+Open data
-Basic information
Entry | Database: PDB / ID: 4uc5 | ||||||
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Title | Neisseria Meningitidis DAH7PS-Phenylalanine regulated | ||||||
Components | PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE | ||||||
Keywords | TRANSFERASE / DAHPS SHIKIMATE PATHWAY PHENYLALANINE TYPE 1A | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.19 Å | ||||||
Authors | Heyes, L.C. / Lang, E.J.M. / Parker, E.J. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2016 Title: Calculated Pka Variations Expose Dynamic Allosteric Communication Networks. Authors: Lang, E.J. / Heyes, L.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 "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 "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 "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 | 4uc5.cif.gz | 525.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uc5.ent.gz | 434 KB | Display | PDB format |
PDBx/mmJSON format | 4uc5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/4uc5 ftp://data.pdbj.org/pub/pdb/validation_reports/uc/4uc5 | HTTPS FTP |
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-Related structure data
Related structure data | 4hsnS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
NCS oper:
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-Components
-Protein , 1 types, 4 molecules ABCD
#1: Protein | Mass: 38712.133 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) NEISSERIA MENINGITIDIS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 References: UniProt: Q9K169, 3-deoxy-7-phosphoheptulonate synthase |
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-Non-polymers , 5 types, 343 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-PEG / | #4: Chemical | ChemComp-SO4 / #5: Chemical | ChemComp-PHE / #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: 2.6 Å3/Da / Density % sol: 52.65 % / Description: NONE |
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Crystal grow | pH: 7.3 Details: 0.1 M TRIS HCL (PH 7.3), 0.2 M TRIMETHYL-AMINO-N-OXIDE (TMAO), 600UM MNSO4 AND 15-20% (W/V) PEG 2000MME |
-Data collection
Diffraction | Mean temperature: 120 K |
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.953 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 26, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.953 Å / Relative weight: 1 |
Reflection | Resolution: 2.19→47.82 Å / Num. obs: 79522 / % possible obs: 99.9 % / Observed criterion σ(I): 1.2 / Redundancy: 3.8 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.19→2.23 Å / Redundancy: 3.8 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 1.2 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4HSN Resolution: 2.19→74.74 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.94 / SU B: 16.258 / SU ML: 0.194 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.2 / 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: 48.584 Å2
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Refinement step | Cycle: LAST / Resolution: 2.19→74.74 Å
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Refine LS restraints |
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