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- PDB-7orx: Rhodococcus jostii RHA1 thiamine diphosphate-dependent 4-hydroxyb... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7orx | |||||||||
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Title | Rhodococcus jostii RHA1 thiamine diphosphate-dependent 4-hydroxybenzoylformate decarboxylase | |||||||||
![]() | Probable benzoylformate decarboxylase | |||||||||
![]() | OXIDOREDUCTASE / benzoylformate decarboxylase / thaimine diphosphate / Rhodococcus jostii RHA1 / lignin degradation | |||||||||
Function / homology | ![]() benzoylformate decarboxylase activity / acetolactate synthase / thiamine pyrophosphate binding / magnesium ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Wilkinson, R.C. / Fulop, V. | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Characterization of Thiamine Diphosphate-Dependent 4-Hydroxybenzoylformate Decarboxylase Enzymes from Authors: Wei, Z. / Wilkinson, R.C. / Rashid, G.M.M. / Brown, D. / Fulop, V. / Bugg, T.D.H. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 730.8 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.5 MB | Display | ![]() |
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Full document | ![]() | 1.5 MB | Display | |
Data in XML | ![]() | 71.4 KB | Display | |
Data in CIF | ![]() | 96.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6qsiS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS ensembles :
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Components
#1: Protein | Mass: 55524.004 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Details: MATVSEVTYELLRARGLTTVFGNPGSNELPFLSGMPDDFRYVLGLHEGAVLSMADGYSLV TGEATLVNLHAASGSGNAMGALTNSVYSHSPLVVTAGQQVRSTIGQEVMLSNVDAGTLMK PLVKWSSEPTCAEDVPRTINQAIHTALLPAKGPVYVSVPYDDWAAEAPPESAGLLAREVH ...Details: MATVSEVTYELLRARGLTTVFGNPGSNELPFLSGMPDDFRYVLGLHEGAVLSMADGYSLV TGEATLVNLHAASGSGNAMGALTNSVYSHSPLVVTAGQQVRSTIGQEVMLSNVDAGTLMK PLVKWSSEPTCAEDVPRTINQAIHTALLPAKGPVYVSVPYDDWAAEAPPESAGLLAREVH SAASLSGDQINDLIETLESATNPVLVLGPAVDADRANADAVLLAEKLRAPVWIAPSPSRC PFPTRHPSFRGVLPAGVADLSKTLEGHDLILVVGAPVFRYHQYVPGNYLPGGARLIHVTD DGGEAARAPIGEAYVAPVGSTLEILANMVKPSDRSPLPPLGDFEEAVSVGAGLDPAQLFA LVRAGAPDDAIYVNESTSTSDAFWSQMDLSHQGSYYFPASGGLGFGLPAAVGAQLASPDR QVIGLIGDGSANYGITALWSAAQYKIPVVIIILNNGTYGALRGFSKILNTGETPGLDVPG IDFVHLAEGYGVRGTAVATAEDFTTAFKSALAADAPTLIEVRTNFDES Source: (gene. exp.) ![]() Strain: RHA1 / Gene: RHA1_ro02985 / Production host: ![]() ![]() #2: Chemical | ChemComp-TPP / #3: Chemical | ChemComp-NA / #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.57 Å3/Da / Density % sol: 52 % / Description: square plates |
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Crystal grow | Temperature: 300 K / Method: vapor diffusion / pH: 6.5 Details: 0.16 M ammonium sulfate, 20% PEG8000, 0.1 mM Mes pH 6.5 |
-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 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97948 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→123.5 Å / Num. obs: 70459 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10 % / CC1/2: 0.997 / Rmerge(I) obs: 0.154 / Net I/σ(I): 11.5 |
Reflection shell | Resolution: 2.6→2.74 Å / Redundancy: 10.2 % / Rmerge(I) obs: 2.187 / Num. unique obs: 10199 / CC1/2: 0.461 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 6QSI Resolution: 2.6→90.423 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.811 / SU B: 36.895 / SU ML: 0.319 / Cross valid method: THROUGHOUT / ESU R: 0.952 / ESU R Free: 0.297 Details: Hydrogens have been added in their 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 BULK SOLVENT | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 81.639 Å2
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Refinement step | Cycle: LAST / Resolution: 2.6→90.423 Å
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Refine LS restraints |
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