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Yorodumi- PDB-6nck: Crystal structure of H108A peptidylglycine alpha-hydroxylating mo... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6nck | |||||||||
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Title | Crystal structure of H108A peptidylglycine alpha-hydroxylating monooxygenase (PHM) | |||||||||
Components | Peptidyl-glycine alpha-amidating monooxygenase | |||||||||
Keywords | HYDROLASE / PHM / peptidylglycine alpha-hydroxylating monooxygenase / PAL | |||||||||
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 / 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 | Rattus norvegicus (Norway rat) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å | |||||||||
Authors | Miller, M.S. / Maheshwari, S. / Gabelli, S.B. | |||||||||
Funding support | United States, 2items
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Citation | Journal: Molecules / Year: 2019 Title: Getting the Most Out of Your Crystals: Data Collection at the New High-Flux, Microfocus MX Beamlines at NSLS-II. Authors: Miller, M.S. / Maheshwari, S. / Shi, W. / Gao, Y. / Chu, N. / Soares, A.S. / Cole, P.A. / Amzel, L.M. / Fuchs, M.R. / Jakoncic, J. / Gabelli, S.B. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6nck.cif.gz | 76.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6nck.ent.gz | 53.3 KB | Display | PDB format |
PDBx/mmJSON format | 6nck.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nc/6nck ftp://data.pdbj.org/pub/pdb/validation_reports/nc/6nck | HTTPS FTP |
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-Related structure data
Related structure data | 6nchC 6nciC 6nctC 6ao6S 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
#1: Protein | Mass: 34706.812 Da / Num. of mol.: 1 / Mutation: H108A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Pam / Production host: Cricetulus griseus (Chinese hamster) References: UniProt: P14925, peptidylglycine monooxygenase, peptidylamidoglycolate lyase |
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#2: Chemical | ChemComp-CU / |
#3: Chemical | ChemComp-NI / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.96 Å3/Da / Density % sol: 37.35 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 19-24% PEG 4000, Tris HCl |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: Y | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.9184 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 3, 2018 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→44.08 Å / Num. obs: 7872 / % possible obs: 99.6 % / Redundancy: 4.873 % / Biso Wilson estimate: 53.452 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.13 / Rrim(I) all: 0.145 / Χ2: 0.975 / Net I/σ(I): 8.19 / Num. measured all: 38364 / Scaling rejects: 36 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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Serial crystallography sample delivery | Method: fixed target |
-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.506
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6AO6 Resolution: 2.7→44.08 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.871 / SU B: 18.766 / SU ML: 0.376 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.457 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 134.89 Å2 / Biso mean: 54.282 Å2 / Biso min: 29.71 Å2
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Refinement step | Cycle: final / Resolution: 2.7→44.08 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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