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Yorodumi- PDB-2ypp: 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase in complex w... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2ypp | ||||||
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Title | 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase in complex with 3 tyrosine molecules | ||||||
Components | PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE AROG | ||||||
Keywords | TRANSFERASE / SHIKIMATE PATHWAY / AROMATIC AMINO ACID BIOSYNTHESIS / ALLOSTERY | ||||||
Function / homology | Function and homology information 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / Chorismate via Shikimate Pathway / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / peptidoglycan-based cell wall / protein homooligomerization / manganese ion binding / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | MYCOBACTERIUM TUBERCULOSIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Authors | Blackmore, N.J. / Reichau, S. / Jiao, W. / Hutton, R.D. / Baker, E.N. / Jameson, G.B. / Parker, E.J. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2013 Title: Three Sites and You are Out: Ternary Synergistic Allostery Controls Aromatic Aminoacid Biosynthesis in Mycobacterium Tuberculosis. Authors: Blackmore, N.J. / Reichau, S. / Jiao, W. / Hutton, R.D. / Baker, E.N. / 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 "BA" 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 | 2ypp.cif.gz | 358.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ypp.ent.gz | 295.4 KB | Display | PDB format |
PDBx/mmJSON format | 2ypp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ypp_validation.pdf.gz | 484.3 KB | Display | wwPDB validaton report |
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Full document | 2ypp_full_validation.pdf.gz | 503.8 KB | Display | |
Data in XML | 2ypp_validation.xml.gz | 36.9 KB | Display | |
Data in CIF | 2ypp_validation.cif.gz | 51.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yp/2ypp ftp://data.pdbj.org/pub/pdb/validation_reports/yp/2ypp | HTTPS FTP |
-Related structure data
Related structure data | 2ypoC 2ypqC 3nv8S 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 on special symmetry positions |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 50700.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) References: UniProt: O53512, 3-deoxy-7-phosphoheptulonate synthase |
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-Non-polymers , 6 types, 171 molecules
#2: Chemical | #3: Chemical | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-GOL / #6: Chemical | #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | L-TYROSINE (TYR): 3 TYROSINE LIGANDS ARE BOUND IN THE TWO MONOMERS OF THE ASYMMETRIC UNIT, 1 IN ...L-TYROSINE (TYR): 3 TYROSINE LIGANDS ARE BOUND IN THE TWO MONOMERS OF THE ASYMMETRIC |
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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: 3.92 Å3/Da / Density % sol: 68.6 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.1 M TRIS-HCL PH 7.5, 1.5 M AMMONIUM SULFATE, 12% V/V GLYCEROL |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953697 | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Aug 19, 2011 | |||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength | Wavelength: 0.953697 Å / Relative weight: 1 | |||||||||||||||
Reflection twin |
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Reflection | Resolution: 2.3→47.03 Å / Num. obs: 67961 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 7.6 % / Rmerge(I) obs: 0.13 / Rsym value: 0.126 / Net I/σ(I): 10.7 | |||||||||||||||
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3.1 / Rsym value: 0.237 / % possible all: 86.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NV8 Resolution: 2.3→44.02 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 6.144 / SU ML: 0.078 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.028 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. CHAIN A RESIDUES 11-12 AND CHAIN B RESIDUES 10-12 ARE DISORDERED.
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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: 29.829 Å2
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Refinement step | Cycle: LAST / Resolution: 2.3→44.02 Å
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Refine LS restraints |
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