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Yorodumi- PDB-4c1k: Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4c1k | ||||||
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Title | Crystal structure of pyrococcus furiosus 3-deoxy-D-arabino- heptulosonate 7-phosphate synthase | ||||||
Components | 2-DEHYDRO-3-DEOXYPHOSPHOHEPTONATE ALDOLASE | ||||||
Keywords | TRANSFERASE / SHIKIMATE PATHWAY | ||||||
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: 2.15 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.J. / 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. THE SHEETS PRESENTED AS "CB" 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 "DB" 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 "EB" 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 "FB" 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 | 4c1k.cif.gz | 322.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4c1k.ent.gz | 261.3 KB | Display | PDB format |
PDBx/mmJSON format | 4c1k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4c1k_validation.pdf.gz | 776.6 KB | Display | wwPDB validaton report |
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Full document | 4c1k_full_validation.pdf.gz | 791.5 KB | Display | |
Data in XML | 4c1k_validation.xml.gz | 60.1 KB | Display | |
Data in CIF | 4c1k_validation.cif.gz | 80.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c1/4c1k ftp://data.pdbj.org/pub/pdb/validation_reports/c1/4c1k | HTTPS FTP |
-Related structure data
Related structure data | 4c1lC 1zcoS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 6 molecules ABCDEF
#1: Protein | Mass: 29260.713 Da / Num. of mol.: 6 / Source method: isolated from a natural source / Source: (natural) PYROCOCCUS FURIOSUS (archaea) References: UniProt: Q8U0A9, 3-deoxy-7-phosphoheptulonate synthase |
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-Non-polymers , 6 types, 435 molecules
#2: Chemical | ChemComp-CO3 / #3: Chemical | ChemComp-PEP / #4: Chemical | ChemComp-CD / #5: Chemical | #6: Chemical | ChemComp-2PE / | #7: 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: 2.57 Å3/Da / Density % sol: 52.19 % / Description: NONE |
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Crystal grow | pH: 6.5 Details: PROTEIN SOLUTION WAS MIXED 1:1 WITH CRYSTALIZATION SLUTION CONTAINING 100 MICROMCDCL2, 0.2M SODIUM CITRATE, 0.1M BTP, PH 6.5, 20% PEG3350. DROP SIZE WAS 2 MICRO L AND PROTEIN CONCENTRATION ...Details: PROTEIN SOLUTION WAS MIXED 1:1 WITH CRYSTALIZATION SLUTION CONTAINING 100 MICROMCDCL2, 0.2M SODIUM CITRATE, 0.1M BTP, PH 6.5, 20% PEG3350. 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: MX1 / Wavelength: 0.97948 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 13, 2011 |
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: 2.15→19.67 Å / Num. obs: 97252 / % possible obs: 98 % / Observed criterion σ(I): 2 / Redundancy: 3.6 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.15→19.67 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.9 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1ZCO Resolution: 2.15→19.65 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.583 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.235 / ESU R Free: 0.191 / 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: 33.719 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→19.65 Å
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Refine LS restraints |
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