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- PDB-8tcl: Crystal Structure of modified HIV reverse transcriptase p51 domai... -

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Basic information

Entry
Database: PDB / ID: 8tcl
TitleCrystal Structure of modified HIV reverse transcriptase p51 domain (FPC2) with picrate bound
Componentsp51 subunit
KeywordsDNA BINDING PROTEIN / P51 subunit / HIV / AIDS / transferase / picric acid
Function / homologyPICRIC ACID
Function and homology information
Biological speciesHIV whole-genome vector AA1305#18 (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsPedersen, L.C. / London, R.E.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIA-ES050111 United States
National Institutes of Health/National Institute of Environmental Health Sciences (NIH/NIEHS)ZIC-ES102645 United States
CitationJournal: Biomolecules / Year: 2023
Title: Targeting the Structural Maturation Pathway of HIV-1 Reverse Transcriptase.
Authors: Kirby, T.W. / Gabel, S.A. / DeRose, E.F. / Perera, L. / Krahn, J.M. / Pedersen, L.C. / London, R.E.
History
DepositionJul 2, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 17, 2024Provider: repository / Type: Initial release
Revision 1.1Feb 12, 2025Group: Database references / Structure summary / Category: citation / citation_author / pdbx_entry_details
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: p51 subunit
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,4934
Polymers39,8051
Non-polymers6873
Water2,648147
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.579, 99.624, 104.161
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-503-

TNF

21B-503-

TNF

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Components

#1: Protein p51 subunit


Mass: 39805.246 Da / Num. of mol.: 1 / Mutation: E203S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HIV whole-genome vector AA1305#18 (others)
Production host: Escherichia coli (E. coli) / References: RNA-directed DNA polymerase
#2: Chemical ChemComp-TNF / PICRIC ACID / 2,4,6-TRINITROPHENOL


Mass: 229.104 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H3N3O7 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.53 Å3/Da / Density % sol: 51.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: protein: 25mg/ml 10mM Tris pH 7.4, 40mM NaCl, 1mM TCEP, 0.25mM azide, 10mM picric acid ML: 20%PEG3350, 0.2M trisodium citrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.514 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Sep 19, 2019 / Details: VarimaxHF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 28616 / % possible obs: 96.1 % / Redundancy: 4.2 % / Rpim(I) all: 0.024 / Rrim(I) all: 0.054 / Rsym value: 0.048 / Net I/σ(I): 10.7
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 1214 / CC1/2: 0.862 / Rpim(I) all: 9.268 / Rrim(I) all: 0.473 / Rsym value: 0.386 / % possible all: 84.1

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→21.62 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 26.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2288 1428 5 %
Rwork0.1982 --
obs0.1998 28558 95.91 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.95→21.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2490 0 48 147 2685
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011
X-RAY DIFFRACTIONf_angle_d1.16
X-RAY DIFFRACTIONf_dihedral_angle_d14.139925
X-RAY DIFFRACTIONf_chiral_restr0.06383
X-RAY DIFFRACTIONf_plane_restr0.009462
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.95-2.020.28911190.25482375X-RAY DIFFRACTION86
2.02-2.10.25681490.23082722X-RAY DIFFRACTION97
2.1-2.190.25381390.21392772X-RAY DIFFRACTION100
2.19-2.310.28191510.21422792X-RAY DIFFRACTION99
2.31-2.460.28911520.22222743X-RAY DIFFRACTION98
2.46-2.640.27831410.22882768X-RAY DIFFRACTION97
2.64-2.910.24671470.21792731X-RAY DIFFRACTION97
2.91-3.330.2491400.21242720X-RAY DIFFRACTION96
3.33-4.190.1871430.17772730X-RAY DIFFRACTION96
4.19-21.620.19471470.17382777X-RAY DIFFRACTION93
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
13.0221-0.4315-0.09731.00020.39191.49080.12760.0553-0.0271-0.0463-0.02180.01380.15430.0974-00.2399-0.018-0.01330.19220.00760.2335-14.0116-3.3345-23.4762
22.28320.5699-0.97080.5819-0.81841.3288-0.0139-0.0730.08490.06750.0205-0.01790.1130.089100.22840.0092-0.0040.2065-0.02940.1951-22.6734-5.9697-15.937
32.2433-2.2212-0.16632.64220.28641.5806-0.2176-0.1625-0.35980.16550.21920.24030.37840.1412-0.00740.32940.00330.00270.24270.00630.2647-34.041-19.1858-11.5517
44.1011-1.3829-1.44312.92671.66042.9607-0.1736-0.27580.0958-0.11310.4707-0.6630.48990.23860.00380.5190.12520.04080.3573-0.04340.4184-12.6236-27.8239-16.0903
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 0 through 83 )
2X-RAY DIFFRACTION2chain 'B' and (resid 84 through 174 )
3X-RAY DIFFRACTION3chain 'B' and (resid 175 through 325 )
4X-RAY DIFFRACTION4chain 'B' and (resid 326 through 417 )

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