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- PDB-1opm: OXIDIZED (CU2+) PEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1opm | ||||||
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Title | OXIDIZED (CU2+) PEPTIDYLGLYCINE ALPHA-HYDROXYLATING MONOOXYGENASE (PHM) WITH BOUND SUBSTRATE | ||||||
![]() | PROTEIN (PEPTIDYLGLYCINE ALPHA-HYDROXYLATING 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 | ![]() ![]() ![]() | ||||||
![]() | Prigge, S.T. / Amzel, L.M. | ||||||
![]() | ![]() Title: Substrate-mediated electron transfer in peptidylglycine alpha-hydroxylating monooxygenase. Authors: Prigge, S.T. / Kolhekar, A.S. / 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 | ![]() | 81.8 KB | Display | ![]() |
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PDB format | ![]() | 59.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3phmC ![]() 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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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 34577.641 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Details: OXIDIZED (CU2+), SUBSTRATE BOUND / Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 162 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/IYG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/AZI.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/IYG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-AZI / | #4: Chemical | ChemComp-NI / | #5: Chemical | #6: Chemical | ChemComp-GOL / #7: Water | ChemComp-HOH / | |
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-Details
Nonpolymer details | CU 357 IS ACTIVE SITE COPPER CUA 1CU 358 IS ACTIVE SITE COPPER CUB NI1 359 FORMS A CRYSTAL CONTACT |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 63 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 5.5 / Details: pH 5.5 | |||||||||||||||||||||||||||||||||||
Crystal | *PLUS | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / pH: 5.5 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 1998 / Details: SPHERICAL RH COATED MIRROR |
Radiation | Monochromator: SAGITTALLY FOCUSED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0093 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→20 Å / Num. obs: 22493 / % possible obs: 96.6 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Rsym value: 0.07 / Net I/σ(I): 14 |
Reflection shell | Resolution: 2.1→2.175 Å / Redundancy: 4.55 % / Mean I/σ(I) obs: 3.9 / Rsym value: 0.358 / % possible all: 98.7 |
Reflection | *PLUS Redundancy: 4.61 % / Num. measured all: 103719 / Rmerge(I) obs: 0.07 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PHM Resolution: 2.1→10 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.16 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 12
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Xplor file |
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.1 Å / Lowest resolution: 10 Å / σ(F): 2 / % reflection Rfree: 5 % / Rfactor obs: 0.2 / Rfactor Rwork: 0.2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Highest resolution: 2.1 Å / Rfactor Rfree: 0.292 / % reflection Rfree: 4.4 % / Rfactor Rwork: 0.249 |