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Open data
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Basic information
Entry | Database: PDB / ID: 7yvv | ||||||
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Title | AcmP1, R-4-hydroxymandelate synthase | ||||||
![]() | 4-hydroxyphenylpyruvate dioxygenase![]() | ||||||
![]() | ![]() | ||||||
Function / homology | ![]() aromatic amino acid metabolic process / ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhang, B. / Ge, H.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Characterization of AcmP1 as the native R-4-hydroxymandelate synthase from biosynthetic pathway of Amycolamycins Authors: Zhang, B. / Ge, H.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 148 KB | Display | ![]() |
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PDB format | ![]() | 112.9 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 2r5vS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 40268.621 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Production host: ![]() ![]() ![]() References: UniProt: A0A7H8HIR4, ![]() | ||||||||
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#2: Chemical | ![]() #3: Chemical | ChemComp-FE / | ![]() #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.04 Å3/Da / Density % sol: 39.74 % |
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Crystal grow![]() | Temperature: 295.15 K / Method: vapor diffusion, sitting drop Details: 0.1 M HEPES sodium pH 7.5, 10% v/v 2-Propanol, 20% w/v Polyethylene glycol 4,000 |
-Data collection
Diffraction | Mean temperature: 77.15 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 22, 2017 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||||||||
Reflection twin | Operator: h,-h-k,-l / Fraction: 0.33 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.1→61.6 Å / Num. obs: 18285 / % possible obs: 98.3 % / Redundancy: 4.7 % / CC1/2: 0.985 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.087 / Rrim(I) all: 0.192 / Net I/σ(I): 6.9 / Num. measured all: 85544 / Scaling rejects: 7 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 2R5V Resolution: 2.1→61.6 Å / Cross valid method: THROUGHOUT / σ(F): 84.32 / Phase error: 27.38 / Stereochemistry target values: TWIN_LSQ_F
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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: 92.28 Å2 / Biso mean: 25.5535 Å2 / Biso min: 4.86 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→61.6 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 13
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Refinement TLS params. | Method: refined / Origin x: 10.019 Å / Origin y: 20.4105 Å / Origin z: 0.9351 Å
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Refinement TLS group |
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