+Open data
-Basic information
Entry | Database: PDB / ID: 1kbp | ||||||
---|---|---|---|---|---|---|---|
Title | KIDNEY BEAN PURPLE ACID PHOSPHATASE | ||||||
Components | PURPLE ACID PHOSPHATASE | ||||||
Keywords | HYDROLASE (PHOSPHORIC MONOESTER) / PURPLE ACID PHOSPHATASE | ||||||
Function / homology | Function and homology information acid phosphatase / acid phosphatase activity / ferric iron binding / zinc ion binding / extracellular region Similarity search - Function | ||||||
Biological species | Phaseolus vulgaris (French bean) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.65 Å | ||||||
Authors | Klabunde, T. / Strater, N. / Krebs, B. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 1996 Title: Mechanism of Fe(III)-Zn(II) purple acid phosphatase based on crystal structures. Authors: Klabunde, T. / Strater, N. / Frohlich, R. / Witzel, H. / Krebs, B. #1: Journal: Science / Year: 1995 Title: Crystal Structure of a Purple Acid Phosphatase Containing a Dinuclear Fe(III)-Zn(II) Active Site Authors: Strater, N. / Klabunde, T. / Tucker, P. / Witzel, H. / Krebs, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1kbp.cif.gz | 347.4 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1kbp.ent.gz | 291.6 KB | Display | PDB format |
PDBx/mmJSON format | 1kbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/1kbp ftp://data.pdbj.org/pub/pdb/validation_reports/kb/1kbp | HTTPS FTP |
---|
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||||||||||
2 |
| ||||||||||||||||
Unit cell |
| ||||||||||||||||
Noncrystallographic symmetry (NCS) | NCS oper:
|
-Components
#1: Protein | Mass: 50304.262 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (French bean) / References: UniProt: P80366, acid phosphatase #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-ZN / #5: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 64 % | |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal | *PLUS | |||||||||||||||||||||||||
Crystal grow | *PLUS pH: 5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 298 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.95 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Num. obs: 79375 / % possible obs: 93.7 % / Observed criterion σ(I): 0 / Redundancy: 3.9 % / Rmerge(I) obs: 0.066 |
Reflection | *PLUS Highest resolution: 2.65 Å / % possible obs: 93 % / Num. measured all: 312508 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Resolution: 2.65→10 Å / σ(F): 3
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 38.5 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.3 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.65→10 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Xplor file |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.196 / Rfactor Rfree: 0.223 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|