+Open data
-Basic information
Entry | Database: PDB / ID: 6rze | ||||||
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Title | Crystal structure of E. coli Adenylate kinase R119A mutant | ||||||
Components | Adenylate kinase | ||||||
Keywords | TRANSFERASE / ADENYLATE KINASE / R119A VARIANT | ||||||
Function / homology | Function and homology information purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / phosphorylation ...purine ribonucleotide interconversion / ADP biosynthetic process / nucleoside monophosphate metabolic process / nucleoside diphosphate metabolic process / adenylate kinase / adenylate kinase activity / AMP salvage / nucleoside diphosphate kinase activity / AMP binding / phosphorylation / magnesium ion binding / ATP binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.69 Å | ||||||
Authors | Grundstrom, C. / Rogne, P. / Wolf-Watz, M. / Sauer-Eriksson, A.E. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Biochemistry / Year: 2019 Title: Nucleation of an Activating Conformational Change by a Cation-pi Interaction. Authors: Rogne, P. / Andersson, D. / Grundstrom, C. / Sauer-Eriksson, E. / Linusson, A. / 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 | 6rze.cif.gz | 66.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6rze.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 6rze.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rz/6rze ftp://data.pdbj.org/pub/pdb/validation_reports/rz/6rze | HTTPS FTP |
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-Related structure data
Related structure data | 6s36C 4x8hS 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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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 23533.914 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) Gene: adk, D9E35_07195, D9H53_18240, D9H70_06005, D9I87_03740, EB509_06410, EB510_02065, EB515_08900, EC382_09075, ED225_07155, ED607_06260, ED611_06205, ED903_02730, ED944_09135, EEA45_02410, EF173_ ...Gene: adk, D9E35_07195, D9H53_18240, D9H70_06005, D9I87_03740, EB509_06410, EB510_02065, EB515_08900, EC382_09075, ED225_07155, ED607_06260, ED611_06205, ED903_02730, ED944_09135, EEA45_02410, EF173_11005, EIA21_12240, NCTC10444_03756, NCTC9112_04001, NCTC9119_03910, NCTC9969_03944, SAMEA3472056_03545, SAMEA3485101_03900, SAMEA3485113_01288 Production host: Escherichia coli (E. coli) References: UniProt: A0A234NPI7, UniProt: P69441*PLUS, adenylate kinase | ||||||
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#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | Has ligand of interest | N | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.23 Å3/Da / Density % sol: 44.92 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: PURIFIED ADK IN 50 MM NACL AND 30 MM MES BUFFER, PH 6.0 WAS CONCENTRATED TO 18 MG/ML AND CO- CRYSTALLIZED WITH A 5 MOLAR EXCESS OF AP5A. A TYPICAL DROP CONTAINED 2 MICROL OF PROTEIN MIXED ...Details: PURIFIED ADK IN 50 MM NACL AND 30 MM MES BUFFER, PH 6.0 WAS CONCENTRATED TO 18 MG/ML AND CO- CRYSTALLIZED WITH A 5 MOLAR EXCESS OF AP5A. A TYPICAL DROP CONTAINED 2 MICROL OF PROTEIN MIXED WITH 2 MICROL OF PRECIPITANT AND EQUILIBRATED AGAINST 1 ML RESERVOIR SOLUTION CONTAINING 28-30% PEG 4K, 0.2 M MgCL2 AND 0.1 M Tris-HCl, PH 8.5). |
-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: 0.873 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 11, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→48.221 Å / Num. obs: 22857 / % possible obs: 99.9 % / Redundancy: 4.7 % / CC1/2: 0.994 / Rmerge(I) obs: 0.122 / Rpim(I) all: 0.09 / Net I/σ(I): 7.2 |
Reflection shell | Resolution: 1.7→1.75 Å / Rmerge(I) obs: 0.824 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2087 / CC1/2: 0.598 / Rpim(I) all: 0.568 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4x8h Resolution: 1.69→48.221 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 24.52
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.69→48.221 Å
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Refine LS restraints |
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LS refinement shell |
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