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- PDB-4zv5: Crystal structure of N-myristoylated mouse mammary tumor virus ma... -

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Basic information

Entry
Database: PDB / ID: 4zv5
TitleCrystal structure of N-myristoylated mouse mammary tumor virus matrix protein
ComponentsMatrix protein p10
KeywordsVIRAL PROTEIN / retroviral matrix protein / N-myristoylation
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / structural constituent of virion / viral translational frameshifting / nucleotide binding / DNA binding / zinc ion binding
Similarity search - Function
Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / : / 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 ...Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / GAG-polyprotein viral zinc-finger / : / 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
MYRISTIC ACID / Gag polyprotein / Gag polyprotein
Similarity search - Component
Biological speciesMouse mammary tumor virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 1.57 Å
AuthorsZabransky, A. / Dolezal, M. / Dostal, J. / Vanek, O. / Hadravova, R. / Stokrova, J. / Brynda, J. / Pichova, I.
Citation
Journal: Retrovirology / Year: 2016
Title: Myristoylation drives dimerization of matrix protein from mouse mammary tumor virus.
Authors: Dolezal, M. / Zabransky, A. / Dostal, J. / Vanek, O. / Brynda, J. / Lepsik, M. / Hadravova, R. / Pichova, I.
#1: Journal: Protein Expr.Purif. / Year: 2013
Title: One-step separation of myristoylated and nonmyristoylated retroviral matrix proteins.
Authors: Dolezal, M. / Zabransky, A. / Hrabal, R. / Ruml, T. / Pichova, I. / Rumlova, M.
History
DepositionMay 18, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 27, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein p10
B: Matrix protein p10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,4354
Polymers20,9782
Non-polymers4572
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2240 Å2
ΔGint-2 kcal/mol
Surface area10400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.927, 61.927, 90.054
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Matrix protein p10


Mass: 10489.055 Da / Num. of mol.: 2 / Fragment: UNP residues 2-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mouse mammary tumor virus / Gene: gag / Plasmid: pET-22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: P10258, UniProt: P11284*PLUS
#2: Chemical ChemComp-MYR / MYRISTIC ACID


Mass: 228.371 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H28O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.38 Å3/Da / Density % sol: 48.24 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M potassium chloride, 20% PEG 3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.9184 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 29, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionRmerge(I) obs: 0.036 / D res high: 1.9 Å
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)IDRmerge(I) obs
4.025.6610.022
3.284.0210.029
2.853.2810.031
2.552.8510.041
2.332.5510.057
2.152.3310.08
2.012.1510.143
1.92.0110.201
ReflectionResolution: 1.57→46.08 Å / Num. all: 28486 / Num. obs: 28486 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.2 % / Biso Wilson estimate: 30.3 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 23.9
Reflection shellResolution: 1.57→1.611 Å / Mean I/σ(I) obs: 2.4

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Phasing

PhasingMethod: SIRAS

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Processing

Software
NameVersionClassification
XDSdata reduction
PDB_EXTRACT3.11data extraction
XSCALEdata scaling
REFMAC5.6.0117refinement
SHELXDphasing
XSCALEdata reduction
RefinementMethod to determine structure: SIRAS / Resolution: 1.57→46.08 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.938 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 2.115 / SU ML: 0.076 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.2627 1423 5 %RANDOM
Rwork0.2257 ---
obs0.2275 27039 99.77 %-
all-27039 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 67.27 Å2 / Biso mean: 24.1833 Å2 / Biso min: 7.55 Å2
Baniso -1Baniso -2Baniso -3
1--0.15 Å2-0.08 Å20 Å2
2---0.15 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 1.57→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1473 0 30 87 1590
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191581
X-RAY DIFFRACTIONr_angle_refined_deg1.5751.972127
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5595190
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.64823.15173
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.47615287
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.4441513
X-RAY DIFFRACTIONr_chiral_restr0.0950.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0211173
LS refinement shellResolution: 1.57→1.611 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 92 -
Rwork0.294 1826 -
all-1918 -
obs--98.87 %

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