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Yorodumi- PDB-4c1l: Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptu... -
+Open data
-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 | ||||||
Components | 2-dehydro-3-deoxyphosphoheptonate aldolase | ||||||
Keywords | TRANSFERASE / SHIKIMATE PATHWAY / INTERFACE MUTANT | ||||||
Function / homology | Function and homology information 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / aldehyde-lyase activity / aromatic amino acid family biosynthetic process / metal ion binding Similarity search - Function | ||||||
Biological species | Pyrococcus furiosus (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Nazmi, A.R. / Schofield, L.R. / Dobson, R.C.J. / Jameson, G.B. / Parker, E.J. | ||||||
Citation | Journal: J. Mol. Biol. / Year: 2014 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. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4c1l.cif.gz | 127.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c1l.ent.gz | 100 KB | Display | PDB format |
PDBx/mmJSON format | 4c1l.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c1l_validation.pdf.gz | 438.3 KB | Display | wwPDB validaton report |
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Full document | 4c1l_full_validation.pdf.gz | 439.9 KB | Display | |
Data in XML | 4c1l_validation.xml.gz | 25 KB | Display | |
Data in CIF | 4c1l_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/4c1l ftp://data.pdbj.org/pub/pdb/validation_reports/c1/4c1l | HTTPS FTP |
-Related structure data
Related structure data | 4c1kC 1zcoS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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.) Pyrococcus furiosus (archaea) / Gene: PF1690 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): RIL/pT7 References: UniProt: Q8U0A9, 3-deoxy-7-phosphoheptulonate synthase |
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-Non-polymers , 5 types, 431 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.97948 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 20, 2012 / Details: 0 |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 |
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 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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