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- PDB-3hyf: Crystal structure of HIV-1 RNase H p15 with engineered E. coli lo... -

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Basic information

Entry
Database: PDB / ID: 3hyf
TitleCrystal structure of HIV-1 RNase H p15 with engineered E. coli loop and active site inhibitor
ComponentsReverse transcriptase/RNaseH
KeywordsHYDROLASE / RNase H / HIV-1 / di-valent metal nucleic acid cleavage mechanism / di-valent metal coordination / Aspartyl protease / DNA integration / DNA recombination / Endonuclease / Multifunctional enzyme / Nuclease / Nucleotidyltransferase / Protease / RNA-directed DNA polymerase / Transferase / Magnesium / Metal-binding
Function / homology
Function and homology information


DNA replication, removal of RNA primer / ribonuclease H / DNA integration / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / endonuclease activity / nucleic acid binding / aspartic-type endopeptidase activity / magnesium ion binding / proteolysis ...DNA replication, removal of RNA primer / ribonuclease H / DNA integration / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / endonuclease activity / nucleic acid binding / aspartic-type endopeptidase activity / magnesium ion binding / proteolysis / identical protein binding / metal ion binding / cytoplasm
Similarity search - Function
Ribonuclease HI / : / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain ...Ribonuclease HI / : / Ribonuclease H-like superfamily/Ribonuclease H / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / RNase H / RNase H type-1 domain profile. / Ribonuclease H domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Reverse transcriptase (RNA-dependent DNA polymerase) / Nucleotidyltransferase; domain 5 / 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
ACETATE ION / : / Chem-ON1 / Ribonuclease HI / Reverse transcriptase/RNaseH
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
Escherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLansdon, E.B. / Kirschberg, T.A.
CitationJournal: J.Med.Chem. / Year: 2009
Title: RNase H active site inhibitors of human immunodeficiency virus type 1 reverse transcriptase: design, biochemical activity, and structural information.
Authors: Kirschberg, T.A. / Balakrishnan, M. / Squires, N.H. / Barnes, T. / Brendza, K.M. / Chen, X. / Eisenberg, E.J. / Jin, W. / Kutty, N. / Leavitt, S. / Liclican, A. / Liu, Q. / Liu, X. / Mak, J. ...Authors: Kirschberg, T.A. / Balakrishnan, M. / Squires, N.H. / Barnes, T. / Brendza, K.M. / Chen, X. / Eisenberg, E.J. / Jin, W. / Kutty, N. / Leavitt, S. / Liclican, A. / Liu, Q. / Liu, X. / Mak, J. / Perry, J.K. / Wang, M. / Watkins, W.J. / Lansdon, E.B.
History
DepositionJun 22, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Nov 16, 2011Group: Atomic model
Revision 1.3Aug 16, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / 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_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Mar 13, 2024Group: Source and taxonomy / Category: entity_src_gen

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Reverse transcriptase/RNaseH
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5907
Polymers16,9211
Non-polymers6686
Water3,405189
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.717, 90.326, 113.334
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11A-116-

HOH

21A-606-

HOH

31A-608-

HOH

41A-609-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Reverse transcriptase/RNaseH


Mass: 16921.463 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1, (gene. exp.) Escherichia coli (E. coli)
Gene: pol, Reverse Transcriptase (amino acids 427-560) / Plasmid: pET30b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3
References: UniProt: Q72547, UniProt: P0A7Y4, ribonuclease H

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Non-polymers , 5 types, 195 molecules

#2: Chemical ChemComp-MN / MANGANESE (II) ION / RNase HI / Ribonuclease H / RNase H


Mass: 54.938 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mn
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-ON1 / 2-(3,4-dichlorobenzyl)-5,6-dihydroxypyrimidine-4-carboxylic acid


Mass: 315.109 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H8Cl2N2O4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3 Å3/Da / Density % sol: 59.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 1.0M MgSO4, 100mM sodium acetate pH 4.6, 5mM manganese chloride, 5mM TCEP, 1.5mM inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 2, 2008
RadiationMonochromator: Single crystal, cylindrically bent, Si(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.6→29.1 Å / Num. all: 26856 / Num. obs: 26856 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Biso Wilson estimate: 17.8 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 37.5
Reflection shellResolution: 1.6→1.63 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.347 / Mean I/σ(I) obs: 2.9 / Num. unique all: 1019 / % possible all: 76.4

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Processing

Software
NameVersionClassification
BOSdata collection
AMoREphasing
CNX2005refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB code 1HRH

1hrh


Resolution: 1.7→29.1 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 78272.72 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1050 4.8 %RANDOM
Rwork0.196 ---
obs0.198 22030 96.1 %-
all-22881 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 70.5694 Å2 / ksol: 0.396692 e/Å3
Displacement parametersBiso mean: 30.3 Å2
Baniso -1Baniso -2Baniso -3
1-8.19 Å20 Å20 Å2
2---6.18 Å20 Å2
3----2.01 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.22 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.1 Å0.13 Å
Refinement stepCycle: LAST / Resolution: 1.7→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1135 0 38 189 1362
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg0.9
X-RAY DIFFRACTIONc_dihedral_angle_d19.4
X-RAY DIFFRACTIONc_improper_angle_d0.62
X-RAY DIFFRACTIONc_mcbond_it5.541.5
X-RAY DIFFRACTIONc_mcangle_it7.152
X-RAY DIFFRACTIONc_scbond_it9.932
X-RAY DIFFRACTIONc_scangle_it11.212.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.218 168 5 %
Rwork0.247 3192 -
obs--89 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.pprotein.top
X-RAY DIFFRACTION2on1.paron1.top
X-RAY DIFFRACTION3water_rep.parwater.top
X-RAY DIFFRACTION4ion.paramion.top

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