+Open data
-Basic information
Entry | Database: PDB / ID: 1pb0 | ||||||
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Title | YCDX PROTEIN IN AUTOINHIBITED STATE | ||||||
Components | Hypothetical protein ycdXHypothesis | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta-alpha-barrel / trinuclear zinc / autoinhibition | ||||||
Function / homology | Function and homology information phosphoric ester hydrolase activity / bacterial-type flagellum-dependent swarming motility / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatase activity / zinc ion binding / identical protein binding / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å | ||||||
Authors | Teplyakov, A. / Obmolova, G. / Khil, P.P. / Camerini-Otero, R.D. / Gilliland, G.L. | ||||||
Citation | Journal: To be Published Title: Autoregulation of YcdX protein Authors: Teplyakov, A. / Obmolova, G. / Khil, P.P. / Camerini-Otero, R.D. / Gilliland, G.L. #1: Journal: Proteins / Year: 2003 Title: Crystal structure of the Escherichia coli YcdX protein reveals a trinuclear zinc active site. Authors: Teplyakov, A. / Obmolova, G. / Khil, P.P. / Howard, A.J. / Camerini-Otero, R.D. / Gilliland, G.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pb0.cif.gz | 165.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pb0.ent.gz | 128.9 KB | Display | PDB format |
PDBx/mmJSON format | 1pb0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/1pb0 ftp://data.pdbj.org/pub/pdb/validation_reports/pb/1pb0 | HTTPS FTP |
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-Related structure data
Related structure data | 1m65S S: Starting model for refinement |
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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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Details | The asymmetric unit contains the entire trimer that corresponds to the oligomeric state of the protein in solution |
-Components
#1: Protein | Mass: 26925.529 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Gene: YCDX / Plasmid: pDEST14 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 Star (DE3) / References: UniProt: P75914 #2: Chemical | ChemComp-ZN / #3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-FMT / #5: 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: 2.57 Å3/Da / Density % sol: 52.15 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris, 60% AS, 3% MPD, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-BM / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 15, 2003 / Details: mirror |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.95→30 Å / Num. all: 59787 / Num. obs: 59787 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Biso Wilson estimate: 17.5 Å2 / Rmerge(I) obs: 0.081 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.95→2 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.212 / Mean I/σ(I) obs: 3.3 / Num. unique all: 7470 / % possible all: 98.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1M65 Resolution: 1.95→10 Å / Cor.coef. Fo:Fc: 0.949 / SU B: 1.628 / SU ML: 0.05 / σ(F): 0 / ESU R: 0.135 / Stereochemistry target values: Engh & Huber
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.717 Å2
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Refine analyze | Luzzati coordinate error obs: 0.135 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.95→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.95→2 Å / Total num. of bins used: 20 /
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