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Yorodumi- PDB-3l5k: The crystal structure of human Haloacid Dehalogenase-like Hydrola... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3l5k | ||||||
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Title | The crystal structure of human Haloacid Dehalogenase-like Hydrolase Domain containing 1A (HDHD1A) | ||||||
Components | Haloacid dehalogenase-like hydrolase domain-containing protein 1A | ||||||
Keywords | HYDROLASE / HDHD1A / Haloacid Dehalogenase-like Hydrolase Domain containing 1A / Structural Genomics / Structural Genomics Consortium / SGC / Polymorphism | ||||||
Function / homology | Function and homology information pseudouridine 5'-phosphatase / pseudouridine 5'-phosphatase activity / pyrimidine nucleoside salvage / Pyrimidine salvage / nucleotide metabolic process / phosphatase activity / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||
Authors | Ugochukwu, E. / Guo, K. / Picaud, S. / Muniz, J. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. ...Ugochukwu, E. / Guo, K. / Picaud, S. / Muniz, J. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Yue, W.W. / Kavanagh, K.L. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
Citation | Journal: To be Published Title: The crystal structure of human Haloacid Dehalogenase-like Hydrolase Domain containing 1A (HDHD1A) Authors: Ugochukwu, E. / Guo, K. / Picaud, S. / Muniz, J. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Yue, W.W. / Kavanagh, K.L. / Oppermann, U. / ...Authors: Ugochukwu, E. / Guo, K. / Picaud, S. / Muniz, J. / Allerston, C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. / Edwards, A. / Yue, W.W. / Kavanagh, K.L. / Oppermann, U. / Structural Genomics Consortium (SGC) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3l5k.cif.gz | 67.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l5k.ent.gz | 47.9 KB | Display | PDB format |
PDBx/mmJSON format | 3l5k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3l5k_validation.pdf.gz | 435.7 KB | Display | wwPDB validaton report |
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Full document | 3l5k_full_validation.pdf.gz | 436 KB | Display | |
Data in XML | 3l5k_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 3l5k_validation.cif.gz | 19.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l5/3l5k ftp://data.pdbj.org/pub/pdb/validation_reports/l5/3l5k | HTTPS FTP |
-Related structure data
Related structure data | 2pib 2w4mS 3hltS 3k1zS 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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Unit cell |
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-Components
#1: Protein | Mass: 27936.121 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: HDHD1A / Plasmid: pNIC28-Bsa4 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3 / References: UniProt: Q08623 | ||
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#2: Chemical | ChemComp-K / | ||
#3: Chemical | ChemComp-GOL / | ||
#4: Chemical | ChemComp-CL / #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.86 Å3/Da / Density % sol: 68.16 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M Sodium dihydrogen phosphate, 1.344 M di-potassium hydrogen phosphate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 14, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2→42.59 Å / Num. obs: 29508 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Rmerge(I) obs: 0.107 / Rsym value: 0.107 / Net I/σ(I): 9.4 |
Reflection shell | Resolution: 2→2.11 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.855 / Mean I/σ(I) obs: 2 / Num. unique all: 17548 / Rsym value: 0.855 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2PIB, 3HLT, 3K1Z, 2W4M Resolution: 2→42.6 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.94 / SU B: 6.824 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.109 / ESU R Free: 0.118 / 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: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 15.171 Å2
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Refinement step | Cycle: LAST / Resolution: 2→42.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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