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- PDB-2xgv: Structure of the N-terminal domain of capsid protein from Rabbit ... -

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Basic information

Entry
Database: PDB / ID: 2xgv
TitleStructure of the N-terminal domain of capsid protein from Rabbit Endogenous Lentivirus (RELIK)
ComponentsPSIV CAPSID N-TERMINAL DOMAIN
KeywordsVIRAL PROTEIN / RETROVIRAL CAPSID
Function / homologyHuman Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesMICROCEBUS MURINUS (gray mouse lemur)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsGoldstone, D.C. / Robertson, L.E. / Haire, L.F. / Stoye, J.P. / Taylor, I.A.
CitationJournal: Cell Host Microbe / Year: 2010
Title: Structural and Functional Analysis of Prehistoric Lentiviruses Uncovers an Ancient Molecular Interface.
Authors: Goldstone, D.C. / Yap, M.W. / Robertson, L.E. / Haire, L.F. / Taylor, W.R. / Katzourakis, A. / Stoye, J.P. / Taylor, I.A.
History
DepositionJun 7, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 22, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PSIV CAPSID N-TERMINAL DOMAIN


Theoretical massNumber of molelcules
Total (without water)15,9941
Polymers15,9941
Non-polymers00
Water1,982110
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)80.250, 62.710, 26.870
Angle α, β, γ (deg.)90.00, 102.11, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2026-

HOH

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Components

#1: Protein PSIV CAPSID N-TERMINAL DOMAIN


Mass: 15993.886 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MICROCEBUS MURINUS (gray mouse lemur) / Production host: ESCHERICHIA COLI (E. coli)
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 110 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 40.67 % / Description: NONE
Crystal growpH: 4.6 / Details: 24% PEG6000, 0.1M NA-ACETATE PH4.6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Wavelength: 1.5418
DetectorType: RIGAKU-MSC / Detector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 8728 / % possible obs: 98.7 % / Observed criterion σ(I): 2 / Redundancy: 3.5 % / Biso Wilson estimate: 23.3 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 11.6
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 4.3 / % possible all: 96.9

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→24.529 Å / SU ML: 0.31 / σ(F): 1.43 / Phase error: 22.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2239 417 4.8 %
Rwork0.1837 --
obs0.1858 8728 98.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.914 Å2 / ksol: 0.339 e/Å3
Displacement parametersBiso mean: 26.7 Å2
Baniso -1Baniso -2Baniso -3
1-2.9265 Å2-0 Å2-1.3127 Å2
2--0.7177 Å2-0 Å2
3----3.6442 Å2
Refinement stepCycle: LAST / Resolution: 2→24.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1018 0 0 110 1128
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071047
X-RAY DIFFRACTIONf_angle_d0.8921430
X-RAY DIFFRACTIONf_dihedral_angle_d14.72371
X-RAY DIFFRACTIONf_chiral_restr0.058158
X-RAY DIFFRACTIONf_plane_restr0.004187
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0002-2.28950.26131170.19362726X-RAY DIFFRACTION97
2.2895-2.88380.25241670.17542732X-RAY DIFFRACTION99
2.8838-24.53120.18971330.17942853X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.91981.37970.94476.06371.83780.80720.3854-0.4898-0.2919-0.3896-0.2965-0.0190.1705-0.5071-0.06310.1884-0.0528-0.10980.21320.05170.14785.3069-10.19514.8075
20.7683-0.07890.67530.833-0.00520.21120.15060.12030.0826-0.1485-0.17530.0304-0.00510.09190.05520.07070.04430.00840.12590.01520.07896.80748.9945-2.8734
30.5238-0.49170.80761.10170.07320.85930.1880.1966-0.0366-0.1208-0.1247-0.16340.08150.175-0.04090.09130.0430.02850.12550.0030.135815.64547.1392.2026
41.6287-1.42-2.46891.52031.26666.72880.25760.08660.24280.06510.2405-0.7596-1.2337-0.226-0.29370.1268-0.0007-0.03960.1117-0.0730.251320.857410.130116.2226
52.35010.9865-1.4164.9908-0.65430.84970.6702-1.3303-0.17770.5934-0.4363-0.29790.6619-0.0804-0.05710.3644-0.1413-0.19830.64960.04660.209120.68852.686625.9139
61.99551.6908-0.38691.9842-0.62520.3896-0.1702-0.1623-0.5752-0.20370.0153-0.56850.1272-0.0050.12490.11850.04070.02780.0960.00280.228317.2839-4.324513.1932
70.2049-0.33320.36171.06340.04580.05030.0127-0.11550.11460.23250.0021-0.2322-0.04280.051-0.02590.09310.0155-0.0030.0946-0.03110.09110.52536.878611.5047
84.8944-3.71523.38853.1321-3.09373.2055-0.6001-0.07281.34970.39060.2905-0.9545-0.4910.06450.27190.1593-0.0411-0.00310.1118-0.01910.352911.223123.78556.1152
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:14)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 15:44)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 45:72)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 73:80)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 81:88)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 89:109)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 110:127)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 128:133)

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