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- PDB-7tm5: Crystal structure of shikimate-3-phosphate bound 3-phosphoshikima... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7tm5 | ||||||
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Title | Crystal structure of shikimate-3-phosphate bound 3-phosphoshikimate 1-carboxyvinyltransferase from Klebsiella pneumoniae | ||||||
![]() | 3-phosphoshikimate 1-carboxyvinyltransferase | ||||||
![]() | TRANSFERASE / shikimate-3-phosphate / 3-phosphoshikimate 1-carboxyvinyltransferase / SSGCID / STRUCTURAL GENOMICS / SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE | ||||||
Function / homology | ![]() 3-phosphoshikimate 1-carboxyvinyltransferase / 3-phosphoshikimate 1-carboxyvinyltransferase activity / shikimate kinase activity / shikimate 3-dehydrogenase (NADP+) activity / 3-dehydroquinate dehydratase activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process / cytoplasm Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Seattle Structural Genomics Center for Infectious Disease (SSGCID) | ||||||
Funding support | ![]()
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![]() | ![]() Title: Crystal structure of shikimate-3-phosphate bound 3-phosphoshikimate 1-carboxyvinyltransferase from Klebsiella pneumoniae Authors: Liu, L. / Lovell, S. / Battaile, K.P. / Tillery, L. / Shek, R. / Craig, J.K. / Barrett, L.K. / Van Voorhis, W.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 370.9 KB | Display | ![]() |
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PDB format | ![]() | 297 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.2 MB | Display | ![]() |
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Full document | ![]() | 1.2 MB | Display | |
Data in XML | ![]() | 43.1 KB | Display | |
Data in CIF | ![]() | 68.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1g6tS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 47115.641 Da / Num. of mol.: 2 / Fragment: KlpnC.18288.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Strain: HS11286 / Gene: aroA, KPHS_18160 / Plasmid: KlpnC.18288.a.B1 / Production host: ![]() ![]() References: UniProt: A0A0H3GV01, 3-phosphoshikimate 1-carboxyvinyltransferase |
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-Non-polymers , 7 types, 1254 molecules ![](data/chem/img/S3P.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/PO4.gif)
![](data/chem/img/1PE.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NO3.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | #4: Chemical | #5: Chemical | #6: Chemical | ChemComp-GOL / | #7: Chemical | ChemComp-NO3 / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.49 Å3/Da / Density % sol: 50.55 % / Mosaicity: 0.12 ° |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Morpheus C5: 12% (v/v) PEG 500 MME: 8% (w/v) PEG 20000, 0.1M (Sodium HEPES: MOPS), 0.03 M Sodium nitrate, 0.03 M Sodium phosphate dibasic, 0.03 M Ammonium sulfate, KlpnC.18288.a.B1.PW39049 ...Details: Morpheus C5: 12% (v/v) PEG 500 MME: 8% (w/v) PEG 20000, 0.1M (Sodium HEPES: MOPS), 0.03 M Sodium nitrate, 0.03 M Sodium phosphate dibasic, 0.03 M Ammonium sulfate, KlpnC.18288.a.B1.PW39049 at 20 mg/mL, Tray: plate 12156 well C5 drop 1, Puck: PSL0602, Cryo: direct |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 19, 2021 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 1.41→97.7 Å / Num. obs: 181399 / % possible obs: 100 % / Redundancy: 6.5 % / Biso Wilson estimate: 14.56 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.028 / Rrim(I) all: 0.072 / Net I/σ(I): 14.3 / Num. measured all: 1180504 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Redundancy: 6.2 % / % possible all: 99.9
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-Phasing
Phasing | Method: ![]() |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1G6T Resolution: 1.41→35.86 Å / SU ML: 0.13 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 13.7 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 71.61 Å2 / Biso mean: 18.4412 Å2 / Biso min: 8.51 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.41→35.86 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30
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