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Yorodumi- PDB-5d57: In meso X-ray crystallography structure of diacylglycerol kinase,... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d57 | ||||||
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Title | In meso X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K | ||||||
Components | Diacylglycerol kinase | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information diacylglycerol kinase (ATP) / ATP-dependent diacylglycerol kinase activity / phosphatidic acid biosynthetic process / response to UV / ATP binding / identical protein binding / membrane / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Huang, C.-Y. / Howe, N. / Olieric, V. / Wang, M. / Caffrey, M. | ||||||
Funding support | Ireland, 1items
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Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: In meso in situ serial X-ray crystallography of soluble and membrane proteins at cryogenic temperatures. Authors: Huang, C.Y. / Olieric, V. / Ma, P. / Howe, N. / Vogeley, L. / Liu, X. / Warshamanage, R. / Weinert, T. / Panepucci, E. / Kobilka, B. / Diederichs, K. / Wang, M. / Caffrey, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5d57.cif.gz | 132.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d57.ent.gz | 106 KB | Display | PDB format |
PDBx/mmJSON format | 5d57.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5d57_validation.pdf.gz | 2.5 MB | Display | wwPDB validaton report |
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Full document | 5d57_full_validation.pdf.gz | 2.5 MB | Display | |
Data in XML | 5d57_validation.xml.gz | 26.6 KB | Display | |
Data in CIF | 5d57_validation.cif.gz | 34.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/5d57 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/5d57 | HTTPS FTP |
-Related structure data
Related structure data | 5d52C 5d53C 5d54C 5d56C 5d58C 5d59C 5d5aC 5d5bC 5d5cC 5d5dC 5d5eC 5d5fC 3ze3S S: Starting model for refinement C: citing same article (ref.) |
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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
#1: Protein | Mass: 14204.451 Da / Num. of mol.: 6 / Mutation: A41C, C46A, I53V, I70L, M96L, V107D and C113A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: dgkA, b4042, JW4002 / Production host: Escherichia coli (E. coli) / References: UniProt: P0ABN1, diacylglycerol kinase (ATP) #2: Chemical | ChemComp-78M / ( #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.89 Å3/Da / Density % sol: 57.49 % |
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Crystal grow | Temperature: 277 K / Method: lipidic cubic phase Details: 3-6 %(v/v) MPD, 0.1 M NaCl, 60 mM Mg(CH3COO)2 and 50 mM Na3C6H5O7, pH 5.6 PH range: 5.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Feb 18, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.8→50 Å / Num. obs: 24904 / % possible obs: 99.6 % / Redundancy: 6.23 % / Net I/σ(I): 7.71 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 5.63 % / Mean I/σ(I) obs: 1.61 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ze3 Resolution: 2.8→45.67 Å / SU ML: 0.45 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 28.57 / 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: 2.8→45.67 Å
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Refine LS restraints |
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LS refinement shell |
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