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Yorodumi- PDB-1vs1: Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1vs1 | ||||||
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Title | Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Aeropyrum pernix in complex with Mn2+ and PEP | ||||||
Components | 3-deoxy-7-phosphoheptulonate synthase | ||||||
Keywords | TRANSFERASE / (beta/alpha)8 barrel | ||||||
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 | Aeropyrum pernix (archaea) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Shumilin, I.A. / Zhou, L. / Wu, J. / Woodard, R.W. / Bauerle, R. / Kretsinger, R.H. | ||||||
Citation | Journal: TO BE PUBLISHED Title: Crystal structure of 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase (DAHP synthase) from Aeropyrum pernix in complex with Mn2+ and PEP Authors: Shumilin, I.A. / Zhou, L. / Wu, J. / Woodard, R.W. / Bauerle, R. / Kretsinger, R.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1vs1.cif.gz | 214.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1vs1.ent.gz | 171.6 KB | Display | PDB format |
PDBx/mmJSON format | 1vs1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1vs1_validation.pdf.gz | 473.1 KB | Display | wwPDB validaton report |
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Full document | 1vs1_full_validation.pdf.gz | 486.9 KB | Display | |
Data in XML | 1vs1_validation.xml.gz | 41.2 KB | Display | |
Data in CIF | 1vs1_validation.cif.gz | 56.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/vs/1vs1 ftp://data.pdbj.org/pub/pdb/validation_reports/vs/1vs1 | HTTPS FTP |
-Related structure data
Related structure data | 1rzmS 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / Ens-ID: 1 / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: 2
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-Components
#1: Protein | Mass: 30037.719 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Aeropyrum pernix (archaea) / Gene: APE0581 / Plasmid: pT7-7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 References: UniProt: Q9YEJ7, 3-deoxy-7-phosphoheptulonate synthase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-PEP / #4: 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: 2.18 Å3/Da / Density % sol: 43.55 % |
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Crystal grow | Details: 0.1 M HEPES, 0.2 M lithium sulfate, 0.2 M magnesium chloride, 30% v/v 2-propanol, 10% v/v butanol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.92015 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 18, 2004 |
Radiation | Monochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.92015 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→90.7 Å / Num. all: 47755 / Num. obs: 47755 / % possible obs: 90.7 % / Observed criterion σ(F): -3 / Observed criterion σ(I): 0 / Redundancy: 7.4 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 19.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 6.1 % / Rmerge(I) obs: 0.344 / Mean I/σ(I) obs: 8.6 / Num. unique all: 2403 / % possible all: 46 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: FRAGMENT OF PDB ENTRY 1RZM Resolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.937 / SU B: 6.72 / SU ML: 0.164 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.417 / ESU R Free: 0.231 / 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: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.141 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→20 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.3→2.36 Å / Total num. of bins used: 20
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