+Open data
-Basic information
Entry | Database: PDB / ID: 1m68 | ||||||
---|---|---|---|---|---|---|---|
Title | YCDX PROTEIN, TRINUCLEAR ZINC SITE | ||||||
Components | Hypothetical protein ycdX | ||||||
Keywords | STRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta-alpha-barrel / trinuclear zinc | ||||||
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 / FOURIER SYNTHESIS / Resolution: 2.3 Å | ||||||
Authors | Teplyakov, A. / Obmolova, G. / Khil, P.P. / Camerini-Otero, R.D. / Gilliland, G.L. | ||||||
Citation | Journal: PROTEINS: STRUCT.,FUNCT.,GENET. / 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 1m68.cif.gz | 63.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb1m68.ent.gz | 45.9 KB | Display | PDB format |
PDBx/mmJSON format | 1m68.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1m68_validation.pdf.gz | 423.6 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 1m68_full_validation.pdf.gz | 424.8 KB | Display | |
Data in XML | 1m68_validation.xml.gz | 13 KB | Display | |
Data in CIF | 1m68_validation.cif.gz | 18.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m6/1m68 ftp://data.pdbj.org/pub/pdb/validation_reports/m6/1m68 | HTTPS FTP |
-Related structure data
Related structure data | 1m65SC S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
| ||||||||
Details | The protein forms a trimer in solution that sits on the 3-fold crystal axis |
-Components
#1: Protein | Mass: 26925.529 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: pDEST14 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P75914 | ||||
---|---|---|---|---|---|
#2: Chemical | #3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52.07 % | ||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: 0.1 M Tris, 60% AS, 5 mM Zinc Acetate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K | ||||||||||||||||||||||||
Crystal grow | *PLUS | ||||||||||||||||||||||||
Components of the solutions | *PLUS
|
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.9795 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jul 2, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→20 Å / Num. all: 12703 / Num. obs: 12596 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8.5 % / Biso Wilson estimate: 34 Å2 / Rmerge(I) obs: 0.041 / Net I/σ(I): 33.7 |
Reflection shell | Resolution: 2.3→2.35 Å / Redundancy: 9.5 % / Rmerge(I) obs: 0.102 / Mean I/σ(I) obs: 12.8 / Num. unique all: 757 / % possible all: 89.8 |
Reflection | *PLUS Lowest resolution: 20 Å |
-Processing
Software |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1M65 Resolution: 2.3→10 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.372 / SU ML: 0.156 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.276 / ESU R Free: 0.217 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 38.198 Å2
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.28 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→10 Å
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.3→2.361 Å / Total num. of bins used: 20 /
| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / % reflection Rfree: 5 % / Rfactor Rfree: 0.225 / Rfactor Rwork: 0.165 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
|