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- PDB-8ere: HTLV-1 capsid protein N-terminal domain triclinic crystal form -

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Basic information

Entry
Database: PDB / ID: 8ere
TitleHTLV-1 capsid protein N-terminal domain triclinic crystal form
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 / molecular replacement / Resolution: 0.87 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
Authors: Yu, R.J. / Li, N. / Jacques, D.A.
History
DepositionOct 11, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2023Provider: 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


Theoretical massNumber of molelcules
Total (without water)14,1451
Polymers14,1451
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)30.070, 30.560, 35.010
Angle α, β, γ (deg.)75.030, 68.460, 89.620
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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / Source method: isolated from a natural source / Formula: H2O

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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: 2.03 Å3/Da / Density % sol: 39.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting 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: 0.7999 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7999 Å / Relative weight: 1
ReflectionResolution: 0.87→31.31 Å / Num. obs: 84819 / % possible obs: 93 % / Redundancy: 6.7 % / Biso Wilson estimate: 8.41 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.054 / Rpim(I) all: 0.022 / Rrim(I) all: 0.058 / Net I/σ(I): 17.8 / Num. measured all: 565868 / Scaling rejects: 1937
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
0.87-0.893.50.2711330238380.9420.1690.3214.185.4
4.77-31.316.20.03533785450.9990.0170.03940.698.7

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation4.4 Å31.31 Å

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Processing

Software
NameVersionClassification
PHENIX1.20.1refinement
Aimless0.7.4data scaling
PHASER2.8.3phasing
PDB_EXTRACT3.27data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Alphafold2 prediction

Resolution: 0.87→31.31 Å / SU ML: 0.06 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 11.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.131 4178 4.93 %
Rwork0.1204 80629 -
obs0.1209 84807 93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 38.79 Å2 / Biso mean: 10.5308 Å2 / Biso min: 5.3 Å2
Refinement stepCycle: final / Resolution: 0.87→31.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms996 0 0 159 1155
Biso mean---21.03 -
Num. residues----127
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
0.87-0.880.22941330.17652402253585
0.88-0.890.16681110.15932562267387
0.89-0.90.16291310.1482490262187
0.9-0.910.16771140.14172636275090
0.91-0.930.14181400.12992538267888
0.93-0.940.13531380.12762605274391
0.94-0.950.14631320.12192643277590
0.95-0.970.12141240.11812624274891
0.97-0.980.12881250.10682636276191
0.98-10.11261430.10472671281492
1-1.010.09991380.09532576271491
1.01-1.030.10581280.09262703283193
1.03-1.050.10731310.09132706283792
1.05-1.070.10791400.08632671281193
1.07-1.10.09381620.08772653281593
1.1-1.120.10111450.08762709285493
1.12-1.150.09981140.08552725283994
1.15-1.180.08881590.08282682284194
1.18-1.220.1011500.0912712286294
1.22-1.260.10581360.09492754289095
1.26-1.30.10971680.09712737290595
1.3-1.350.11600.09772718287895
1.35-1.410.11791430.10532752289596
1.41-1.490.12491480.10542792294096
1.49-1.580.1031640.10482773293797
1.58-1.70.10841370.11032769290696
1.7-1.880.12851440.1272847299198
1.88-2.150.12011300.1282851298198
2.15-2.70.15521580.1332830298898
2.71-31.310.18071320.15252862299499

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