+Open data
-Basic information
Entry | Database: PDB / ID: 3hfw | ||||||
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Title | Crystal Structure of human ADP-ribosylhydrolase 1 (hARH1) | ||||||
Components | Protein ADP-ribosylarginine hydrolase | ||||||
Keywords | HYDROLASE / all alpha-helical / Magnesium | ||||||
Function / homology | Function and homology information [protein ADP-ribosylarginine] hydrolase / ADP-ribosylarginine hydrolase activity / protein de-ADP-ribosylation / potassium ion binding / protein modification process / magnesium ion binding / extracellular space Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.92 Å | ||||||
Authors | Mueller-Dieckmann, C. / Weiss, M.S. / Mueller-Dieckmann, J. / Koch-Nolte, F. | ||||||
Citation | Journal: To be Published Title: Crystal Structure of human ADP-ribosylhydrolase 1 Authors: Koch-Nolte, F. / Mueller-Dieckmann, J. / Weiss, M.S. / Mueller-Dieckmann, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hfw.cif.gz | 85.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hfw.ent.gz | 63.5 KB | Display | PDB format |
PDBx/mmJSON format | 3hfw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hf/3hfw ftp://data.pdbj.org/pub/pdb/validation_reports/hf/3hfw | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 39553.566 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) References: UniProt: P54922, [protein ADP-ribosylarginine] hydrolase |
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-Non-polymers , 5 types, 134 molecules
#2: Chemical | ChemComp-ADP / |
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#3: Chemical | ChemComp-K / |
#4: Chemical | ChemComp-CL / |
#5: Chemical | ChemComp-MG / |
#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 3 |
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-Sample preparation
Crystal | Density Matthews: 2.12 Å3/Da / Density % sol: 41.99 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 150 mM Li-acetate, 25% PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.8505 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jan 1, 2008 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.8505 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→50 Å / Num. obs: 26290 / % possible obs: 95.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 29.9 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.153 / Net I/σ(I): 29.7 |
Reflection shell | Resolution: 1.92→1.97 Å / Redundancy: 9.9 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 3 / Num. unique all: 0 / % possible all: 71.1 |
-Processing
Software | Name: REFMAC / Version: 5.5.0070 / Classification: refinement | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: SAD / Resolution: 1.92→30 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.951 / SU B: 6.007 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.141 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 10.114 Å2
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Refinement step | Cycle: LAST / Resolution: 1.92→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.92→1.971 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 27.9549 Å / Origin y: 12.5936 Å / Origin z: 16.7918 Å
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