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- PDB-8tmw: HTLV-1 capsid protein N-terminal domain triclinic crystal form wi... -

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Basic information

Entry
Database: PDB / ID: 8tmw
TitleHTLV-1 capsid protein N-terminal domain triclinic crystal form with sulphate ion
Componentscapsid protein p24
KeywordsVIRAL PROTEIN / capsid
Function / homology
Function and homology information


viral nucleocapsid / nucleic acid binding / viral translational frameshifting / structural molecule activity / zinc ion binding
Similarity search - Function
Delta-retroviral matrix protein / Major core protein p19 / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger ...Delta-retroviral matrix protein / Major core protein p19 / : / gag protein p24 N-terminal domain / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile.
Similarity search - Domain/homology
Biological speciesHTLV-1 subtype C (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 Å
AuthorsYu, R.J. / Li, N. / Jacques, D.A.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
Wellcome Trust214344/Z/18/Z United Kingdom
CitationJournal: To Be Published
Title: HTLV-1 capsid protein N-terminal domain triclinic crystal form with sulphate ion
Authors: Yu, R.J. / Li, N. / Jacques, D.A.
History
DepositionJul 31, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 7, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2412
Polymers14,1451
Non-polymers961
Water91951
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)28.659, 30.604, 36.388
Angle α, β, γ (deg.)65.62, 70.73, 72.03
Int Tables number1
Space group name H-MP1

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Components

#1: Protein capsid protein p24


Mass: 14144.993 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HTLV-1 subtype C (virus) / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Rosetta2 / References: UniProt: U3RC00
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 51 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 1.9 Å3/Da / Density % sol: 35.28 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% ethylene glycol, 10% PEG 8K, 0.1 M HEPES, pH7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 1, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.71→32.22 Å / Num. obs: 10396 / % possible obs: 91.6 % / Redundancy: 3.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.031 / Rrim(I) all: 0.059 / Χ2: 0.52 / Net I/σ(I): 10.2 / Num. measured all: 37131
Reflection shellResolution: 1.71→1.74 Å / % possible obs: 78.3 % / Redundancy: 3.2 % / Rmerge(I) obs: 1.571 / Num. measured all: 1521 / Num. unique obs: 475 / CC1/2: 0.378 / Rpim(I) all: 0.986 / Rrim(I) all: 1.861 / Χ2: 0.42 / Net I/σ(I) obs: 0.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 8ERE

8ere


Resolution: 1.71→32.22 Å / SU ML: 0.27 / Cross valid method: THROUGHOUT / σ(F): 1.96 / Phase error: 30.6 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2472 1035 10.01 %
Rwork0.1995 --
obs0.2042 10339 91.76 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.71→32.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms965 0 5 51 1021
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.547
X-RAY DIFFRACTIONf_dihedral_angle_d3.738130
X-RAY DIFFRACTIONf_chiral_restr0.034146
X-RAY DIFFRACTIONf_plane_restr0.005180
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.71-1.80.38411410.351270X-RAY DIFFRACTION88
1.8-1.910.3131400.27991260X-RAY DIFFRACTION86
1.91-2.060.31071500.24641339X-RAY DIFFRACTION94
2.06-2.270.26751530.19531379X-RAY DIFFRACTION95
2.27-2.60.26071520.1991370X-RAY DIFFRACTION94
2.6-3.270.20981480.19921327X-RAY DIFFRACTION92
3.27-32.220.23231510.17591359X-RAY DIFFRACTION93

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