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- PDB-1rnh: STRUCTURE OF RIBONUCLEASE H PHASED AT 2 ANGSTROMS RESOLUTION BY M... -

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Basic information

Entry
Database: PDB / ID: 1rnh
TitleSTRUCTURE OF RIBONUCLEASE H PHASED AT 2 ANGSTROMS RESOLUTION BY MAD ANALYSIS OF THE SELENOMETHIONYL PROTEIN
ComponentsRIBONUCLEASE HI
KeywordsHYDROLASE(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
Ribonuclease HI / : / Ribonuclease H-like superfamily/Ribonuclease H / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Nucleotidyltransferase; domain 5 / Ribonuclease H superfamily / Ribonuclease H-like superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribonuclease HI / Ribonuclease HI
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsYang, 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
DepositionJul 11, 1990Processing site: BNL
Revision 1.0Oct 15, 1991Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 5, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE HI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,9072
Polymers17,8111
Non-polymers961
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.790, 86.340, 36.310
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Atom site foot note1: 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.

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Components

#1: Protein RIBONUCLEASE HI


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
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 33.09 %
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
21.5 %satammonium sulfate1drop
310 mMHEPES1dropr
420-25 %(w/w)PEG33501reservoir
51.5 %satammonium sulfate1reservoir
61 mMEDTA1reservoir
71 mMdithiothreitol1reservoir
810 mMTris-HCl1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementResolution: 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 stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1209 0 5 86 1300
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0150.02
X-RAY DIFFRACTIONp_angle_d0.0340.03
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0130.02
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr0.1720.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
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

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