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Yorodumi- PDB-5wja: Crystal structure of H107A peptidylglycine alpha-hydroxylating mo... -
+Open data
-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 | ||||||
Components | Peptidyl-glycine alpha-amidating monooxygenase | ||||||
Keywords | OXIDOREDUCTASE / PEPTIDYLGLYCINE MONOOXYGENASE / PEPTIDYLGLYCINE 2-HYDROXYLASE / PHM / METAL BINDING PROTEIN / LYASE | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.3 Å | ||||||
Model details | copper M is present in both molecules: copper H is present in only one molecule | ||||||
Authors | Maheshwari, S. / Rudzka, K. / Gabelli, S.B. / Amzel, L.M. | ||||||
Funding support | United States, 1items
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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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5wja.cif.gz | 140.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5wja.ent.gz | 106.8 KB | Display | PDB format |
PDBx/mmJSON format | 5wja.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wj/5wja ftp://data.pdbj.org/pub/pdb/validation_reports/wj/5wja | HTTPS FTP |
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-Related structure data
Related structure data | 5wkwC 5wm0C 6alaC 6alvC 6ampC 6an3C 6ao6C 6ay0C 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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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.) Rattus norvegicus (Norway rat) / Gene: Pam / Plasmid: PCIS / Production host: Cricetulus griseus (Chinese hamster) / Strain (production host): CHO References: UniProt: P14925, peptidylglycine monooxygenase, peptidylamidoglycolate lyase |
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-Non-polymers , 5 types, 153 molecules
#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: X-RAY DIFFRACTION / Number of used crystals: 1 |
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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: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||
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
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT 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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