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Yorodumi- PDB-6hwr: Red kidney bean purple acid phosphatase in complex with adenosine... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hwr | ||||||||||||
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Title | Red kidney bean purple acid phosphatase in complex with adenosine divanadate | ||||||||||||
Components | (Fe(3+)-Zn(2+) purple acid ...) x 2 | ||||||||||||
Keywords | METAL BINDING PROTEIN / Purple acid phosphatase / metallohydrolases / transition state / catalysis / osteoporosis | ||||||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||||||||
Authors | Feder, D. / Gahan, L.R. / McGeary, R.P. / Guddat, L.W. / Schenk, G. | ||||||||||||
Funding support | Australia, 1items
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Citation | Journal: Chembiochem / Year: 2019 Title: The Binding Mode of an ADP Analogue to a Metallohydrolase Mimics the Likely Transition State. Authors: Feder, D. / Gahan, L.R. / McGeary, R.P. / Guddat, L.W. / Schenk, G. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hwr.cif.gz | 433.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hwr.ent.gz | 344.5 KB | Display | PDB format |
PDBx/mmJSON format | 6hwr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6hwr_validation.pdf.gz | 2.4 MB | Display | wwPDB validaton report |
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Full document | 6hwr_full_validation.pdf.gz | 2.4 MB | Display | |
Data in XML | 6hwr_validation.xml.gz | 87 KB | Display | |
Data in CIF | 6hwr_validation.cif.gz | 134.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/6hwr ftp://data.pdbj.org/pub/pdb/validation_reports/hw/6hwr | HTTPS FTP |
-Related structure data
Related structure data | 4dhlS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Fe(3+)-Zn(2+) purple acid ... , 2 types, 4 molecules CBAD
#1: Protein | Mass: 49555.398 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (French bean) / References: UniProt: P80366, acid phosphatase #2: Protein | | Mass: 49556.383 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Phaseolus vulgaris (French bean) / References: UniProt: P80366, acid phosphatase |
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-Sugars , 3 types, 12 molecules
#3: Polysaccharide | #4: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | #11: Sugar | ChemComp-NAG / |
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-Non-polymers , 14 types, 2307 molecules
#5: Chemical | ChemComp-ZN / #6: Chemical | ChemComp-FE / #7: Chemical | ChemComp-SO4 / #8: Chemical | ChemComp-GOL / #9: Chemical | ChemComp-EDO / #10: Chemical | #12: Chemical | ChemComp-NA / #13: Chemical | ChemComp-H1T / [[[[ | #14: Chemical | ChemComp-VV6 / [[[[ | #15: Chemical | ChemComp-H1Q / | #16: Chemical | ChemComp-H1W / | #17: Chemical | ChemComp-IPA / | #18: Chemical | ChemComp-VN3 / | #19: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.45 Å3/Da / Density % sol: 64.35 % / Description: Hexagonal |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5 Details: 2.3 M ammonium sulfate, 0.1 M sodium acetate, pH 4.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9 Å |
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Dec 18, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→19.97 Å / Num. obs: 199405 / % possible obs: 99.9 % / Redundancy: 10.4 % / Biso Wilson estimate: 19.55 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.214 / Rpim(I) all: 0.07 / Rrim(I) all: 0.226 / Net I/σ(I): 10.6 |
Reflection shell | Resolution: 1.95→2.06 Å / Redundancy: 9 % / Rmerge(I) obs: 1.193 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 28831 / CC1/2: 0.585 / Rpim(I) all: 0.419 / Rrim(I) all: 1.265 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4DHL Resolution: 1.95→19.966 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 18.12 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→19.966 Å
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Refine LS restraints |
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LS refinement shell |
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