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Yorodumi- PDB-6pbj: The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synt... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6pbj | ||||||
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Title | The structure of 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase with Gly190Pro mutation | ||||||
Components | Phospho-2-dehydro-3-deoxyheptonate aldolase | ||||||
Keywords | TRANSFERASE / DAH7PS / Allostery / shipmate pathway / TIM barrel | ||||||
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: 1.9 Å | ||||||
Authors | Jiao, W. / Fan, Y. / Blackmore, N.J. / Parker, E.J. | ||||||
Funding support | New Zealand, 1items
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Citation | Journal: J.Biol.Chem. / Year: 2020 Title: A single amino acid substitution uncouples catalysis and allostery in an essential biosynthetic enzyme in Mycobacterium tuberculosis . Authors: Jiao, W. / Fan, Y. / Blackmore, N.J. / Parker, E.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6pbj.cif.gz | 194.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6pbj.ent.gz | 150.8 KB | Display | PDB format |
PDBx/mmJSON format | 6pbj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6pbj_validation.pdf.gz | 293.5 KB | Display | wwPDB validaton report |
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Full document | 6pbj_full_validation.pdf.gz | 293.9 KB | Display | |
Data in XML | 6pbj_validation.xml.gz | 1.8 KB | Display | |
Data in CIF | 6pbj_validation.cif.gz | 13 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pb/6pbj ftp://data.pdbj.org/pub/pdb/validation_reports/pb/6pbj | HTTPS FTP |
-Related structure data
Related structure data | 3nv8S 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: ASP / End label comp-ID: ASP / Refine code: _ / Auth seq-ID: -1 - 462 / Label seq-ID: 1 - 464
NCS oper:
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 50868.457 Da / Num. of mol.: 2 / Mutation: G190P Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) Gene: aroG_1, ERS027644_03091, ERS031537_02142, ERS124361_01166 Production host: Escherichia coli (E. coli) References: UniProt: A0A0T9FW33, UniProt: O53512*PLUS, 3-deoxy-7-phosphoheptulonate synthase |
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-Non-polymers , 7 types, 550 molecules
#2: Chemical | #3: Chemical | ChemComp-SO4 / #4: Chemical | #5: Chemical | ChemComp-CL / #6: Chemical | ChemComp-PEG / #7: Chemical | ChemComp-PG4 / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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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: 3.94 Å3/Da / Density % sol: 68.77 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 20 mM BTP, 150 mM NaCl, 0.5 mM TCEP, 0.2 mM PEP, 0.1 mM MnCl2, 2M Li2SO4, 2% PEG 400 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å | ||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jan 24, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection twin |
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Reflection | Resolution: 1.9→51.06 Å / Num. obs: 124730 / % possible obs: 99.9 % / Redundancy: 14.3 % / CC1/2: 0.995 / Rmerge(I) obs: 0.131 / Rpim(I) all: 0.035 / Rrim(I) all: 0.136 / Net I/σ(I): 16.9 / Num. measured all: 1783055 / Scaling rejects: 491 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3NV8 Resolution: 1.9→36.83 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.229 / SU ML: 0.039 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.018 / ESU R Free: 0.018 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 81.26 Å2 / Biso mean: 20.536 Å2 / Biso min: 6.3 Å2
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Refinement step | Cycle: final / Resolution: 1.9→36.83 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 12838 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05
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LS refinement shell | Resolution: 1.9→1.949 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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