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Yorodumi- PDB-4x8l: Crystal structure of E. coli Adenylate kinase P177A mutant in com... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4x8l | ||||||
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Title | Crystal structure of E. coli Adenylate kinase P177A mutant in complex with inhibitor Ap5a | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / Adenylate Kinase / P177A / Ap5a / Protein Dynamics | ||||||
Function / homology | Function and homology information purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / CDP biosynthetic process / nucleoside diphosphate metabolic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage ...purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / CDP biosynthetic process / nucleoside diphosphate metabolic process / (d)CMP kinase activity / UMP kinase activity / adenylate kinase / adenylate kinase activity / AMP salvage / UDP biosynthetic process / nucleoside diphosphate kinase activity / AMP binding / phosphorylation / magnesium ion binding / ATP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli K-12 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å | ||||||
Authors | Sauer-Eriksson, A.E. / Kovermann, M. / Aden, J. / Grundstrom, C. / Wolf-Watz, M. / Sauer, U.H. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Nat Commun / Year: 2015 Title: Structural basis for catalytically restrictive dynamics of a high-energy enzyme state. Authors: Kovermann, M. / Aden, J. / Grundstrom, C. / Elisabeth Sauer-Eriksson, A. / 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 | 4x8l.cif.gz | 196.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4x8l.ent.gz | 158.6 KB | Display | PDB format |
PDBx/mmJSON format | 4x8l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4x8l_validation.pdf.gz | 1005.2 KB | Display | wwPDB validaton report |
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Full document | 4x8l_full_validation.pdf.gz | 1014.3 KB | Display | |
Data in XML | 4x8l_validation.xml.gz | 27.8 KB | Display | |
Data in CIF | 4x8l_validation.cif.gz | 43.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/x8/4x8l ftp://data.pdbj.org/pub/pdb/validation_reports/x8/4x8l | HTTPS FTP |
-Related structure data
Related structure data | 4x8hC 4x8mC 4x8oC 1akeS 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 23593.992 Da / Num. of mol.: 2 / Mutation: P177A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: adk, dnaW, plsA, b0474, JW0463 / Production host: Escherichia coli (E. coli) / References: UniProt: P69441, adenylate kinase #2: Chemical | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51.21 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 30% PEG 4K, 0.2 M AmAc, 0.1 M Tris-HCl, Ap5a in five time stoichiometric excess |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR-H / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Apr 22, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→27.25 Å / Num. obs: 52935 / % possible obs: 99.4 % / Redundancy: 7.1 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 19.5 |
Reflection shell | Resolution: 1.7→1.74 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.267 / Mean I/σ(I) obs: 5 / % possible all: 96.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ake Resolution: 1.7→27 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / Phase error: 22.73 / 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: 1.7→27 Å
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Refine LS restraints |
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LS refinement shell |
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