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Yorodumi- PDB-5lcd: Structure of Polyphosphate Kinase from Meiothermus ruber bound to AMP -
+Open data
-Basic information
Entry | Database: PDB / ID: 5lcd | ||||||
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Title | Structure of Polyphosphate Kinase from Meiothermus ruber bound to AMP | ||||||
Components | Polyphosphate:AMP phosphotransferase | ||||||
Keywords | TRANSFERASE / Polyphosphate Kinase | ||||||
Function / homology | Function and homology information phosphotransferase activity, phosphate group as acceptor / polyphosphate metabolic process / kinase activity Similarity search - Function | ||||||
Biological species | Meiothermus ruber H328 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.66 Å | ||||||
Authors | Gerhardt, S. / Einsle, O. / Kemper, F. / Schwarzer, N. | ||||||
Citation | Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2018 Title: Substrate recognition and mechanism revealed by ligand-bound polyphosphate kinase 2 structures. Authors: Parnell, A.E. / Mordhorst, S. / Kemper, F. / Giurrandino, M. / Prince, J.P. / Schwarzer, N.J. / Hofer, A. / Wohlwend, D. / Jessen, H.J. / Gerhardt, S. / Einsle, O. / Oyston, P.C.F. / Andexer, J.N. / Roach, P.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5lcd.cif.gz | 447.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5lcd.ent.gz | 364.9 KB | Display | PDB format |
PDBx/mmJSON format | 5lcd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5lcd_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 5lcd_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 5lcd_validation.xml.gz | 37 KB | Display | |
Data in CIF | 5lcd_validation.cif.gz | 49.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lc/5lcd ftp://data.pdbj.org/pub/pdb/validation_reports/lc/5lcd | HTTPS FTP |
-Related structure data
Related structure data | 5lc9SC 5ld1C 5ldbC 5ll0C 5llbC 5llfC 5maqC 5o6kC 5o6mC 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
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 33778.340 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: the residues Met -19 to His 0 have been introduced by the expression tag of pET28A MET 1 in chains A,B,C and D is the initiating methionine Source: (gene. exp.) Meiothermus ruber H328 (bacteria) / Gene: MrH_2468 / Plasmid: pET28A / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0S7ASE9 |
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-Non-polymers , 5 types, 95 molecules
#2: Chemical | ChemComp-AMP / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-MG / | #6: Water | ChemComp-HOH / | |
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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: 2.62 Å3/Da / Density % sol: 53.08 % / Mosaicity: 0.53 ° |
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Crystal grow | Temperature: 298 K / Method: evaporation / pH: 8.5 / Details: PEG3350, Li2SO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.00001 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Aug 28, 2015 / Details: MIRROR |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.00001 Å / Relative weight: 1 |
Reflection | Resolution: 2.66→116.28 Å / Num. obs: 37790 / % possible obs: 99.6 % / Redundancy: 44 % / Biso Wilson estimate: 54.44 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.322 / Rpim(I) all: 0.049 / Rrim(I) all: 0.329 / Rsym value: 0.33 / Net I/σ(I): 17.3 / Num. measured all: 1661253 / Scaling rejects: 14 |
Reflection shell | Resolution: 2.66→2.68 Å / Redundancy: 31.2 % / Rmerge(I) obs: 2.089 / Mean I/σ(I) obs: 2.4 / % possible all: 99.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5LC9 Resolution: 2.66→116.28 Å / Cor.coef. Fo:Fc: 0.904 / Cor.coef. Fo:Fc free: 0.885 / Rfactor Rfree error: 0 / SU R Cruickshank DPI: 1.089 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 1.069 / SU Rfree Blow DPI: 0.32 / SU Rfree Cruickshank DPI: 0.326
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Displacement parameters | Biso max: 160.66 Å2 / Biso mean: 46.39 Å2 / Biso min: 14.39 Å2
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Refine analyze | Luzzati coordinate error obs: 0.37 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.66→116.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.66→2.73 Å / Total num. of bins used: 19
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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