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Yorodumi- PDB-8crv: Crystal Structure of the Carbamate Kinase from Pseudomonas aeruginosa -
+Open data
-Basic information
Entry | Database: PDB / ID: 8crv | ||||||
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Title | Crystal Structure of the Carbamate Kinase from Pseudomonas aeruginosa | ||||||
Components | Carbamate kinase | ||||||
Keywords | TRANSFERASE / Carbamate Kinase / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID | ||||||
Function / homology | Function and homology information : / carbamate kinase / carbamate kinase activity / arginine deiminase pathway / phosphorylation / ATP binding / cytosol Similarity search - Function | ||||||
Biological species | Pseudomonas aeruginosa PAO1 (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Kim, Y. / Skarina, T. / Mesa, N. / Stogios, P. / Savchenko, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
Funding support | United States, 1items
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Citation | Journal: To Be Published Title: Crystal Structure of the Carbamate Kinase from Pseudomonas aeruginosa Authors: Kim, Y. / Skarina, T. / Mesa, N. / Stogios, P. / Savchenko, S. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID) | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8crv.cif.gz | 167.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8crv.ent.gz | 108.5 KB | Display | PDB format |
PDBx/mmJSON format | 8crv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8crv_validation.pdf.gz | 464.3 KB | Display | wwPDB validaton report |
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Full document | 8crv_full_validation.pdf.gz | 465.4 KB | Display | |
Data in XML | 8crv_validation.xml.gz | 16 KB | Display | |
Data in CIF | 8crv_validation.cif.gz | 23.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/8crv ftp://data.pdbj.org/pub/pdb/validation_reports/cr/8crv | HTTPS FTP |
-Related structure data
Similar structure data | Similarity search - Function & homologyF&H Search |
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-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
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 33419.277 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas aeruginosa PAO1 (bacteria) Strain: ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1 Gene: arcC, PA5173 / Plasmid: pMCSG53 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P13982, carbamate kinase |
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-Non-polymers , 5 types, 279 molecules
#2: Chemical | ChemComp-EDO / | ||
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#3: Chemical | ChemComp-FMT / | ||
#4: Chemical | ChemComp-OO9 / | ||
#5: Chemical | ChemComp-SO4 / #6: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | N |
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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: 3 Å3/Da / Density % sol: 58.94 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 2.0 M ammonium sulfate, 0.1 M Hepes pH 7.5, 2 %(v/v) PEG400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Oct 15, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→46.82 Å / Num. obs: 55145 / % possible obs: 99.9 % / Redundancy: 19.1 % / Biso Wilson estimate: 24.55 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.097 / Rpim(I) all: 0.022 / Rrim(I) all: 0.1 / Net I/σ(I): 18.8 |
Reflection shell | Resolution: 1.6→1.63 Å / Redundancy: 8.1 % / Rmerge(I) obs: 1.469 / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2654 / CC1/2: 0.623 / Rpim(I) all: 0.533 / Rrim(I) all: 1.566 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: swiss pro Resolution: 1.6→39.99 Å / SU ML: 0.174 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 19.3603 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.14 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.6→39.99 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A
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