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- PDB-4htw: SIVmac239 capsid N-terminal domain -

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Basic information

Entry
Database: PDB / ID: 4htw
TitleSIVmac239 capsid N-terminal domain
ComponentsGag protein
KeywordsVIRAL PROTEIN / SIV capsid protein
Function / homologyHuman Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / gag protein p24 N-terminal domain / viral process / Retrovirus capsid, N-terminal / Orthogonal Bundle / Mainly Alpha / Gag protein
Function and homology information
Biological speciesSimian immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.9 Å
AuthorsSchmidt, A.G.
CitationJournal: Plos Pathog. / Year: 2013
Title: Gain-of-Sensitivity Mutations in a Trim5-Resistant Primary Isolate of Pathogenic SIV Identify Two Independent Conserved Determinants of Trim5alpha Specificity.
Authors: McCarthy, K.R. / Schmidt, A.G. / Kirmaier, A. / Wyand, A.L. / Newman, R.M. / Johnson, W.E.
History
DepositionNov 2, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 22, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 19, 2013Group: Database references
Revision 1.2Nov 15, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Gag protein


Theoretical massNumber of molelcules
Total (without water)16,1981
Polymers16,1981
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)24.614, 56.663, 102.566
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Gag protein


Mass: 16198.291 Da / Num. of mol.: 1 / Fragment: N-terminal domain, UNP residues 3-145
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Simian immunodeficiency virus / Gene: synthetic / Plasmid: pET303 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8Q5M0

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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: 2.21 Å3/Da / Density % sol: 44.29 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 10% PEG 2000 MME, 10mM nickel chloride and 100mM Tris., pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 30, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 3537 / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.063 / Χ2: 3.954 / Net I/σ(I): 10.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.9-2.954.10.3651710.674198.8
2.95-34.30.3291790.7481100
3-3.064.40.3131720.7711100
3.06-3.124.40.2981650.8541100
3.12-3.194.60.2161610.7991100
3.19-3.274.60.1991770.8721100
3.27-3.354.60.1651660.9921100
3.35-3.444.60.1471811.1471100
3.44-3.544.50.1191751.2521100
3.54-3.654.60.0931661.2081100
3.65-3.784.60.0861721.5241100
3.78-3.944.60.0921732.2621100
3.94-4.114.40.0731872.8281100
4.11-4.334.50.0651632.3861100
4.33-4.64.40.0771726.851100
4.6-4.964.20.0671885.447199.5
4.96-5.464.40.0741764.071100
5.46-6.244.10.0631928.348199.5
6.24-7.864.20.0431848.2341100
7.86-503.60.03621728.6611100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
PHENIX1.7.3_928refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→29.273 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.12 / σ(F): 1.36 / Phase error: 38.15 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2927 152 4.35 %
Rwork0.2542 --
obs0.2558 3497 99.23 %
Solvent computationShrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 69.574 Å2 / ksol: 0.298 e/Å3
Displacement parametersBiso max: 205.94 Å2 / Biso mean: 109.2306 Å2 / Biso min: 68.37 Å2
Baniso -1Baniso -2Baniso -3
1--10.6185 Å2-0 Å2-0 Å2
2--42.6382 Å20 Å2
3----32.0197 Å2
Refinement stepCycle: LAST / Resolution: 2.9→29.273 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1130 0 0 0 1130

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