+Open data
-Basic information
Entry | Database: PDB / ID: 2au9 | ||||||
---|---|---|---|---|---|---|---|
Title | Inorganic pyrophosphatase complexed with substrate | ||||||
Components | Inorganic pyrophosphatase | ||||||
Keywords | HYDROLASE / substrate complex / inorganic pyrophosphatase | ||||||
Function / homology | Function and homology information inorganic triphosphate phosphatase activity / inorganic diphosphatase / inorganic diphosphate phosphatase activity / phosphate-containing compound metabolic process / magnesium ion binding / zinc ion binding / membrane / cytosol Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å | ||||||
Authors | Samygina, V.R. / Popov, A.N. / Avaeva, S.M. / Bartunik, H.D. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2007 Title: Reversible inhibition of Escherichia coli inorganic pyrophosphatase by fluoride: trapped catalytic intermediates in cryo-crystallographic studies Authors: Samygina, V.R. / Moiseev, V.M. / Rodina, E.V. / Vorobyeva, N.N. / Popov, A.N. / Kurilova, S.A. / Nazarova, T.I. / Avaeva, S.M. / Bartunik, H.D. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2au9.cif.gz | 104.7 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2au9.ent.gz | 80 KB | Display | PDB format |
PDBx/mmJSON format | 2au9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2au9_validation.pdf.gz | 446.7 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2au9_full_validation.pdf.gz | 452 KB | Display | |
Data in XML | 2au9_validation.xml.gz | 13.4 KB | Display | |
Data in CIF | 2au9_validation.cif.gz | 19.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/2au9 ftp://data.pdbj.org/pub/pdb/validation_reports/au/2au9 | HTTPS FTP |
-Related structure data
Related structure data | 2au6C 2au7C 2au8C 2auuC 1i6tS C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| x 6||||||||
Unit cell |
| ||||||||
Components on special symmetry positions |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 19585.279 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Plasmid: PUC19 / Production host: Escherichia coli (E. coli) / Strain (production host): JM109 / References: UniProt: P0A7A9, inorganic diphosphatase |
---|
-Non-polymers , 6 types, 266 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | #4: Chemical | #5: Chemical | ChemComp-F / | #6: Chemical | ChemComp-POP / | #7: Water | ChemComp-HOH / | |
---|
-Details
Sequence details | THERE IS THR IN THE POSITION 85 ACCORDING TO: OGANESSYAN V.YU., KURILOVA S.A., VOROBEVA N.N., ...THERE IS THR IN THE POSITION 85 ACCORDING TO: OGANESSYAN |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.62 % |
---|---|
Crystal grow | pH: 5 / Details: pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05 / Wavelength: 1.05 Å | |||||||||
Detector | Type: MARRESEARCH / Detector: CCD / Date: Oct 25, 2003 / Details: DOUBLE FOCUSSING X-RAY OPTICS | |||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
| |||||||||
Reflection | Resolution: 1.3→20 Å / Num. all: 46439 / Num. obs: 46439 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.049 / Net I/σ(I): 19 | |||||||||
Reflection shell | Resolution: 1.3→1.32 Å / Rmerge(I) obs: 0.538 / Mean I/σ(I) obs: 2 / % possible all: 100 |
-Processing
Software |
| |||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1I6T Resolution: 1.3→10 Å / Num. parameters: 15911 / Num. restraintsaints: 20127 / σ(F): 0 / Stereochemistry target values: Engh & Huber
| |||||||||||||||||||||||||
Refine analyze | Num. disordered residues: 25 / Occupancy sum hydrogen: 1302.37 / Occupancy sum non hydrogen: 1568.2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.3→10 Å
| |||||||||||||||||||||||||
Refine LS restraints |
|