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- PDB-8tck: Apo crystal Structure of modified HIV reverse transcriptase p51 d... -

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Basic information

Entry
Database: PDB / ID: 8tck
TitleApo crystal Structure of modified HIV reverse transcriptase p51 domain (FPC1)
Componentsp51 subunit
KeywordsDNA BINDING PROTEIN / P51 subunit / HIV / AIDS / transferase
Biological speciesHIV whole-genome vector AA1305#18 (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: p51 subunit


Theoretical massNumber of molelcules
Total (without water)39,8451
Polymers39,8451
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.735, 63.952, 128.296
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein p51 subunit


Mass: 39845.266 Da / Num. of mol.: 1
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
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: 2.77 Å3/Da / Density % sol: 55.54 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Protein: 25mg/ml 50mM NaCl, 10mM Tris pH 8.0, 2mM DTT ML: 11% PEG 6000, 0.1M Tris pH 8.5

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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: Nov 30, 2018 / Details: VariMAX-HF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. obs: 22917 / % possible obs: 98.8 % / Redundancy: 11.8 % / Rpim(I) all: 0.021 / Rrim(I) all: 0.073 / Rsym value: 0.07 / Net I/σ(I): 9.5
Reflection shellResolution: 2.2→2.24 Å / Num. unique obs: 990 / CC1/2: 0.895 / Rpim(I) all: 0.165 / Rrim(I) all: 0.448 / Rsym value: 0.413 / % possible all: 86.1

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→25.259 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.97 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2396 1139 4.99 %
Rwork0.2075 --
obs0.2091 22806 98.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.2→25.259 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2553 0 0 55 2608
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0062629
X-RAY DIFFRACTIONf_angle_d0.733583
X-RAY DIFFRACTIONf_dihedral_angle_d11.5911555
X-RAY DIFFRACTIONf_chiral_restr0.048385
X-RAY DIFFRACTIONf_plane_restr0.005452
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2001-2.30010.30521290.2662446X-RAY DIFFRACTION91
2.3001-2.42130.2721410.24842693X-RAY DIFFRACTION99
2.4213-2.57290.34121430.25042698X-RAY DIFFRACTION100
2.5729-2.77130.28061420.25152704X-RAY DIFFRACTION100
2.7713-3.04980.29581440.2632711X-RAY DIFFRACTION99
3.0498-3.49010.25891410.22332750X-RAY DIFFRACTION100
3.4901-4.39340.20861460.17822768X-RAY DIFFRACTION100
4.3934-25.250.20021530.17642897X-RAY DIFFRACTION100
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)
12.34020.20280.64691.9023-0.70432.30120.10590.0149-0.0702-0.1566-0.1524-0.05220.10390.05790.04850.29260.03620.01750.30840.02970.324826.2466-12.9055-10.9251
21.5527-0.25051.14631.1803-0.42691.70120.13190.2506-0.1403-0.2222-0.1227-0.00260.07760.2018-0.00250.37520.05460.03910.40470.00660.330524.6938-8.8426-26.8888
32.06810.213-0.62631.17030.11532.30850.03720.0227-0.010.00470.13910.1664-0.1079-0.0449-0.15750.33530.02790.00990.33330.09580.37258.15-0.0092-16.8543
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 5 through 83 )
2X-RAY DIFFRACTION2chain 'B' and (resid 84 through 212 )
3X-RAY DIFFRACTION3chain 'B' and (resid 213 through 417 )

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