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Yorodumi- PDB-8q2b: E. coli Adenylate Kinase variant D158A (AK D158A) showing signifi... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8q2b | ||||||
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Title | E. coli Adenylate Kinase variant D158A (AK D158A) showing significant changes to the stacking of catalytic arginine side chains | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / PHOSPHOTRANSFERASE / ADENYLATE KINASE / D158A VARIANT / AP5A LIGAND / PROTEIN DYNAMICS | ||||||
Function / homology | Function and homology information CDP biosynthetic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 Å | ||||||
Authors | Sauer, U.H. / Wolf-Watz, M. / Nam, K. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: J.Chem.Inf.Model. / Year: 2024 Title: Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. Authors: Nam, K. / Arattu Thodika, A.R. / Grundstrom, C. / Sauer, U.H. / Wolf-Watz, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8q2b.cif.gz | 183.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8q2b.ent.gz | 146.8 KB | Display | PDB format |
PDBx/mmJSON format | 8q2b.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8q2b_validation.pdf.gz | 986.3 KB | Display | wwPDB validaton report |
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Full document | 8q2b_full_validation.pdf.gz | 988.6 KB | Display | |
Data in XML | 8q2b_validation.xml.gz | 22.8 KB | Display | |
Data in CIF | 8q2b_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q2/8q2b ftp://data.pdbj.org/pub/pdb/validation_reports/q2/8q2b | HTTPS FTP |
-Related structure data
Related structure data | |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Experimental dataset #1 | Data reference: 10.1016/s0969-2126(96)00018-4 / Data set type: other data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23576.020 Da / Num. of mol.: 2 / Mutation: D158A Source method: isolated from a genetically manipulated source Details: AK D158A variant / Source: (gene. exp.) Escherichia coli (E. coli) / Gene: adk / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C3TLA2 #2: Chemical | #3: Chemical | ChemComp-SO4 / | #4: Chemical | ChemComp-MPO / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.84 Å3/Da / Density % sol: 56.62 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: Crystallization: 2 ul of purified AK-D158A at 16.4 mg/ml, mixed with the non-hydrolysable inhibitor Ap5A at a final concentration of 5 mM and 2 ul of precipitant buffer containing 32% PEG ...Details: Crystallization: 2 ul of purified AK-D158A at 16.4 mg/ml, mixed with the non-hydrolysable inhibitor Ap5A at a final concentration of 5 mM and 2 ul of precipitant buffer containing 32% PEG 8K, 0.2 M AmSO4, 0.1 M Cacodylate at pH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.87293 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: May 2, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.87293 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→47.45 Å / Num. obs: 52176 / % possible obs: 100 % / Redundancy: 6.9 % / Biso Wilson estimate: 22.1 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.109 / Rpim(I) all: 0.045 / Rrim(I) all: 0.118 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 1.76→1.82 Å / Redundancy: 7.1 % / Rmerge(I) obs: 1.097 / Mean I/σ(I) obs: 1.82 / Num. unique obs: 5114 / CC1/2: 0.627 / Rpim(I) all: 0.44 / Rrim(I) all: 1.183 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.76→40.08 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 22.02 / Stereochemistry target values: ML Details: Iterative rounds of AK-D158A structure refinement against data extending to 0.176 nm using phenix.refine (Afonine, 2010; Afonine, 2012) of the Phenix program package (version 1.19.2-4158-000) ...Details: Iterative rounds of AK-D158A structure refinement against data extending to 0.176 nm using phenix.refine (Afonine, 2010; Afonine, 2012) of the Phenix program package (version 1.19.2-4158-000) and manual model building with Coot (version 0.9.8.1-EL (Emsley, 2010)) were carried out until the R-free factor and R-factor converged.
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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: 1.76→40.08 Å
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Refine LS restraints |
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LS refinement shell |
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