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

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Basic information

Entry
Database: PDB / ID: 8tcj
TitleApo crystal Structure of modified HIV reverse transcriptase p51 domain (FPC2)
Componentsp51 subunit
KeywordsDNA BINDING PROTEIN / P51 subunit / HIV / AIDS / transferase
Biological speciesHIV whole-genome vector AA1305#18 (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.848 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)40,3321
Polymers40,3321
Non-polymers00
Water1,65792
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.080, 105.080, 54.531
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein p51 subunit


Mass: 40331.938 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.: 92 / 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: 2.15 Å3/Da / Density % sol: 42.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein: 25mg/ml FPC2, 50mM NaCl, 10mM Tris pH 7.0, 1mM TCEP, 5%DMSO, 0.25mM azide, 5mM fisetin Res: 25% PEG1500, 0.1M TBG pH 7.0
Temp details: room temp

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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: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Sep 4, 2019 / Details: VariMAX-HF mirrors
RadiationMonochromator: VariMAX-HF mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 1.848→50 Å / Num. obs: 29994 / % possible obs: 100 % / Redundancy: 11.2 % / Rrim(I) all: 0.039 / Rsym value: 0.038 / Net I/σ(I): 24.3
Reflection shellResolution: 1.85→1.88 Å / Redundancy: 2.2 % / Num. unique obs: 1497 / CC1/2: 0.883 / CC star: 0.968 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.16_3549: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.848→46.776 Å / SU ML: 0.27 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2523 1491 5.01 %
Rwork0.2158 --
obs0.2177 29756 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.848→46.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2471 0 0 92 2563
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0162546
X-RAY DIFFRACTIONf_angle_d1.2573469
X-RAY DIFFRACTIONf_dihedral_angle_d11.2621497
X-RAY DIFFRACTIONf_chiral_restr0.073372
X-RAY DIFFRACTIONf_plane_restr0.01434
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.848-1.90720.37921330.35972545X-RAY DIFFRACTION99
1.9072-1.97540.34551360.30112550X-RAY DIFFRACTION100
1.9754-2.05450.30391340.26852552X-RAY DIFFRACTION100
2.0545-2.1480.28761310.24572580X-RAY DIFFRACTION100
2.148-2.26120.31191370.24312574X-RAY DIFFRACTION100
2.2612-2.40290.26331330.2542548X-RAY DIFFRACTION99
2.4029-2.58840.26251300.2562523X-RAY DIFFRACTION98
2.5884-2.84880.26561340.24922526X-RAY DIFFRACTION98
2.8488-3.2610.28691330.22442563X-RAY DIFFRACTION99
3.261-4.10810.23581440.19752617X-RAY DIFFRACTION100
4.1081-46.7760.20991460.1752687X-RAY DIFFRACTION99
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)
14.1438-0.26650.71333.8186-1.85924.242-0.1234-0.170.06360.215-0.1312-0.2829-0.4848-0.1045-0.02380.32830.0155-0.08750.2627-0.01930.220441.0699-15.95268.9717
21.2951-0.71852.08361.2183-1.57593.5112-0.2154-0.4684-0.06530.32050.16390.2332-0.4371-0.5908-0.01410.38880.079-0.02950.46-0.04760.374132.3588-16.82948.2356
32.0854-2.0023-0.00663.7721-1.38962.5438-0.0418-0.2825-0.24670.0720.3460.37540.0422-0.08010.00070.2523-0.0245-0.03570.45940.02930.509519.3516-13.0834-3.486
44.8688-1.121.74573.60830.71073.08590.28370.6741-0.6723-0.5416-0.0036-0.16280.00690.45360.0140.39450.034-0.07460.3568-0.12090.354637.7204-25.4522-12.1625
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'B' and (resid 6 through 83 )
2X-RAY DIFFRACTION2chain 'B' and (resid 84 through 153 )
3X-RAY DIFFRACTION3chain 'B' and (resid 154 through 325 )
4X-RAY DIFFRACTION4chain 'B' and (resid 326 through 417 )

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