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- PDB-8erg: HTLV-1 capsid protein N-terminal domain hexagonal crystal form -

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Basic information

Entry
Database: PDB / ID: 8erg
TitleHTLV-1 capsid protein N-terminal domain hexagonal crystal form
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 / Zinc knuckle ...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: 2.1 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 hexagonal 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2412
Polymers14,1451
Non-polymers961
Water36020
1
A: capsid protein p24
hetero molecules

A: capsid protein p24
hetero molecules

A: capsid protein p24
hetero molecules

A: capsid protein p24
hetero molecules

A: capsid protein p24
hetero molecules

A: capsid protein p24
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,44612
Polymers84,8706
Non-polymers5766
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
crystal symmetry operation4_555-x,-y,z1
crystal symmetry operation5_555y,-x+y,z1
crystal symmetry operation6_555x-y,x,z1
Unit cell
Length a, b, c (Å)74.620, 74.620, 73.782
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number177
Space group name H-MP622

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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 / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.1 Å3/Da / Density % sol: 41.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 2 M (NH4)SO4, 2% PEG 400, 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: MX2 / Wavelength: 0.9537 Å
DetectorType: DECTRIS EIGER2 S 16M / Detector: PIXEL / Date: Apr 8, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.05→48.61 Å / Num. obs: 7949 / % possible obs: 98.6 % / Redundancy: 33.2 % / Biso Wilson estimate: 32.81 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.15 / Rpim(I) all: 0.026 / Rrim(I) all: 0.152 / Net I/σ(I): 17.4 / Num. measured all: 263835 / Scaling rejects: 74
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
2.05-2.1125.51.549126194940.4880.3011.5842.481.7
8.95-48.6126.40.08536501380.9990.0160.08737.799.5

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.82 Å49.08 Å
Translation3.82 Å49.08 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: 2.1→48.61 Å / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 1.38 / Phase error: 28.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2711 738 9.79 %
Rwork0.24 6797 -
obs0.243 7535 99.96 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 124.27 Å2 / Biso mean: 43.7232 Å2 / Biso min: 18.59 Å2
Refinement stepCycle: final / Resolution: 2.1→48.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms975 0 5 20 1000
Biso mean--37 37.81 -
Num. residues----124
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 5 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.1-2.260.36471460.273513071453
2.26-2.490.28821390.263613331472
2.49-2.850.29831400.255313331473
2.85-3.590.26671530.244813511504
3.59-48.610.24221600.22114731633
Refinement TLS params.Method: refined / Origin x: -4.4039 Å / Origin y: 26.1514 Å / Origin z: 17.0932 Å
111213212223313233
T0.1653 Å2-0.0147 Å20.0354 Å2-0.232 Å2-0.028 Å2--0.2638 Å2
L1.819 °20.7231 °20.8345 °2-4.0928 °22.1044 °2--3.7007 °2
S0.0922 Å °-0.1033 Å °0.1171 Å °-0.2754 Å °-0.1779 Å °-0.012 Å °-0.1162 Å °0.0198 Å °0.0715 Å °
Refinement TLS groupSelection details: (chain 'A' and resid 1 through 127)

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