+Open data
-Basic information
Entry | Database: PDB / ID: 8dsj | ||||||
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Title | Peptidylglycine alpha hydroxylating monooxygenase anaerobic | ||||||
Components | Peptidylglycine alpha-amidating monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / copper / monooxygenase / peptidylglycine alpha hydroxylating | ||||||
Function / homology | Function and homology information peptidylglycine monooxygenase / peptidylamidoglycolate lyase / peptide amidation / peptidylglycine monooxygenase activity / peptidylamidoglycolate lyase activity / fatty acid primary amide biosynthetic process / toxin metabolic process / ovulation cycle process / long-chain fatty acid metabolic process / peptide metabolic process ...peptidylglycine monooxygenase / peptidylamidoglycolate lyase / peptide amidation / peptidylglycine monooxygenase activity / peptidylamidoglycolate lyase activity / fatty acid primary amide biosynthetic process / toxin metabolic process / ovulation cycle process / long-chain fatty acid metabolic process / peptide metabolic process / mitotic chromosome condensation / L-ascorbic acid binding / response to pH / response to copper ion / limb development / transport vesicle membrane / response to zinc ion / maternal process involved in female pregnancy / response to glucocorticoid / condensed chromosome / lactation / secretory granule / regulation of actin cytoskeleton organization / trans-Golgi network / response to estradiol / heart development / perikaryon / response to hypoxia / response to xenobiotic stimulus / copper ion binding / neuronal cell body / calcium ion binding / chromatin binding / chromatin / regulation of transcription by RNA polymerase II / protein kinase binding / perinuclear region of cytoplasm / cell surface / extracellular space / zinc ion binding / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Arias, R.J. / Blackburn, N.J. | ||||||
Funding support | United States, 1items
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Citation | Journal: Protein Sci. / Year: 2023 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8dsj.cif.gz | 135.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8dsj.ent.gz | 103.7 KB | Display | PDB format |
PDBx/mmJSON format | 8dsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ds/8dsj ftp://data.pdbj.org/pub/pdb/validation_reports/ds/8dsj | HTTPS FTP |
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-Related structure data
Related structure data | 8dslC 8dsnC 1phmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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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.) Rattus norvegicus (Norway rat) / Gene: Pam / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: P14925, peptidylglycine monooxygenase, peptidylamidoglycolate lyase #2: Chemical | ChemComp-CU / #3: Chemical | ChemComp-GOL / Has ligand of interest | Y | |
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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: 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: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 1 Å | ||||||||||||||||||||||||
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: 1 Å / Relative weight: 1 | ||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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