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- PDB-5wja: Crystal structure of H107A peptidylglycine alpha-hydroxylating mo... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5wja | ||||||
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Title | Crystal structure of H107A peptidylglycine alpha-hydroxylating monooxygenase (PHM) in complex with citrate | ||||||
![]() | Peptidyl-glycine alpha-amidating monooxygenase | ||||||
![]() | OXIDOREDUCTASE / PEPTIDYLGLYCINE MONOOXYGENASE / PEPTIDYLGLYCINE 2-HYDROXYLASE / PHM / METAL BINDING PROTEIN / LYASE | ||||||
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 / condensed chromosome / 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 / 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 | ![]() ![]() | ||||||
Model details | copper M is present in both molecules: copper H is present in only one molecule | ||||||
![]() | Maheshwari, S. / Rudzka, K. / Gabelli, S.B. / Amzel, L.M. | ||||||
Funding support | ![]()
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![]() | ![]() Title: Effects of copper occupancy on the conformational landscape of peptidylglycine alpha-hydroxylating monooxygenase. Authors: Maheshwari, S. / Shimokawa, C. / Rudzka, K. / Kline, C.D. / Eipper, B.A. / Mains, R.E. / Gabelli, S.B. / Blackburn, N. / 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 | ![]() | 140.2 KB | Display | ![]() |
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PDB format | ![]() | 106.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 473.6 KB | Display | ![]() |
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Full document | ![]() | 486.2 KB | Display | |
Data in XML | ![]() | 26.5 KB | Display | |
Data in CIF | ![]() | 36.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5wkwC ![]() 5wm0C ![]() 6alaC ![]() 6alvC ![]() 6ampC ![]() 6an3C ![]() 6ao6C ![]() 6ay0C ![]() 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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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein , 1 types, 2 molecules AD
#1: Protein | Mass: 34706.812 Da / Num. of mol.: 2 / Fragment: PHM / Mutation: H107A Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() References: UniProt: P14925, peptidylglycine monooxygenase, peptidylamidoglycolate lyase |
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-Non-polymers , 5 types, 153 molecules ![](data/chem/img/CU.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/NI.gif)
![](data/chem/img/FLC.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | #3: Chemical | ChemComp-GOL / #4: Chemical | ChemComp-NI / | #5: Chemical | ChemComp-FLC / | #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.88 % / Mosaicity: 0.72 ° |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 19-24% PEG 4000, Tris HCL, citrate |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() | ||||||||||||||||||||||||||||||
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jul 22, 2014 | ||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||
Reflection | Resolution: 2.3→29.77 Å / Num. obs: 27694 / % possible obs: 99.6 % / Redundancy: 1.9 % / CC1/2: 0.996 / Rmerge(I) obs: 0.048 / Rpim(I) all: 0.048 / Rrim(I) all: 0.069 / Net I/σ(I): 9.6 / Num. measured all: 52974 / Scaling rejects: 0 | ||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1PHM Resolution: 2.3→29.77 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.922 / WRfactor Rfree: 0.2799 / WRfactor Rwork: 0.201 / FOM work R set: 0.7566 / SU B: 10.497 / SU ML: 0.244 / SU R Cruickshank DPI: 0.4148 / SU Rfree: 0.2795 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.415 / ESU R Free: 0.279 / 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: 148.68 Å2 / Biso mean: 51.392 Å2 / Biso min: 17.72 Å2
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Refinement step | Cycle: final / Resolution: 2.3→29.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.301→2.361 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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