+Open data
-Basic information
Entry | Database: PDB / ID: 1dm5 | ||||||
---|---|---|---|---|---|---|---|
Title | ANNEXIN XII E105K HOMOHEXAMER CRYSTAL STRUCTURE | ||||||
Components | ANNEXIN XII E105K MUTANT HOMOHEXAMER | ||||||
Keywords | UNKNOWN FUNCTION / HOMOHEXAMER / NOVEL PH-DEPENDENT HEXAMERIZATION SWITCH E76 / LOW CALCIUM FORM / MIXED TYPEII/TYPEIII CALCIUM BINDING SITE / E105K EPSILON AMINO GROUP REPLACES INTERMOLECULAR CALCIUM | ||||||
Function / homology | Function and homology information 1-phosphatidylinositol binding / phosphatidylethanolamine binding / calcium-dependent phospholipid binding / phosphatidylserine binding / heparin binding / calcium ion binding / nucleus / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Hydra vulgaris (swiftwater hydra) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.93 Å | ||||||
Authors | Cartailler, J.P. / Haigler, H.T. / Luecke, H. | ||||||
Citation | Journal: Biochemistry / Year: 2000 Title: Annexin XII E105K crystal structure: identification of a pH-dependent switch for mutant hexamerization. Authors: Cartailler, J.P. / Haigler, H.T. / Luecke, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1dm5.cif.gz | 385.3 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1dm5.ent.gz | 314.9 KB | Display | PDB format |
PDBx/mmJSON format | 1dm5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/dm/1dm5 ftp://data.pdbj.org/pub/pdb/validation_reports/dm/1dm5 | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35024.539 Da / Num. of mol.: 6 / Mutation: E105K Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hydra vulgaris (swiftwater hydra) / Production host: Escherichia coli (E. coli) / References: UniProt: P26256 #2: Chemical | ChemComp-CA / #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.13 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2 M AMMONIUM ACETATE 0.1 M SODIUM CITRATE PH 5.6 80 % 2-METHYL-PENTANEDIOL, VAPOR DIFFUSION, HANGING DROP, temperature 4K | |||||||||||||||||||||||||
Crystal grow | *PLUS | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: May 14, 1997 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→25 Å / Num. all: 969367 / Num. obs: 156877 / % possible obs: 93.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.18 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 20.6 |
Reflection shell | Resolution: 1.9→1.93 Å / Rmerge(I) obs: 0.295 / % possible all: 75.6 |
Reflection | *PLUS Lowest resolution: 25 Å / Num. measured all: 969367 |
Reflection shell | *PLUS % possible obs: 93.8 % / Mean I/σ(I) obs: 3.6 |
-Processing
Software |
| |||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 1.93→10 Å / σ(F): 4 / σ(I): 0 / Stereochemistry target values: SHELXL Details: -WATERS WERE ADDED ONCE THE RFREE DROPPED BELOW 30% -NCS RESTRAINTS WERE USED UNTIL CONVERGENCE AT RFREE=32% -NCS RESTRAINTS THEN RELAXED TO ALLOW LOOP INDEPENDENT LOOP MOTIONS IN NCS COPIES ...Details: -WATERS WERE ADDED ONCE THE RFREE DROPPED BELOW 30% -NCS RESTRAINTS WERE USED UNTIL CONVERGENCE AT RFREE=32% -NCS RESTRAINTS THEN RELAXED TO ALLOW LOOP INDEPENDENT LOOP MOTIONS IN NCS COPIES -RANDOM DISPLACEMENT OF ATOMIC POSITIONS AND B-VALUES FROM THEIR CURRENT VALUES (MAIN-"KICKING") WAS USED TO REDUCE MODEL BIAS
| |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.93→10 Å
| |||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||
Software | *PLUS Name: SHELXL-97 / Classification: refinement | |||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 4 / Rfactor obs: 0.208 / Rfactor Rwork: 0.215 | |||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: s_angle_d / Dev ideal: 1.5 |