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Yorodumi- PDB-4csw: Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydr... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4csw | ||||||
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Title | Rhodothermus marinus YCFD-like ribosomal protein L16 Arginyl hydroxylase | ||||||
Components | CUPIN 4 FAMILY PROTEIN | ||||||
Keywords | OXIDOREDUCTASE / 2-OXOGLUTARATE AND IRON DEPENDENT OXYGENASE / DOUBLE STRANDED BETA HELIX FOLD | ||||||
Function / homology | Function and homology information 50S ribosomal protein L16 arginine hydroxylase; Chain A, Domain 2 / ROXA-like, winged helix / ROXA-like winged helix / JmjC domain-containing / JmjC domain / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. ...50S ribosomal protein L16 arginine hydroxylase; Chain A, Domain 2 / ROXA-like, winged helix / ROXA-like winged helix / JmjC domain-containing / JmjC domain / Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 / Cupin / A domain family that is part of the cupin metalloenzyme superfamily. / JmjC domain / JmjC domain profile. / Jelly Rolls / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta Similarity search - Domain/homology | ||||||
Biological species | RHODOTHERMUS MARINUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.821 Å | ||||||
Authors | McDonough, M.A. / Sekirnik, R. / Schofield, C.J. | ||||||
Citation | Journal: Nature / Year: 2014 Title: Ribosomal oxygenases are structurally conserved from prokaryotes to humans. Authors: Chowdhury, R. / Sekirnik, R. / Brissett, N.C. / Krojer, T. / Ho, C.H. / Ng, S.S. / Clifton, I.J. / Ge, W. / Kershaw, N.J. / Fox, G.C. / Muniz, J.R.C. / Vollmar, M. / Phillips, C. / Pilka, E. ...Authors: Chowdhury, R. / Sekirnik, R. / Brissett, N.C. / Krojer, T. / Ho, C.H. / Ng, S.S. / Clifton, I.J. / Ge, W. / Kershaw, N.J. / Fox, G.C. / Muniz, J.R.C. / Vollmar, M. / Phillips, C. / Pilka, E.S. / Kavanagh, K.L. / von Delft, F. / Oppermann, U. / McDonough, M.A. / Doherty, A.J. / Schofield, C.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4csw.cif.gz | 322.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4csw.ent.gz | 262.9 KB | Display | PDB format |
PDBx/mmJSON format | 4csw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cs/4csw ftp://data.pdbj.org/pub/pdb/validation_reports/cs/4csw | HTTPS FTP |
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-Related structure data
Related structure data | 2xdvC 4bu2C 4bxfC 4ccjC 4cckC 4cclSC 4ccmC 4ccnC 4ccoC 4cugC 4litC 4liuC 4livC 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 on special symmetry positions |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.9266, -0.0858, -0.3661), Vector: |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 45803.164 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOTHERMUS MARINUS (bacteria) / Strain: DSM 4252 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: D0MK34 |
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-Non-polymers , 5 types, 146 molecules
#2: Chemical | ChemComp-CIT / | ||||||
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#3: Chemical | #4: Chemical | ChemComp-GOL / | #5: Chemical | ChemComp-MN / | #6: 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.66MM PROTEIN, 1MM MNCL2, 2MM IOX3, 50%(V/V) TACSIMATE, pH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 24, 2013 / Details: MIRRORS |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 2.82→30.21 Å / Num. obs: 27522 / % possible obs: 99.6 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 70.39 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 7.6 |
Reflection shell | Resolution: 2.82→2.89 Å / Redundancy: 5 % / Rmerge(I) obs: 0.8 / Mean I/σ(I) obs: 2.1 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 4CCL Resolution: 2.821→30.206 Å / SU ML: 0.39 / σ(F): 1.34 / Phase error: 23.23 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 78.28 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.821→30.206 Å
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Refine LS restraints |
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LS refinement shell |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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