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Yorodumi- PDB-3mih: Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mih | ||||||
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Title | Oxidized (Cu2+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound azide, obtained in the presence of substrate | ||||||
Components | Peptidyl-glycine alpha-amidating monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / MONOOXYGENASE / BIOACTIVE PEPTIDE ACTIVATION / ASCORBATE | ||||||
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 / condensed chromosome / response to zinc ion / maternal process involved in female pregnancy / response to glucocorticoid / 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 / chromatin binding / neuronal cell body / calcium ion binding / regulation of transcription by RNA polymerase II / chromatin / 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: 2.74 Å | ||||||
Authors | Chufan, E.E. / Eipper, B.A. / Mains, R.E. / Amzel, L.M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mih.cif.gz | 75 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mih.ent.gz | 54.8 KB | Display | PDB format |
PDBx/mmJSON format | 3mih.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mih_validation.pdf.gz | 445.2 KB | Display | wwPDB validaton report |
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Full document | 3mih_full_validation.pdf.gz | 449.5 KB | Display | |
Data in XML | 3mih_validation.xml.gz | 12.9 KB | Display | |
Data in CIF | 3mih_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mi/3mih ftp://data.pdbj.org/pub/pdb/validation_reports/mi/3mih | HTTPS FTP |
-Related structure data
Related structure data | 3mibC 3micC 3midC 3mieC 3mifC 3migC 3mljC 3mlkC 3mllC 1phmS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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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.) Rattus norvegicus (Norway rat) / Strain: SPRAGUE-DAWLEY / Gene: Pam / Plasmid: pCIS / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): Cho Dg44 / References: UniProt: P14925, peptidylglycine monooxygenase |
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-Non-polymers , 6 types, 32 molecules
#2: Chemical | #3: Chemical | ChemComp-NI / | #4: Chemical | ChemComp-IOD / | #5: Chemical | ChemComp-NA / #6: Chemical | ChemComp-AZI / #7: Water | ChemComp-HOH / | |
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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: 2.67 Å3/Da / Density % sol: 53.93 % |
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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 40mM NaN3/1mM substrate for 8 hours at 293K., VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X4C / Wavelength: 0.98 Å |
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: 2.74→52 Å / Num. obs: 8970 / % possible obs: 87.3 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Rsym value: 0.089 / Net I/σ(I): 21.1 |
Reflection shell | Resolution: 2.75→2.85 Å / Redundancy: 3 % / Mean I/σ(I) obs: 1.7 / Num. unique all: 502 / Rsym value: 0.41 / % possible all: 49.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PHM Resolution: 2.74→52 Å / Cor.coef. Fo:Fc: 0.921 / Cor.coef. Fo:Fc free: 0.907 / SU B: 32.622 / SU ML: 0.331 / Cross valid method: THROUGHOUT / ESU R Free: 0.463 / 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: 84.396 Å2
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Refinement step | Cycle: LAST / Resolution: 2.74→52 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.743→2.814 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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