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- PDB-1em9: ROUS SARCOMA VIRUS CAPSID PROTEIN: N-TERMINAL DOMAIN -

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Basic information

Entry
Database: PDB / ID: 1em9
TitleROUS SARCOMA VIRUS CAPSID PROTEIN: N-TERMINAL DOMAIN
ComponentsGAG POLYPROTEIN CAPSID PROTEIN P27
KeywordsVIRAL PROTEIN / VIRUS/VIRAL PROTEIN
Function / homology
Function and homology information


host cell nucleoplasm / viral procapsid maturation / host cell nucleolus / structural constituent of virion / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / viral capsid / nucleic acid binding / aspartic-type endopeptidase activity / zinc ion binding
Retroviral Gag polyprotein, M / Retroviral matrix protein / Zinc finger, CCHC-type superfamily / Retropepsin-like catalytic domain / Aspartic peptidase domain superfamily / Retropepsins / Retroviral nucleocapsid protein Gag, p24 fragment / Zinc finger, CCHC-type / Aspartic peptidase, active site / Peptidase A2A, retrovirus, catalytic ...Retroviral Gag polyprotein, M / Retroviral matrix protein / Zinc finger, CCHC-type superfamily / Retropepsin-like catalytic domain / Aspartic peptidase domain superfamily / Retropepsins / Retroviral nucleocapsid protein Gag, p24 fragment / Zinc finger, CCHC-type / Aspartic peptidase, active site / Peptidase A2A, retrovirus, catalytic / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retrovirus capsid, C-terminal / Retrovirus capsid, N-terminal / Human Immunodeficiency Virus Type 1 Capsid Protein / Human Immunodeficiency Virus Type 1 Capsid Protein / Orthogonal Bundle / Mainly Alpha
Gag polyprotein
Biological speciesRous sarcoma virus - Prague C
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.05 Å
AuthorsKingston, R.L. / Fitzon-Ostendorp, T. / Eisenmesser, E.Z. / Schatz, G.W. / Vogt, V.M. / Post, C.B. / Rossmann, M.G.
CitationJournal: Structure Fold.Des. / Year: 2000
Title: Structure and self-association of the Rous sarcoma virus capsid protein.
Authors: Kingston, R.L. / Fitzon-Ostendorp, T. / Eisenmesser, E.Z. / Schatz, G.W. / Vogt, V.M. / Post, C.B. / Rossmann, M.G.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 16, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 2, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: GAG POLYPROTEIN CAPSID PROTEIN P27
B: GAG POLYPROTEIN CAPSID PROTEIN P27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,0213
Polymers32,9962
Non-polymers241
Water1,820101
1
A: GAG POLYPROTEIN CAPSID PROTEIN P27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,5222
Polymers16,4981
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: GAG POLYPROTEIN CAPSID PROTEIN P27


Theoretical massNumber of molelcules
Total (without water)16,4981
Polymers16,4981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)40.5, 64.5, 108.9
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
DetailsThe 'dimer' found in the asymmetric unit is of unknown biological significance.

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Components

#1: Protein GAG POLYPROTEIN CAPSID PROTEIN P27


Mass: 16498.105 Da / Num. of mol.: 2 / Fragment: N-TERMINAL DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rous sarcoma virus - Prague C / Genus: Alpharetrovirus / Species: Rous sarcoma virus / Strain: PRAGUE C / Plasmid details: PET-3XC (NOVAGEN) / Production host: Escherichia coli (E. coli) / References: UniProt: P03322
#2: Chemical ChemComp-MG / MAGNESIUM ION / Magnesium


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 101 / 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: 2.16 Å3/Da / Density % sol: 43 %
Crystal growTemperature: 277 K / Method: vapor diffusion / pH: 9.1
Details: Boric acid/Potassium Hydroxide, PEG 6000, Magnesium Nitrate, pH 9.1, VAPOR DIFFUSION, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120-30 mg/mlprotein1drop
220 mMTris-HCl1drop
350 mM1dropNaCl
40.15 Mboric acid/KOH1reservoir
516-22 %(v/v)PEG60001reservoir
60.7 M1reservoirMgNO32

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.037
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 3, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.037 Å / Relative weight: 1
ReflectionResolution: 2.05→55 Å / Num. all: 17194 / Num. obs: 17194 / % possible obs: 92.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 25.1 Å2 / Rmerge(I) obs: 0.049
Reflection shellResolution: 2.05→2.11 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.335 / % possible all: 89.8
Reflection shell
*PLUS
% possible obs: 89.8 %

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Processing

Software
NameClassification
MLPHAREphasing
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.05→55.5 Å / Rfactor Rfree error: 0.009 / Isotropic thermal model: restrained / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber (1991)
RfactorNum. reflection% reflectionSelection details
Rfree0.271 875 5.1 %Random
Rwork0.247 ---
All-17194 --
Obs-17194 92.5 %-
Solvent computationSolvent model: flat model / Bsol: 63.4687 Å2 / ksol: 0.373453 e/Å3
Displacement parametersBiso mean: 42.9 Å2
Baniso -1Baniso -2Baniso -3
1--6.77 Å20 Å20 Å2
2--15.61 Å20 Å2
3----8.84 Å2
Refinement stepCycle: LAST / Resolution: 2.05→55.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2155 0 1 101 2257
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_dihedral_angle_d19
X-RAY DIFFRACTIONx_improper_angle_d0.83
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.033 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.323 94 5.6 %
Rwork0.286 1586 -
Obs--51.4 %
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d
X-RAY DIFFRACTIONc_angle_deg
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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