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- PDB-3mig: Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3mig | ||||||
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Title | Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound nitrite, obtained in the presence of substrate | ||||||
![]() | Peptidyl-glycine alpha-amidating monooxygenase | ||||||
![]() | OXIDOREDUCTASE / MONOOXYGENASE / BIOACTIVE PEPTIDE ACTIVATION / ASCORBATE | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chufan, E.E. / Eipper, B.A. / Mains, R.E. / Amzel, L.M. | ||||||
![]() | ![]() Title: Differential Reactivity Between the Two Copper Sites of Peptidylglycine alpha-Hydroxylating Monooxygenase (PHM) Authors: Chufan, E.E. / Prigge, S.T. / Siebert, X. / Eipper, B.A. / Mains, R.E. / Amzel, L.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 | ![]() | 75.6 KB | Display | ![]() |
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PDB format | ![]() | 55.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 449.5 KB | Display | ![]() |
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Full document | ![]() | 454.2 KB | Display | |
Data in XML | ![]() | 13.5 KB | Display | |
Data in CIF | ![]() | 17.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3mibC ![]() 3micC ![]() 3midC ![]() 3mieC ![]() 3mifC ![]() 3mihC ![]() 3mljC ![]() 3mlkC ![]() 3mllC ![]() 1phmS S: Starting model for refinement C: citing same article ( |
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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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Details | The asymmetric unit contains one biological unit |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 35008.133 Da / Num. of mol.: 1 / Fragment: UNP residues 43-356, monooxygenase domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 5 types, 24 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/NO2.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-NI / | #4: Chemical | #5: Chemical | ChemComp-GOL / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.2 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Crystallization: 0.1-0.5mM CuSO4, 1.25mM NiCl2, 100mM sodium cacodylate pH=5.5, 3mM sodium azide and 5% glycerol. The crystal was first soaked in 1mM substrate (Ac-3,5-diI-YG) for 1 hour and ...Details: Crystallization: 0.1-0.5mM CuSO4, 1.25mM NiCl2, 100mM sodium cacodylate pH=5.5, 3mM sodium azide and 5% glycerol. The crystal was first soaked in 1mM substrate (Ac-3,5-diI-YG) for 1 hour and then soaked in 300mM NaNO2/1mM substrate for 14 hours at 293K., VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 16, 2007 |
Radiation | Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2. ...Monochromator: Monochromator system consisting of a horizontally deflecting and focusing crystal preceded by a vertically focusing mirror. Distance from monochromator to sample is variable between 2.5 and 4.5 m. Distance from the monochromator to source is ~10.5 m Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→52 Å / Num. obs: 10776 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 7 % / Rsym value: 0.085 / Net I/σ(I): 35.7 |
Reflection shell | Resolution: 2.7→2.8 Å / Redundancy: 5.6 % / Mean I/σ(I) obs: 2.1 / Num. unique all: 970 / Rsym value: 0.53 / % possible all: 91.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1PHM Resolution: 2.7→52 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.914 / SU B: 27.487 / SU ML: 0.285 / Cross valid method: THROUGHOUT / ESU R: 1.43 / ESU R Free: 0.367 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.565 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.697→2.767 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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