[English] 日本語
Yorodumi- PDB-5wm0: Crystal structure of apo wild type peptidylglycine alpha-hydroxyl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5wm0 | ||||||
---|---|---|---|---|---|---|---|
Title | Crystal structure of apo wild type peptidylglycine alpha-hydroxylating monooxygenase (PHM) soaked with peptide (peptide not observed) | ||||||
Components | Peptidyl-glycine alpha-amidating monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / PEPTIDYLGLYCINE MONOOXYGENASE / PEPTIDYLGLYCINE 2-HYDROXYLASE / PHM / METAL BINDING PROTEIN | ||||||
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 / response to pH / mitotic chromosome condensation / L-ascorbic acid binding / 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 / chromatin binding / calcium ion 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 | Rattus norvegicus (Norway rat) | ||||||
Method | X-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2.4 Å | ||||||
Model details | no copper bound | ||||||
Authors | Maheshwari, S. / Rudzka, K. / Gabelli, S.B. / Amzel, L.M. | ||||||
Funding support | United States, 1items
| ||||||
Citation | Journal: Commun Biol / Year: 2018 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 5wm0.cif.gz | 88.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb5wm0.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 5wm0.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wm/5wm0 ftp://data.pdbj.org/pub/pdb/validation_reports/wm/5wm0 | HTTPS FTP |
---|
-Related structure data
Related structure data | 5wjaC 5wkwC 6alaC 6alvC 6ampC 6an3C 6ao6C 6ay0C 1phmS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 108810.148 Da / Num. of mol.: 1 / Fragment: PHM Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pam / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO References: UniProt: P14925, peptidylglycine monooxygenase, peptidylamidoglycolate lyase |
---|---|
#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Mosaicity: 1.141 ° / Mosaicity esd: 0.02 ° |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 8.5 / Details: 19-24% PEG 4000, Tris HCL |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Nov 28, 2016 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.4→50 Å / Num. obs: 11068 / % possible obs: 99.2 % / Redundancy: 5.5 % / Rmerge(I) obs: 0.075 / Rpim(I) all: 0.034 / Rrim(I) all: 0.082 / Χ2: 2.251 / Net I/σ(I): 15.2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 1PHM Resolution: 2.4→47.93 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.898 / SU B: 11.01 / SU ML: 0.258 / SU R Cruickshank DPI: 0.934 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.934 / ESU R Free: 0.333 Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 164.8 Å2 / Biso mean: 51.291 Å2 / Biso min: 23.93 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.4→47.93 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.4→2.462 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
|