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Open data
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Basic information
Entry | Database: PDB / ID: 4zci | ||||||
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Title | Crystal Structure of Escherichia coli GTPase BipA/TypA | ||||||
![]() | GTP-binding protein TypA/BipA | ||||||
![]() | GTP-BINDING PROTEIN / BipA / GTPase / Nucleotide | ||||||
Function / homology | ![]() guanosine tetraphosphate binding / protein folding chaperone / response to cold / ribosomal large subunit assembly / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome biogenesis / ribosome binding / response to heat / tRNA binding / rRNA binding ...guanosine tetraphosphate binding / protein folding chaperone / response to cold / ribosomal large subunit assembly / Hydrolases; Acting on acid anhydrides; Acting on GTP to facilitate cellular and subcellular movement / ribosome biogenesis / ribosome binding / response to heat / tRNA binding / rRNA binding / ribonucleoprotein complex / GTPase activity / GTP binding / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Fan, H.T. / Hahm, J. / Diggs, S. / Blaha, G. | ||||||
![]() | ![]() Title: Structural and Functional Analysis of BipA, a Regulator of Virulence in Enteropathogenic Escherichia coli. Authors: Fan, H. / Hahm, J. / Diggs, S. / Perry, J.J. / Blaha, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 447.9 KB | Display | ![]() |
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PDB format | ![]() | 366.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4zckC ![]() 4zclC ![]() 4zcmC ![]() 3cb4S ![]() 3e3xS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 70307.547 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() Strain: K12 / Gene: typA, bipA, yihK, b3871, JW5571 / Production host: ![]() ![]() #2: Chemical | ChemComp-NCO / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.02 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8 Details: 100 mM Tris-HCl, 2 % PEG 6000, and 5 mM [Co(NH3)6]Cl3, pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 7, 2014 |
Radiation | Monochromator: Double-crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.627→46.004 Å / Num. all: 46793 / Num. obs: 46760 / % possible obs: 99.7 % / Redundancy: 3.7 % / Biso Wilson estimate: 58.9 Å2 / Rmerge(I) obs: 0.106 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 2.63→2.68 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.919 / Mean I/σ(I) obs: 1.4 / % possible all: 96.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3CB4, 3E3X Resolution: 2.627→46.004 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 27.9 / Stereochemistry target values: ML
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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: 78 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.627→46.004 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 |
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