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- PDB-3nrj: Crystal structure of probable yrbi family phosphatase from pseudo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3nrj | ||||||
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Title | Crystal structure of probable yrbi family phosphatase from pseudomonas syringae pv.phaseolica 1448a complexed with magnesium | ||||||
![]() | PROBABLE YRBI FAMILY PHOSPHATASE | ||||||
![]() | HYDROLASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / PHOSPHATASE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / NEW YORK SGX RESEARCH CENTER FOR STRUCTURAL GENOMICS | ||||||
Function / homology | ![]() 3-deoxy-manno-octulosonate-8-phosphatase / 3-deoxy-manno-octulosonate-8-phosphatase activity / lipopolysaccharide biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Patskovsky, Y. / Ramagopal, U. / Toro, R. / Freeman, J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC) | ||||||
![]() | ![]() Title: Crystal Structure of Had Family Hydrolase from Pseudomonas Syringae Pv.Phaseolica 1448A Authors: Patskovsky, Y. / Ramagopal, U. / Toro, R. / Freeman, J. / Sauder, J.M. / Burley, S.K. / Almo, S.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 426.4 KB | Display | ![]() |
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PDB format | ![]() | 349.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 554.3 KB | Display | ![]() |
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Full document | ![]() | 581.5 KB | Display | |
Data in XML | ![]() | 82.6 KB | Display | |
Data in CIF | ![]() | 113.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mn1S S: Starting model for refinement |
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Similar structure data | |
Other databases |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 12 molecules ABCDEFGHIJKL
#1: Protein | Mass: 20673.576 Da / Num. of mol.: 12 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: 1448A / Race 6 / Gene: PSPPH_4147 / Production host: ![]() ![]() |
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-Non-polymers , 5 types, 833 molecules ![](data/chem/img/CL.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/MG.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CL / #3: Chemical | ChemComp-MG / #4: Chemical | ChemComp-PO4 / #5: Chemical | ChemComp-UNL / | Num. of mol.: 1 / Source method: obtained synthetically #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.11 Å3/Da / Density % sol: 41.64 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 100MM TRIS-HCL, PH 7.0, 30% PEG 3K, 200MM SODIUM CHLORIDE, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 29, 2010 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.88→40 Å / Num. obs: 163907 / % possible obs: 95.6 % / Observed criterion σ(I): -5 / Redundancy: 2 % / Biso Wilson estimate: 32.512 Å2 / Rsym value: 0.064 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.88→1.91 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 0.95 / % possible all: 71.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3MN1 Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.954 / SU B: 5.318 / SU ML: 0.145 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.157 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 52.477 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.9→1.949 Å / Total num. of bins used: 20
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