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Yorodumi- PDB-1j1f: Crystal structure of the RNase MC1 mutant N71T in complex with 5'-GMP -
+Open data
-Basic information
Entry | Database: PDB / ID: 1j1f | ||||||
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Title | Crystal structure of the RNase MC1 mutant N71T in complex with 5'-GMP | ||||||
Components | RIBONUCLEASE MC1 | ||||||
Keywords | HYDROLASE / Nucleic acid / RNA | ||||||
Function / homology | Function and homology information ribonuclease T2 / ribonuclease T2 activity / organic substance metabolic process / RNA binding Similarity search - Function | ||||||
Biological species | Momordica charantia (bitter melon) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Numata, T. / Suzuki, A. / Kakuta, Y. / Kimura, K. / Yao, M. / Tanaka, I. / Yoshida, Y. / Ueda, T. / Kimura, M. | ||||||
Citation | Journal: Biochemistry / Year: 2003 Title: Crystal Structures of the Ribonuclease MC1 Mutants N71T and N71S in Complex with 5'-GMP: Structural Basis for Alterations in Substrate Specificity Authors: Numata, T. / Suzuki, A. / Kakuta, Y. / Kimura, K. / Yao, M. / Tanaka, I. / Yoshida, Y. / Ueda, T. / Kimura, M. #1: Journal: BIOCHIM.BIOPHYS.ACTA / Year: 1999 Title: Crystal structure of a ribonuclease from the seeds of bitter gourd (Momordica charantia) at 1.75 A resolution Authors: Nakagawa, A. / Tanaka, I. / Sakai, R. / Nakashima, T. / Funatsu, G. / Kimura, M. #2: Journal: Biochem.Biophys.Res.Commun. / Year: 2000 Title: Crystal structures of the ribonuclease MC1 from bitter gourd seeds, complexed with 2'-UMP or 3'-UMP, reveal structural basis for uridine specificity Authors: Suzuki, A. / Yao, M. / Tanaka, I. / Numata, T. / Kikukawa, S. / Yamasaki, N. / Kimura, M. #3: Journal: BIOCHEMISTRY / Year: 2001 Title: Amino acid residues in ribonuclease MC1 from bitter gourd seeds which are essential for uridine specificity Authors: Numata, T. / Suzuki, A. / Yao, M. / Tanaka, I. / Kimura, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1j1f.cif.gz | 55.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1j1f.ent.gz | 38.7 KB | Display | PDB format |
PDBx/mmJSON format | 1j1f.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j1/1j1f ftp://data.pdbj.org/pub/pdb/validation_reports/j1/1j1f | HTTPS FTP |
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-Related structure data
Related structure data | 1j1gC 1ucgC 1bk7S C: citing same article (ref.) S: Starting model for refinement |
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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: 21344.109 Da / Num. of mol.: 1 / Mutation: N71T Source method: isolated from a genetically manipulated source Source: (gene. exp.) Momordica charantia (bitter melon) / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / References: UniProt: P23540, EC: 3.1.27.1 |
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#2: Chemical | ChemComp-5GP / |
#3: 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: 2.06 Å3/Da / Density % sol: 39.69 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.6 Details: 0.2M ammonium acetate, 0.1M tri-sodium citrate, 27.5% PEG8000, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Mar 1, 2002 / Details: mirrors |
Radiation | Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→50 Å / Num. all: 31008 / Num. obs: 31008 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.1 % / Biso Wilson estimate: 15.8 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.201 / Mean I/σ(I) obs: 3 / Num. unique all: 2890 / % possible all: 92.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1BK7 Resolution: 1.6→19.04 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 36.1703 Å2 / ksol: 0.367496 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 1.6→19.04 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.6→1.7 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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