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Yorodumi- PDB-1rnh: STRUCTURE OF RIBONUCLEASE H PHASED AT 2 ANGSTROMS RESOLUTION BY M... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1rnh | ||||||
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Title | STRUCTURE OF RIBONUCLEASE H PHASED AT 2 ANGSTROMS RESOLUTION BY MAD ANALYSIS OF THE SELENOMETHIONYL PROTEIN | ||||||
Components | RIBONUCLEASE HI | ||||||
Keywords | HYDROLASE(ENDORIBONUCLEASE) | ||||||
Function / homology | Function and homology information DNA replication, removal of RNA primer / RNA catabolic process / ribonuclease H / RNA-DNA hybrid ribonuclease activity / endonuclease activity / nucleic acid binding / magnesium ion binding / cytoplasm Similarity search - Function | ||||||
Biological species | Escherichia coli (E. coli) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 2 Å | ||||||
Authors | Yang, W. / Hendrickson, W.A. / Crouch, R.J. / Satow, Y. | ||||||
Citation | Journal: Science / Year: 1990 Title: Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein. Authors: Yang, W. / Hendrickson, W.A. / Crouch, R.J. / Satow, Y. #1: Journal: J.Biol.Chem. / Year: 1990 Title: Expression, Purification, and Crystallization of Natural and Selenomethionyl Recombinant Ribonuclease H from Escherichia Coli Authors: Yang, W. / Hendrickson, W.A. / Kalman, E.T. / Crouch, R.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1rnh.cif.gz | 40.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1rnh.ent.gz | 31.9 KB | Display | PDB format |
PDBx/mmJSON format | 1rnh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/rn/1rnh ftp://data.pdbj.org/pub/pdb/validation_reports/rn/1rnh | 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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Atom site foot note | 1: RESIDUE 17 IS A CIS PROLINE. 2: THERE ARE THREE REGIONS OF LOW (OR NO) DENSITY, CONSISTING OF MSE 1 - LYS 3 (N TERMINUS), TYR 28 - ARG 31 (LOOP BETWEEN BETA STRAND 1 AND BETA STRAND 2), AND VAL 153 - VAL 155 (C TERMINUS). NO ...2: THERE ARE THREE REGIONS OF LOW (OR NO) DENSITY, CONSISTING OF MSE 1 - LYS 3 (N TERMINUS), TYR 28 - ARG 31 (LOOP BETWEEN BETA STRAND 1 AND BETA STRAND 2), AND VAL 153 - VAL 155 (C TERMINUS). NO COORDINATES ARE PRESENT IN THIS ENTRY FOR MSE 1 AND THE THREE C-TERMINAL RESIDUES. |
-Components
#1: Protein | Mass: 17810.578 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Production host: Escherichia coli (E. coli) References: UniProt: P00647, UniProt: P0A7Y4*PLUS, ribonuclease H |
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#2: Chemical | ChemComp-SO4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 1.84 Å3/Da / Density % sol: 33.09 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | *PLUS pH: 7.5 / Method: vapor diffusion, hanging drop | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Radiation | Scattering type: x-ray |
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Radiation wavelength | Relative weight: 1 |
-Processing
Software | Name: PROLSQ / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Resolution: 2→10 Å / Rfactor obs: 0.198 / σ(F): 4 Details: THERE ARE THREE REGIONS OF LOW (OR NO) DENSITY, CONSISTING OF MSE 1 - LYS 3 (N TERMINUS), TYR 28 - ARG 31 (LOOP BETWEEN BETA STRAND 1 AND BETA STRAND 2), AND VAL 153 - VAL 155 (C TERMINUS). ...Details: THERE ARE THREE REGIONS OF LOW (OR NO) DENSITY, CONSISTING OF MSE 1 - LYS 3 (N TERMINUS), TYR 28 - ARG 31 (LOOP BETWEEN BETA STRAND 1 AND BETA STRAND 2), AND VAL 153 - VAL 155 (C TERMINUS). NO COORDINATES ARE PRESENT IN THIS ENTRY FOR MSE 1 AND THE THREE C-TERMINAL RESIDUES. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→10 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Lowest resolution: 10 Å / Rfactor all: 0.198 / Num. reflection obs: 8646 / Rfactor Rfree: 0.198 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |