+Open data
-Basic information
Entry | Database: PDB / ID: 2oda | ||||||
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Title | Crystal Structure of PSPTO_2114 | ||||||
Components | Hypothetical protein PSPTO_2114 | ||||||
Keywords | PROTEIN BINDING / Haloacid dehalogenase / phosphonoacetaldehyde hydrolase | ||||||
Function / homology | HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta / Uncharacterized protein Function and homology information | ||||||
Biological species | Pseudomonas syringae pv. tomato (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å | ||||||
Authors | Peisach, E. / Allen, K.N. / Dunaway-Mariano, D. / Wang, L. / Burroughs, A.M. / Aravind, L. | ||||||
Citation | Journal: Proteins / Year: 2007 Title: The X-ray crystallographic structure and activity analysis of a Pseudomonas-specific subfamily of the HAD enzyme superfamily evidences a novel biochemical function. Authors: Peisach, E. / Wang, L. / Burroughs, A.M. / Aravind, L. / Dunaway-Mariano, D. / Allen, K.N. #1: Journal: Biochemistry / Year: 2000 Title: The crystal structure of bacillus cereus phosphonoacetaldehyde hydrolase: insight into catalysis of phosphorus bond cleavage and catalytic diversification within the HAD enzyme superfamily Authors: Morais, M.C. / Zhang, W. / Baker, A.S. / Zhang, G. / Dunaway-Mariano, D. / Allen, K.N. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2oda.cif.gz | 99.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2oda.ent.gz | 74.5 KB | Display | PDB format |
PDBx/mmJSON format | 2oda.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2oda_validation.pdf.gz | 443.4 KB | Display | wwPDB validaton report |
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Full document | 2oda_full_validation.pdf.gz | 444.3 KB | Display | |
Data in XML | 2oda_validation.xml.gz | 21.1 KB | Display | |
Data in CIF | 2oda_validation.cif.gz | 33.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/od/2oda ftp://data.pdbj.org/pub/pdb/validation_reports/od/2oda | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 21084.283 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Pseudomonas syringae pv. tomato (bacteria) Species: Pseudomonas syringae group genomosp. 3 / Gene: PSPTO_2114 / Plasmid: pET23b / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q884H9 #2: Chemical | ChemComp-MG / | #3: Chemical | #4: 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: 2.3 Å3/Da / Density % sol: 46.9 % Description: THE STRUCTURE FACTOR FILE CONTAINS FRIEDEL PAIRS |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.3 Details: 15-20% PEG 3350, 150-200mM Sodium formate, 100mM Hepes pH 7.3, 5mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.97980, 0.97786, 0.95000 | ||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Nov 9, 2005 | ||||||||||||
Radiation | Monochromator: Si(111) crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.9→60 Å / Num. all: 30874 / Num. obs: 30874 / % possible obs: 98 % / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 13.45 Å2 / Rsym value: 0.065 / Net I/σ(I): 41 | ||||||||||||
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 6.6 % / Mean I/σ(I) obs: 7.3 / Num. unique all: 2580 / Rsym value: 0.183 / % possible all: 83.8 |
-Phasing
Phasing | Method: MAD | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Phasing set |
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Phasing MAD | D res high: 2.1 Å / D res low: 20 Å / FOM : 0.77 / Reflection: 22986 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing MAD set |
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Phasing MAD set site |
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Phasing MAD shell |
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Phasing dm | FOM : 0.84 / FOM acentric: 0.85 / FOM centric: 0.79 / Reflection: 22988 / Reflection acentric: 20209 / Reflection centric: 2779 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Phasing dm shell |
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-Processing
Software |
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Refinement | Method to determine structure: MAD / Resolution: 1.9→43.27 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / SU B: 2.958 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.165 / ESU R Free: 0.153 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FRIEDEL PAIRS WERE USED FOR PHASING
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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: 13.815 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→43.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.95 Å / Total num. of bins used: 20
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