+Open data
-Basic information
Entry | Database: PDB / ID: 4ucg | ||||||
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Title | NmeDAH7PS R126S variant | ||||||
Components | PHOSPHO-2-DEHYDRO-3-DEOXYHEPTONATE ALDOLASE | ||||||
Keywords | TRANSFERASE / SHIKIMATE PATHWAY / DAHPS / DAH7PS | ||||||
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 Å | ||||||
Authors | Cross, P.J. / Heyes, L.C. / Zhang, S. / Nazmi, A.R. / Parker, E.J. | ||||||
Citation | Journal: Plos One / Year: 2016 Title: The Functional Unit of Neisseria Meningitidis 3-Deoxy-D-Arabino-Heptulosonate 7-Phosphate Synthase is Dimeric. Authors: Cross, P.J. / Heyes, L.C. / Zhang, S. / Nazmi, A.R. | ||||||
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 | 4ucg.cif.gz | 520.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4ucg.ent.gz | 427.7 KB | Display | PDB format |
PDBx/mmJSON format | 4ucg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uc/4ucg ftp://data.pdbj.org/pub/pdb/validation_reports/uc/4ucg | HTTPS FTP |
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-Related structure data
Related structure data | 5dceC 4hsnS 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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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: 38642.020 Da / Num. of mol.: 4 / Mutation: YES 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, 750 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | ChemComp-PEP / #4: Chemical | #5: Chemical | ChemComp-PEG / #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: 2.54 Å3/Da / Density % sol: 51.69 % / 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: MX1 / Wavelength: 0.953 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Oct 5, 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→48.03 Å / Num. obs: 105375 / % possible obs: 100 % / Observed criterion σ(I): 1.5 / Redundancy: 14.8 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 15.2 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 14.4 % / Mean I/σ(I) obs: 1.5 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4HSN Resolution: 2→98.7 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.942 / SU B: 8.44 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.163 / ESU R Free: 0.149 / 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: 34.949 Å2
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Refinement step | Cycle: LAST / Resolution: 2→98.7 Å
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Refine LS restraints |
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