+Open data
-Basic information
Entry | Database: PDB / ID: 3kbp | ||||||
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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: 3 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kbp.cif.gz | 347.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kbp.ent.gz | 291.4 KB | Display | PDB format |
PDBx/mmJSON format | 3kbp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/3kbp ftp://data.pdbj.org/pub/pdb/validation_reports/kb/3kbp | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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3 |
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4 |
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5 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
#1: Protein | Mass: 50304.262 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: 111KDA DIMER, COMPLEX WITH TUNGSTATE / Source: (natural) Phaseolus vulgaris (French bean) / References: UniProt: P80366, acid phosphatase #2: Sugar | ChemComp-NAG / #3: Chemical | ChemComp-FE / #4: Chemical | ChemComp-ZN / #5: Chemical | ChemComp-WO4 / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 3.68 Å3/Da / Density % sol: 64 % | |||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 4 ℃ / pH: 5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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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 | Resolution: 3→35 Å / Num. obs: 50898 / % possible obs: 85.3 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.08 |
Reflection | *PLUS Num. measured all: 153663 |
Reflection shell | *PLUS % possible obs: 79.5 % |
-Processing
Software |
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Refinement | Resolution: 3→10 Å / σ(F): 3
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Displacement parameters | Biso mean: 35.3 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.35 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.188 / Rfactor Rfree: 0.221 / Rfactor Rwork: 0.188 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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