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

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Basic information

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


viral process / viral nucleocapsid / nucleic acid binding / 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: 1.73 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 phosphate 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)14,2402
Polymers14,1451
Non-polymers951
Water1,06359
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)28.195, 30.720, 36.081
Angle α, β, γ (deg.)65.19, 79.30, 89.56
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) / References: UniProt: U3RC00
#2: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 1.96 Å3/Da / Density % sol: 37.39 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% ethylene glycol, 10% PEG 8K, 0.1 M HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95372 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 18, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95372 Å / Relative weight: 1
ReflectionResolution: 1.64→32.08 Å / Num. obs: 12672 / % possible obs: 95.9 % / Redundancy: 3.5 % / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.042 / Rrim(I) all: 0.079 / Χ2: 0.39 / Net I/σ(I): 6.2 / Num. measured all: 43879
Reflection shellResolution: 1.64→1.67 Å / % possible obs: 81 % / Redundancy: 3.1 % / Rmerge(I) obs: 1.007 / Num. measured all: 1657 / Num. unique obs: 532 / CC1/2: 0.456 / Rpim(I) all: 0.648 / Rrim(I) all: 1.203 / Χ2: 0.22 / Net I/σ(I) obs: 0.7

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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: 1.73→27.8 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2.03 / Phase error: 30.52 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2298 538 4.94 %
Rwork0.2 --
obs0.2015 10883 96.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.73→27.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms985 0 5 59 1049
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003
X-RAY DIFFRACTIONf_angle_d0.588
X-RAY DIFFRACTIONf_dihedral_angle_d4.024133
X-RAY DIFFRACTIONf_chiral_restr0.034150
X-RAY DIFFRACTIONf_plane_restr0.007184
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.73-1.90.32241270.2782570X-RAY DIFFRACTION96
1.9-2.180.2661260.20782585X-RAY DIFFRACTION97
2.18-2.750.2171540.21122577X-RAY DIFFRACTION97
2.75-27.80.21861310.18582613X-RAY DIFFRACTION98

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