+Open data
-Basic information
Entry | Database: PDB / ID: 1mas | ||||||
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Title | PURINE NUCLEOSIDE HYDROLASE | ||||||
Components | INOSINE-URIDINE NUCLEOSIDE N-RIBOHYDROLASE | ||||||
Keywords | HYDROLASE / PURINE NUCLEOSIDE HYDROLASE / PURINE NUCLEOSIDASE / IU-NH | ||||||
Function / homology | Function and homology information inosine nucleosidase / uridine nucleosidase / inosine nucleosidase activity / uridine nucleosidase activity / organonitrogen compound metabolic process / nucleotide metabolic process / metal ion binding Similarity search - Function | ||||||
Biological species | Crithidia fasciculata (eukaryote) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2.5 Å | ||||||
Authors | Degano, M. / Gopaul, D.N. / Scapin, G. / Schramm, V.L. / Sacchettini, J.C. | ||||||
Citation | Journal: Biochemistry / Year: 1996 Title: Three-dimensional structure of the inosine-uridine nucleoside N-ribohydrolase from Crithidia fasciculata. Authors: Degano, M. / Gopaul, D.N. / Scapin, G. / Schramm, V.L. / Sacchettini, J.C. #1: Journal: Biochemistry / Year: 1996 Title: Inosine-Uridine Nucleoside Hydrolase from Crithidia Fasciculata. Genetic Characterization, Crystallization, and Identification of Histidine 241 as a Catalytic Site Residue Authors: Gopaul, D.N. / Meyer, S.L. / Degano, M. / Sacchettini, J.C. / Schramm, V.L. #2: Journal: Biochemistry / Year: 1991 Title: Transition-State Analysis of Nucleoside Hydrolase from Crithidia Fasciculata Authors: Horenstein, B.A. / Parkin, D.W. / Estupinan, B. / Schramm, V.L. #3: Journal: J.Biol.Chem. / Year: 1991 Title: Nucleoside Hydrolase from Crithidia Fasciculata Authors: Parkin, D.W. / Horenstein, B.A. / Abdulah, D.R. / Estupinan, B. / Schramm, V.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1mas.cif.gz | 127.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1mas.ent.gz | 99.1 KB | Display | PDB format |
PDBx/mmJSON format | 1mas.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ma/1mas ftp://data.pdbj.org/pub/pdb/validation_reports/ma/1mas | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-0.3301, 0.943796, 0.016835), Vector: |
-Components
#1: Protein | Mass: 34206.480 Da / Num. of mol.: 2 / Mutation: P2A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Crithidia fasciculata (eukaryote) / Gene: IU-NH FROM C.FASCICULATA / Plasmid: PET3D-IUNH / Gene (production host): IU-NH FROM C.FASCICULATA / Production host: Escherichia coli (E. coli) / References: UniProt: Q27546, purine nucleosidase #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.76 Å3/Da / Density % sol: 55.49 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS Temperature: 22 ℃ / pH: 7.4 / Method: vapor diffusion, hanging drop | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction source | Wavelength: 1.5418 |
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Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jan 24, 1995 |
Radiation | Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→99 Å / Num. obs: 25989 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.071 |
Reflection | *PLUS Rmerge(I) obs: 0.075 |
-Processing
Software |
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Refinement | Resolution: 2.5→99 Å / σ(F): 2 Details: TORSION ANGLES NOT RESTRAINED. MEAN B VALUE IS 28.07 ANGSTROMS**. X-PLOR ALSO WAS USED. THE MOLECULE DENOTED BY CHAIN IDENTIFIER B SUFFERS A HIGHER DEGREE OF DISORDER, AS JUDGED FROM THE ...Details: TORSION ANGLES NOT RESTRAINED. MEAN B VALUE IS 28.07 ANGSTROMS**. X-PLOR ALSO WAS USED. THE MOLECULE DENOTED BY CHAIN IDENTIFIER B SUFFERS A HIGHER DEGREE OF DISORDER, AS JUDGED FROM THE TEMPERATURE FACTORS THAT ARE CONSIDERABLY HIGHER.
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Refinement step | Cycle: LAST / Resolution: 2.5→99 Å
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Refine LS restraints |
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Software | *PLUS Name: TNT / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.5 Å / Rfactor obs: 0.17 / Rfactor Rwork: 0.17 | ||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS Type: t_angle_deg / Dev ideal: 1.51 |