information carbon utilization / chloroplast stroma / carbonic anhydrase / carbonate dehydratase activity / zinc ion binding Similarity search - Function | ||||||
Biological species | Pisum sativum (garden pea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.93 Å | ||||||
Authors | Kimber, M.S. / Pai, E.F. | ||||||
Citation | Journal: EMBO J. / Year: 2000 Title: The active site architecture of Pisum sativum beta-carbonic anhydrase is a mirror image of that of alpha-carbonic anhydrases. Authors: Kimber, M.S. / Pai, E.F. #1: Journal: To be Published Title: Beta-Carbonic Anhydrase from Pisum Sativum: Crystallisation and Preliminary X-Ray Analysis Authors: Kimber, M.S. / Coleman, J.R. / Pai, E.F. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1ekj.cif.gz | 349.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1ekj.ent.gz | 285.2 KB | Display | PDB format |
PDBx/mmJSON format | 1ekj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ekj_validation.pdf.gz | 469.9 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1ekj_full_validation.pdf.gz | 499.8 KB | Display | |
Data in XML | 1ekj_validation.xml.gz | 37.7 KB | Display | |
Data in CIF | 1ekj_validation.cif.gz | 60.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/1ekj ftp://data.pdbj.org/pub/pdb/validation_reports/ek/1ekj | HTTPS FTP |
-Related structure data
Similar structure data |
---|
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 8 molecules ABCDEFGH
#1: Protein | Mass: 23967.291 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Pisum sativum (garden pea) / Cellular location: NUCLEAR ENCODED / Organ: LEAF / References: UniProt: P17067, carbonic anhydrase |
---|
-Non-polymers , 8 types, 849 molecules
#2: Chemical | ChemComp-ACT / #3: Chemical | ChemComp-AZI / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-EDO / #7: Chemical | ChemComp-CU / #8: Chemical | ChemComp-CIT / | #9: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.58 Å3/Da / Density % sol: 52.41 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.2 Details: 16% PEG 4000, 0.05 M DITHIOTHREITOL, 0.4 M AMMONIUM ACETATE, 0.1 M SODIUM CITRATE, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K | |||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Type: APS / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 1, 1999 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.93→40 Å / Num. obs: 138484 / % possible obs: 93.2 % / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 13 |
Reflection shell | Highest resolution: 1.93 Å / Rmerge(I) obs: 0.277 / % possible all: 78.5 |
Reflection | *PLUS Num. measured all: 779081 |
Reflection shell | *PLUS % possible obs: 78.5 % |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.93→40 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER Details: TORSION ANGLE ANNEALING REFINEMENT TO MAXIMIMUM LIKELIHOOD TARGETS, FOLLOWED BY INDIVIDUAL TEMPERATURE FACTOR REFINEMENT
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Solvent model: FLAT MODEL / Bsol: 60.75 Å2 / ksol: 0.34 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 45.3 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 1.93→2.05 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: CNS / Version: 0.5 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|