+Open data
-Basic information
Entry | Database: PDB / ID: 7fj7 | |||||||||
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Title | KpAckA (PduW) native structure | |||||||||
Components | Probable propionate kinase | |||||||||
Keywords | TRANSFERASE / Acetate utilization pathway / Acetate kinase / Klebsiella pneumoniae | |||||||||
Function / homology | Function and homology information propionate kinase / propanediol catabolic process / propionate kinase activity / acetate kinase activity / acetate metabolic process / propionate catabolic process / ATP binding / cytoplasm Similarity search - Function | |||||||||
Biological species | Klebsiella pneumoniae (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å | |||||||||
Authors | Wu, W. / Zhang, Q. / Bartlam, M. | |||||||||
Funding support | 2items
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Citation | Journal: To Be Published Title: KpAckA (PduW) native structure Authors: Wu, W. / Zhang, Q. / Bartlam, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7fj7.cif.gz | 360.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7fj7.ent.gz | 246.3 KB | Display | PDB format |
PDBx/mmJSON format | 7fj7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7fj7_validation.pdf.gz | 433.2 KB | Display | wwPDB validaton report |
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Full document | 7fj7_full_validation.pdf.gz | 439.7 KB | Display | |
Data in XML | 7fj7_validation.xml.gz | 27 KB | Display | |
Data in CIF | 7fj7_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fj/7fj7 ftp://data.pdbj.org/pub/pdb/validation_reports/fj/7fj7 | HTTPS FTP |
-Related structure data
Related structure data | 2iirS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 43666.004 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Klebsiella pneumoniae (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A0H3GUQ7, propionate kinase #2: 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: 3.27 Å3/Da / Density % sol: 62.44 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 6.5 Details: 0.1 M BIS-TRIS, 45% v/v Polypropylene glycol P 400, pH 6.5. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL18U1 / Wavelength: 0.97915 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 23, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→50 Å / Num. obs: 38499 / % possible obs: 98.8 % / Redundancy: 6.8 % / Biso Wilson estimate: 34.27 Å2 / Rpim(I) all: 0.032 / Net I/σ(I): 21.45 |
Reflection shell | Resolution: 2.5→2.54 Å / Redundancy: 6.1 % / Mean I/σ(I) obs: 3.5 / Num. unique obs: 1895 / Rpim(I) all: 0.211 / % possible all: 97.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2IIR Resolution: 2.5→45.38 Å / SU ML: 0.296 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 24.1712 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 44.88 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.5→45.38 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Origin x: 29.374470653 Å / Origin y: 29.5826258628 Å / Origin z: 22.0284106591 Å
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Refinement TLS group | Selection details: all |