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Open data
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Basic information
Entry | Database: PDB / ID: 8dsj | ||||||
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Title | Peptidylglycine alpha hydroxylating monooxygenase anaerobic | ||||||
![]() | Peptidylglycine alpha-amidating monooxygenase | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Arias, R.J. / Blackburn, N.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: New structures reveal flexible dynamics between the subdomains of peptidylglycine monooxygenase. Implications for an open to closed mechanism. Authors: Arias, R.J. / Welch, E.F. / Blackburn, N.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 135.3 KB | Display | ![]() |
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PDB format | ![]() | 103.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 8dslC ![]() 8dsnC ![]() 1phmS S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 34577.641 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() References: UniProt: P14925, ![]() ![]() #2: Chemical | ChemComp-CU / ![]() #3: Chemical | ChemComp-GOL / ![]() Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 51.03 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 1.5 uL of WT PHM protein at 17 mg/mL in 20 mM sodium phosphate, pH 7.5 was added to 1.5 uL of mother liquor solution containing 16-18% PEG 20K, 20-250 mM sodium citrate, and 2 mM CuSO4. ...Details: 1.5 uL of WT PHM protein at 17 mg/mL in 20 mM sodium phosphate, pH 7.5 was added to 1.5 uL of mother liquor solution containing 16-18% PEG 20K, 20-250 mM sodium citrate, and 2 mM CuSO4. Plates were sealed using transparent tape. Crystals were formed within one week, and these initial crystals were used to seed succeeding trays using the same crystal conditions. Seeding was performed using a Hampton Research seed bead and Hampton Research seeding tool. Initial crystals (5-7 crystals) were vortexed with seed beads for 30 seconds in 30 uL mother liquor, and streaked into a new drop using the seeding tool. PH range: 4-5 |
-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 27, 2021 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength![]() | ||||||||||||||||||||||||
Reflection | Resolution: 1.8→37.4 Å / Num. obs: 57073 / % possible obs: 92.8 % / Redundancy: 7.9 % / CC1/2: 0.855 / Rmerge(I) obs: 0.169 / Net I/σ(I): 3.6 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: 1phm Resolution: 2.8→37.4 Å / Cor.coef. Fo:Fc: 0.92 / Cor.coef. Fo:Fc free: 0.839 / SU B: 16.595 / SU ML: 0.333 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.437 / 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: 131.81 Å2 / Biso mean: 36.841 Å2 / Biso min: 9.61 Å2
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Refinement step | Cycle: final / Resolution: 2.8→37.4 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.8→2.872 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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