+Open data
-Basic information
Entry | Database: PDB / ID: 2zp2 | ||||||
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Title | C-terminal domain of KipI from Bacillus subtilis | ||||||
Components | Kinase A inhibitor | ||||||
Keywords | TRANSFERASE INHIBITOR / kipI / histidine kinase inhibitor / ATP-binding / Nucleotide-binding / Protein kinase inhibitor / Sporulation | ||||||
Function / homology | Function and homology information 5-oxoprolinase (ATP-hydrolysing) / 5-oxoprolinase (ATP-hydrolyzing) activity / sporulation resulting in formation of a cellular spore / protein kinase inhibitor activity / ATP binding Similarity search - Function | ||||||
Biological species | Bacillus subtilis (bacteria) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.01 Å | ||||||
Authors | Langley, D.B. / Jacques, D.A. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Histidine kinase regulation by a cyclophilin-like inhibitor Authors: Jacques, D.A. / Langley, D.B. / Jeffries, C.M. / Cunningham, K.A. / Burkholder, W.F. / Guss, J.M. / Trewhella, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2zp2.cif.gz | 55 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2zp2.ent.gz | 38.4 KB | Display | PDB format |
PDBx/mmJSON format | 2zp2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2zp2_validation.pdf.gz | 429.8 KB | Display | wwPDB validaton report |
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Full document | 2zp2_full_validation.pdf.gz | 434.8 KB | Display | |
Data in XML | 2zp2_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 2zp2_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zp/2zp2 ftp://data.pdbj.org/pub/pdb/validation_reports/zp/2zp2 | HTTPS FTP |
-Related structure data
Related structure data | 2phcS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15341.532 Da / Num. of mol.: 2 / Fragment: C-terminal domain, UNP residues 100-240 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus subtilis (bacteria) / Strain: 168 / Gene: kipI / Plasmid: pET (novagen) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P60495 |
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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: 2.61 Å3/Da / Density % sol: 52.82 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 15% PEG 8000, 20% glycerol, 40mM potassium phosphate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: May 15, 2008 / Details: Osmic mirror optics |
Radiation | Monochromator: Ni filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3→17 Å / Num. all: 6751 / Num. obs: 6738 / % possible obs: 99.8 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 6 % / Biso Wilson estimate: 78 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 6.7 |
Reflection shell | Resolution: 3→3.11 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 1.5 / Num. unique all: 629 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 2PHC Resolution: 3.01→16.88 Å / Cor.coef. Fo:Fc: 0.872 / Cor.coef. Fo:Fc free: 0.788 / SU B: 21.564 / SU ML: 0.415 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.533 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS but are not displayed in the PDB
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 37.673 Å2
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Refinement step | Cycle: LAST / Resolution: 3.01→16.88 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.007→3.082 Å / Total num. of bins used: 20
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