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- PDB-4qrn: HIGH-RESOLUTION CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXY... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4qrn | |||||||||
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Title | HIGH-RESOLUTION CRYSTAL STRUCTURE of 5-CARBOXYVANILLATE DECARBOXYLASE (TARGET EFI-505250) FROM NOVOSPHINGOBIUM AROMATICIVORANS DSM 12444 COMPLEXED WITH MANGANESE AND 4-HYDROXY-3-METHOXY-5-NITROBENZOIC ACID | |||||||||
![]() | 5-Carboxyvanillate Decarboxylase | |||||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / HYDROLASE / DECARBOXYLASE / ENZYME FUNCTION INITIATIVE / EFI / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | ![]() secondary metabolic process / : / : / carboxy-lyase activity / hydrolase activity / metal ion binding / cytosol Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Patskovsky, Y. / Vladimirova, A. / Toro, R. / Bhosle, R. / Gerlt, J.A. / Raushel, F.M. / Almo, S.C. | |||||||||
![]() | ![]() Title: Crystal Structure of 5-Carboxyvanillate Decarboxylase from Novosphingobium Aromaticivorans Authors: Patskovsky, Y. / Vladimirova, A. / Toro, R. / Bhosle, R. / Raushel, F.M. / 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 | ![]() | 899.1 KB | Display | ![]() |
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PDB format | ![]() | 758.1 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 496.8 KB | Display | ![]() |
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Full document | ![]() | 502.2 KB | Display | |
Data in XML | ![]() | 69.8 KB | Display | |
Data in CIF | ![]() | 109.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2dvtS S: Starting model for refinement |
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Similar structure data |
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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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Unit cell |
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Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 42456.277 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: DSM 12444 / F199 / Gene: Saro_0799 / Plasmid: PET / Production host: ![]() ![]() |
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-Non-polymers , 6 types, 2028 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/1DF.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/1DF.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-1DF / #4: Chemical | ChemComp-GOL / #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-ACT / | #7: 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: 41.6 % |
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Crystal grow | pH: 8.5 Details: 0.085M TRIS-HCL, PH 8.5, 0.17M SODIUM ACETATE, 25% PEG 4000,15% 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 24, 2014 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92 Å / Relative weight: 1 |
Reflection | Resolution: 1.068→50 Å / Num. obs: 614492 / % possible obs: 98.9 % / Observed criterion σ(I): -5 / Redundancy: 3.5 % / Rmerge(I) obs: 0.109 / Rsym value: 0.109 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 1.07→1.09 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.65 / Mean I/σ(I) obs: 2 / Rsym value: 0.65 / % possible all: 99.8 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2DVT Resolution: 1.07→28.14 Å / SU ML: 0.08 / σ(F): 1.34 / Phase error: 15.1 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.07→28.14 Å
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Refine LS restraints |
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LS refinement shell |
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