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

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Basic information

Entry
Database: PDB / ID: 8tcm
TitleCrystal Structure of modified HIV reverse transcriptase p51 domain (FPC1) with picric acid and Xanthene-1,3,6,8-tetrol bound
Componentsp51 subunit
KeywordsDNA BINDING PROTEIN / P51 subunit / HIV / AIDS / transferase / Xanthene-1 / 3 / 6 / 8-tetrol / picric acid
Function / homologyPICRIC ACID / :
Function and homology information
Biological speciesHIV whole-genome vector AA1305#18 (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.82 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)40,9856
Polymers39,8051
Non-polymers1,1805
Water3,495194
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.309, 99.406, 104.747
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number23
Space group name H-MI222
Space group name HallI22
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z
#4: -x,-y,z
#5: x+1/2,y+1/2,z+1/2
#6: x+1/2,-y+1/2,-z+1/2
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-503-

TNF

21B-503-

TNF

31B-503-

TNF

41B-503-

TNF

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Components

#1: Protein p51 subunit


Mass: 39805.246 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)
#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: Chemical ChemComp-ZQT / 9H-xanthene-1,3,6,8-tetrol


Mass: 246.215 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C13H10O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 51.34 %
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: 10% PEG6000, .1M MES pH 6.5

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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: Dec 7, 2019 / Details: VarimaxHF
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.514 Å / Relative weight: 1
ReflectionResolution: 1.82→50 Å / Num. obs: 36046 / % possible obs: 98.7 % / Redundancy: 6.2 % / Biso Wilson estimate: 28.42 Å2 / Rpim(I) all: 0.016 / Rrim(I) all: 0.041 / Rsym value: 0.038 / Net I/σ(I): 15.1
Reflection shellResolution: 1.82→1.85 Å / Redundancy: 2.4 % / Num. unique obs: 1454 / CC1/2: 0.897 / Rpim(I) all: 0.266 / Rrim(I) all: 0.451 / Rsym value: 0.36 / % possible all: 81.2

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
PHENIX1.20.1_4487refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.82→22.52 Å / SU ML: 0.1598 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.1797
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.223 1801 5.01 %
Rwork0.1935 34169 -
obs0.1949 35970 98.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 37.58 Å2
Refinement stepCycle: LAST / Resolution: 1.82→22.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2465 0 84 194 2743
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142701
X-RAY DIFFRACTIONf_angle_d1.20643703
X-RAY DIFFRACTIONf_chiral_restr0.068387
X-RAY DIFFRACTIONf_plane_restr0.0096470
X-RAY DIFFRACTIONf_dihedral_angle_d16.2639942
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.870.31971110.27162206X-RAY DIFFRACTION83.77
1.87-1.920.2611450.23342591X-RAY DIFFRACTION98.35
1.92-1.990.23981340.21562628X-RAY DIFFRACTION99.93
1.99-2.060.23081500.19212647X-RAY DIFFRACTION100
2.06-2.140.19821360.17792644X-RAY DIFFRACTION100
2.14-2.240.25241360.17872638X-RAY DIFFRACTION100
2.24-2.350.22981340.1912667X-RAY DIFFRACTION99.93
2.35-2.50.22971400.21492661X-RAY DIFFRACTION99.96
2.5-2.690.25241420.20752643X-RAY DIFFRACTION99.75
2.69-2.960.22431430.20862665X-RAY DIFFRACTION99.22
2.96-3.390.23011470.19922658X-RAY DIFFRACTION99.19
3.39-4.270.1931360.16872712X-RAY DIFFRACTION99.68
4.27-22.520.21551470.19172809X-RAY DIFFRACTION99.6
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)
13.26584532611-1.21760217555-1.083866657632.273371487120.7043943657732.878507775550.1301463072980.0908341800680.0337404718817-0.112987355649-0.076388513933-0.02332220168360.1040602917260.0470832440259-0.03969431048510.171763921979-0.0274501399363-0.02333347505240.1568171194130.003505141434680.227188017548-15.0302015165-3.32961822567-24.1637274489
22.318957652650.0197645075728-0.4542773736360.848093108494-0.2316758597450.913513476559-0.0336387381703-0.0809371292621-0.1138924349580.03777426153410.05517245678330.03702055699140.1305176704510.0279984631033-0.00588652040080.2102913237690.00896439471877-0.02413627432810.203995590193-0.01498858034560.177634455186-28.1240065601-10.9160549152-15.2307100704
34.81972447064-2.09890204438-3.101805036964.093183227961.617341996055.53358255543-0.172463208095-0.3939621910290.316510534232-0.1141728306210.46872778825-0.5107348321140.5527900656460.530092731738-0.2880622102540.3508491773940.08267063720950.02534976148020.30192888306-0.07422728457520.31185106403-13.4274789864-27.394951723-15.2573842427
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: B / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid -1 through 83 )-1 - 831 - 81
22chain 'B' and (resid 84 through 238 )84 - 23882 - 217
33chain 'B' and (resid 239 through 416 )239 - 416218 - 313

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