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Yorodumi- PDB-3mlj: Reduced (Cu+) peptidylglycine alpha-hydroxylating monooxygenase (... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mlj | ||||||
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Title | Reduced (Cu+) peptidylglycine alpha-hydroxylating monooxygenase (PHM) with bound carbon monooxide (CO) | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.15 Å | ||||||
Authors | Prigge, S.T. / Chufan, E.E. / Eipper, B.A. / Mains, R.E. / Amzel, L.M. | ||||||
Citation | Journal: J.Am.Chem.Soc. / Year: 2010 Title: Differential reactivity between two copper sites in peptidylglycine alpha-hydroxylating monooxygenase 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 | 3mlj.cif.gz | 80 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mlj.ent.gz | 58.6 KB | Display | PDB format |
PDBx/mmJSON format | 3mlj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3mlj_validation.pdf.gz | 462.5 KB | Display | wwPDB validaton report |
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Full document | 3mlj_full_validation.pdf.gz | 468.2 KB | Display | |
Data in XML | 3mlj_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 3mlj_validation.cif.gz | 21.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ml/3mlj ftp://data.pdbj.org/pub/pdb/validation_reports/ml/3mlj | HTTPS FTP |
-Related structure data
Related structure data | 3mibC 3micC 3midC 3mieC 3mifC 3migC 3mihC 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, 162 molecules
#2: Chemical | #3: Chemical | ChemComp-NI / | #4: Chemical | #5: Chemical | ChemComp-ACT / | #6: Chemical | #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: 2.78 Å3/Da / Density % sol: 55.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: Crystallization: 1.8 mM NiCl2, 100mM sodium cacodylate pH=5.5, and 3mM sodium azide. The crystal was soaked in 5mM ascorbic acid and then CO-soaked in a chamber at 50 psi CO for 15 minutes., ...Details: Crystallization: 1.8 mM NiCl2, 100mM sodium cacodylate pH=5.5, and 3mM sodium azide. The crystal was soaked in 5mM ascorbic acid and then CO-soaked in a chamber at 50 psi CO for 15 minutes., VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→53 Å / Num. obs: 21690 / % possible obs: 98.1 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rsym value: 0.046 / Net I/σ(I): 29.7 |
Reflection shell | Highest resolution: 2.15 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.6 / Rsym value: 0.66 / % possible all: 99.4 |
-Processing
Software | Name: REFMAC / Classification: refinement | ||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1PHM Resolution: 2.15→53 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Refinement step | Cycle: LAST / Resolution: 2.15→53 Å
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