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Yorodumi- PDB-5d56: In meso in situ serial X-ray crystallography structure of diacylg... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5d56 | ||||||
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Title | In meso in situ serial 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 / phosphorylation / ATP binding / membrane / identical protein binding / 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. / Warshamanage, R. / Diederichs, K. / 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 | 5d56.cif.gz | 131.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5d56.ent.gz | 103.4 KB | Display | PDB format |
PDBx/mmJSON format | 5d56.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/d5/5d56 ftp://data.pdbj.org/pub/pdb/validation_reports/d5/5d56 | HTTPS FTP |
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-Related structure data
Related structure data | 5d52C 5d53C 5d54C 5d57C 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
-Protein , 1 types, 6 molecules ABCDEF
#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) |
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-Non-polymers , 5 types, 27 molecules
#2: Chemical | ChemComp-78M / ( #3: Chemical | ChemComp-ZN / | #4: Chemical | ChemComp-FLC / | #5: Chemical | ChemComp-ACT / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.92 Å3/Da / Density % sol: 57.88 % |
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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: 25188 / % possible obs: 98.8 % / Redundancy: 9.3 % / Net I/σ(I): 4.42 |
Reflection shell | Resolution: 2.8→2.87 Å / Redundancy: 8.7 % / Mean I/σ(I) obs: 1 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ze3 Resolution: 2.8→46.52 Å / SU ML: 0.49 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.94 / 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→46.52 Å
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Refine LS restraints |
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LS refinement shell |
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