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- PDB-1hrh: CRYSTAL STRUCTURE OF THE RIBONUCLEASE H DOMAIN OF HIV-1 REVERSE T... -

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Basic information

Entry
Database: PDB / ID: 1hrh
TitleCRYSTAL STRUCTURE OF THE RIBONUCLEASE H DOMAIN OF HIV-1 REVERSE TRANSCRIPTASE
ComponentsRIBONUCLEASE H
KeywordsHYDROLASE(ENDORIBONUCLEASE)
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral ...Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Nucleotidyltransferase; domain 5 / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / Resolution: 2.4 Å
AuthorsDavies /II, J.F. / Matthews, D.A.
Citation
Journal: Science / Year: 1991
Title: Crystal structure of the ribonuclease H domain of HIV-1 reverse transcriptase.
Authors: Davies 2nd., J.F. / Hostomska, Z. / Hostomsky, Z. / Jordan, S.R. / Matthews, D.A.
#1: Journal: J.Biol.Chem. / Year: 1991
Title: Proteolytic Release and Crystallization of the Rnase H Domain of Human Immunodeficiency Virus Type I Reverse Transcriptase
Authors: Hostomska, Z. / Matthews, D.A. / Davies /II, J.F. / Nodes, B.R. / Hostomsky, Z.
History
DepositionMar 6, 1991Processing site: BNL
Revision 1.0Jan 15, 1992Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 29, 2017Group: Derived calculations / Other
Category: pdbx_database_status / struct_conf / struct_conf_type
Item: _pdbx_database_status.process_site
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: RIBONUCLEASE H
B: RIBONUCLEASE H


Theoretical massNumber of molelcules
Total (without water)30,0622
Polymers30,0622
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)51.900, 51.900, 114.900
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.3698, -0.78761, 0.49286), (-0.78799, -0.54692, -0.28275), (0.49225, -0.28381, -0.82288)
Vector: 2.0138, 58.7575, 88.1949)
DetailsTHE TRANSFORMATION PRESENTED ON *MTRIX 1* RECORDS BELOW WILL YIELD APPROXIMATE COORDINATES FOR CHAIN *A* WHEN APPLIED TO CHAIN *B*.

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Components

#1: Protein RIBONUCLEASE H


Mass: 15031.130 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / References: UniProt: P03366

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.97 Å3/Da / Density % sol: 58.6 %
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
225 mMpotassium phosphate1drop
30.15 Msodium potassium tartrate1reservoir
420 %PEG80001reservoir
50.1 Msodium citrate1reservoir

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Data collection

RadiationScattering type: x-ray
Radiation wavelengthRelative weight: 1
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Num. obs: 13047 / % possible obs: 93.1 % / Num. measured all: 32084 / Rmerge(I) obs: 0.045
Reflection shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å / % possible obs: 90.4 % / Num. unique obs: 2521 / Num. measured obs: 3359 / Rmerge(I) obs: 0.198 / Mean I/σ(I) obs: 1.6

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Processing

SoftwareName: PROLSQ / Classification: refinement
RefinementRfactor obs: 0.2 / Highest resolution: 2.4 Å
Refinement stepCycle: LAST / Highest resolution: 2.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1803 0 0 0 1803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.022
X-RAY DIFFRACTIONp_angle_d0.051
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
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_restr
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
Software
*PLUS
Name: X-PLOR/PROLSQ / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.2
Solvent computation
*PLUS
Displacement parameters
*PLUS
LS refinement shell
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 2.6 Å / Total num. of bins used: 6 / Rfactor obs: 0.232

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