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Yorodumi- PDB-3rhn: HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN (HINT) FROM RABBIT COM... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3rhn | ||||||
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Title | HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN (HINT) FROM RABBIT COMPLEXED WITH GMP | ||||||
Components | HISTIDINE TRIAD NUCLEOTIDE-BINDING PROTEIN | ||||||
Keywords | NUCLEOTIDE-BINDING PROTEIN / HISTIDINE | ||||||
Function / homology | Function and homology information purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases ...purine ribonucleotide catabolic process / adenylylsulfatase activity / Hydrolases; Acting on phosphorus-nitrogen bonds / adenosine 5'-monophosphoramidase activity / deSUMOylase activity / protein desumoylation / sulfur compound metabolic process / histone deacetylase complex / intrinsic apoptotic signaling pathway by p53 class mediator / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / hydrolase activity / nucleotide binding / regulation of DNA-templated transcription / proteolysis / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / REFINEMENT FROM MIR STRUCTURE OF HINT-ADENOSINE / Resolution: 2.1 Å | ||||||
Authors | Brenner, C. / Garrison, P. / Gilmour, J. / Peisach, D. / Ringe, D. / Petsko, G.A. / Lowenstein, J.M. | ||||||
Citation | Journal: Nat.Struct.Biol. / Year: 1997 Title: Crystal structures of HINT demonstrate that histidine triad proteins are GalT-related nucleotide-binding proteins. Authors: Brenner, C. / Garrison, P. / Gilmour, J. / Peisach, D. / Ringe, D. / Petsko, G.A. / Lowenstein, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3rhn.cif.gz | 36.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3rhn.ent.gz | 24.2 KB | Display | PDB format |
PDBx/mmJSON format | 3rhn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rh/3rhn ftp://data.pdbj.org/pub/pdb/validation_reports/rh/3rhn | HTTPS FTP |
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-Related 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: 12584.530 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Oryctolagus cuniculus (rabbit) Description: RABBIT HINT CDNA WAS CLONED FROM HEART LIBRARY, EXPRESSED IN ESCHERICHIA COLI, AND PURIFIED BY ADENOSINE-AGAROSE AFFINITY CHROMATOGRAPHY Gene: HINT / Organ: HEART / Plasmid: PSGA02-HINT / Gene (production host): HINT / Production host: Escherichia coli (E. coli) / Strain (production host): JM109/DE3/LACIQ / References: UniProt: P80912 |
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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: 2.23 Å3/Da / Density % sol: 45 % Description: HINT-GMP, ISOMORPHOUS WITH HINT-ADENOSINE, WAS DETERMINED BY REFINEMENT FROM THE HINT-ADENOSINE COORDINATES. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: 30% POLYETHYLENE GLYCOL 8000, 0.1 M SODIUM ACETATE, 0.1 M SODIUM CACODYLATE, PH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 7.4 / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 277 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418 |
Detector | Type: RIGAKU / Detector: IMAGE PLATE / Date: Nov 1, 1994 / Details: COLLIMATOR |
Radiation | Monochromator: NI FILTER / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→27.74 Å / Num. obs: 49822 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rsym value: 0.03 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 4 % / Mean I/σ(I) obs: 5 / Rsym value: 0.06 / % possible all: 100 |
Reflection | *PLUS Num. obs: 7463 / Num. measured all: 49822 / Rmerge(I) obs: 0.03 |
-Processing
Software |
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Refinement | Method to determine structure: REFINEMENT FROM MIR STRUCTURE OF HINT-ADENOSINE Resolution: 2.1→10 Å / Rfactor Rfree error: 0.01 / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.1→10 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.19 Å / Rfactor Rfree error: 0.044 / Total num. of bins used: 8
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Xplor file |
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Software | *PLUS Name: X-PLOR / Version: 3.1 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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