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Yorodumi- PDB-4umb: Structural analysis of substrate-mimicking inhibitors in complex ... -
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-Basic information
Entry | Database: PDB / ID: 4umb | ||||||
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Title | Structural analysis of substrate-mimicking inhibitors in complex with Neisseria meningitidis 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase - the importance of accommodating the active site water | ||||||
Components | PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE | ||||||
Keywords | TRANSFERASE / DAH7PS / DAHPS / AROMATIC AMINO ACIDS / SHIKIMATE PATHWAY / OXOCARBENIUM ION / MENINGITIS | ||||||
Function / homology | Function and homology information 3-deoxy-7-phosphoheptulonate synthase / 3-deoxy-7-phosphoheptulonate synthase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / metal ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | NEISSERIA MENINGITIDIS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.17 Å | ||||||
Authors | Heyes, L.C. / Reichau, S. / Cross, P.J. / Parker, E.J. | ||||||
Citation | Journal: Bioorg.Chem. / Year: 2014 Title: Structural Analysis of Substrate-Mimicking Inhibitors in Complex with Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase - the Importance of Accommodating the Active Site Water. Authors: Heyes, L.C. / Reichau, S. / Cross, P.J. / Jameson, G.B. / Parker, E.J. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AA" 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. THE SHEETS PRESENTED AS "CA" 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 "DA" 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 | 4umb.cif.gz | 511.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4umb.ent.gz | 422.8 KB | Display | PDB format |
PDBx/mmJSON format | 4umb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/um/4umb ftp://data.pdbj.org/pub/pdb/validation_reports/um/4umb | HTTPS FTP |
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-Related structure data
Related structure data | 4umaC 4umcC 4hsnS 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
#1: Protein | Mass: 38712.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Strain: MC58 / Plasmid: PT7/7 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9K169, 3-deoxy-7-phosphoheptulonate synthase #2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-PO4 / #4: Chemical | ChemComp-0V5 / ( #5: 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: 52.22 % / Description: NONE |
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Crystal grow | pH: 7.3 / Details: pH 7.3 |
-Data collection
Diffraction | Mean temperature: 110 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 1.3 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 6, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.3 Å / Relative weight: 1 |
Reflection | Resolution: 2.17→48.31 Å / Num. obs: 83610 / % possible obs: 99.9 % / Observed criterion σ(I): 1.2 / Redundancy: 7.4 % / Rmerge(I) obs: 0.3 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 2.17→2.21 Å / Redundancy: 7.2 % / Mean I/σ(I) obs: 1.2 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: MIR Starting model: PDB ENTRY 4HSN Resolution: 2.17→98.99 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.92 / SU B: 12.239 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.186 / 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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.895 Å2
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Refinement step | Cycle: LAST / Resolution: 2.17→98.99 Å
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