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- PDB-4c1l: Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptu... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4c1l | ||||||
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Title | Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptulosonate 7-phosphate synthase I181D interface mutant | ||||||
![]() | 2-dehydro-3-deoxyphosphoheptonate aldolase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nazmi, A.R. / Schofield, L.R. / Dobson, R.C.J. / Jameson, G.B. / Parker, E.J. | ||||||
![]() | ![]() Title: Destabilization of the homotetrameric assembly of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase from the hyperthermophile Pyrococcus furiosus enhances enzymatic activity. Authors: Nazmi, A.R. / Schofield, L.R. / Dobson, R.C. / Jameson, G.B. / Parker, E.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 8-STRANDED BARREL THIS IS REPRESENTED BY A 9-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 127.9 KB | Display | ![]() |
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PDB format | ![]() | 100 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4c1kC ![]() 1zcoS C: citing same article ( 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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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 29262.643 Da / Num. of mol.: 2 / Mutation: I181D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: Q8U0A9, ![]() |
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-Non-polymers , 5 types, 431 molecules ![](data/chem/img/MN.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/K.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-CL / ![]() #4: Chemical | #5: Chemical | ChemComp-1PE / | ![]() #6: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.98 Å3/Da / Density % sol: 58.7 % / Description: NONE |
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Crystal grow![]() | pH: 5.5 Details: PROTEIN SOLUTION WAS MIXED 1:1 WITH CRYSTALIZATION SLUTION CONTAINING, 0.2M MAGNESIUM CHLORIDE, 0.1M SODIUM ACETATE, PH 5.5, 8% PEG 20K AND 8% PEG 550MME. DROP SIZE WAS 2 MICRO L AND PROTEIN ...Details: PROTEIN SOLUTION WAS MIXED 1:1 WITH CRYSTALIZATION SLUTION CONTAINING, 0.2M MAGNESIUM CHLORIDE, 0.1M SODIUM ACETATE, PH 5.5, 8% PEG 20K AND 8% PEG 550MME. DROP SIZE WAS 2 MICRO L AND PROTEIN CONCENTRATION WAS 6.5 MG/ML IN 20 MM BTP, 40 MM KCL, PH 7.5. |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Details: 0 / Detector: CCD / Date: Oct 20, 2012 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.8→44.59 Å / Num. obs: 65170 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 14.9 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 13.4 |
Reflection shell | Resolution: 1.8→44.59 Å / Redundancy: 14.9 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 4.5 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1ZCO Resolution: 1.8→43.97 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.953 / SU B: 1.887 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.099 / ESU R Free: 0.093 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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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: 20.456 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→43.97 Å
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Refine LS restraints |
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