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- PDB-5i27: Crystal structure of non-myristoylated MMTV matrix protein -

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Basic information

Entry
Database: PDB / ID: 5i27
TitleCrystal structure of non-myristoylated MMTV matrix protein
ComponentsMatrix protein
KeywordsVIRAL PROTEIN / non-myristoylated protein / MMTV MA
Function / homology
Function and homology information


viral budding via host ESCRT complex / viral nucleocapsid / structural constituent of virion / nucleotide binding / DNA binding / zinc ion binding
Similarity search - Function
GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / 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 ...GAG-polyprotein viral zinc-finger / Beta-retroviral matrix protein / Beta-retroviral matrix superfamily / Retroviral GAG p10 protein / 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 speciesMouse mammary tumor virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.05 Å
AuthorsBrynda, J. / Dostal, J. / Zabransky, A. / Dolezal, M.
Funding support Czech Republic, 5items
OrganizationGrant numberCountry
RVORVO: 68378050 Czech Republic
Czech Science Foundation (GA CR)15-05677S Czech Republic
RVORVO: 613888963 Czech Republic
NPULO1302 Czech Republic
NPULO1304 Czech Republic
CitationJournal: To Be Published
Title: Crystal structure non-myristoylated MMTV matrix protein
Authors: Brynda, J. / Dostal, J. / Zabransky, A. / Dolezal, M.
History
DepositionFeb 8, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 28, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2019Group: Data collection / Derived calculations
Category: pdbx_data_processing_status / struct_conn / struct_conn_type
Revision 1.2May 8, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Matrix protein
B: Matrix protein


Theoretical massNumber of molelcules
Total (without water)20,3772
Polymers20,3772
Non-polymers00
Water18010
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1660 Å2
ΔGint-5 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.875, 60.875, 91.460
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LYS / Beg label comp-ID: LYS / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 8 - 92 / Label seq-ID: 2 - 86

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Matrix protein


Mass: 10188.742 Da / Num. of mol.: 2 / Fragment: UNP residues 6-92
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mouse mammary tumor virus / Strain: BR6 / Gene: gag
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: P10258
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 10 / 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: 2.4 Å3/Da / Density % sol: 48.76 %
Crystal growTemperature: 292 K / Method: vapor diffusion, hanging drop / Details: 0.2M zinc acetate, 20%(w/v) PEG 33500

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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
ReflectionResolution: 2.05→45.73 Å / Num. obs: 12780 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 7.3 % / Biso Wilson estimate: 49.533 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.071 / Net I/σ(I): 17.06
Reflection shell
Resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
2.05-2.171.0712.01199.1
2.17-2.320.6213.93199.9
2.32-2.510.3456.91199.9
2.51-2.750.19910.98199.9
2.75-3.070.10618.411100
3.07-3.540.06229.741100
3.54-4.330.04539.18199.9
4.33-6.10.04144.041100
6.1-45.730.02944.29197.6

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation45.67 Å3.5 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
MOLREP11.0.02phasing
REFMAC5.6.0117refinement
PDB_EXTRACT3.2data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.05→45.67 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.517 / SU ML: 0.198 / SU R Cruickshank DPI: 0.242 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.242 / ESU R Free: 0.209
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2906 639 5 %RANDOM
Rwork0.244 ---
obs0.2464 12141 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 112.27 Å2 / Biso mean: 44.758 Å2 / Biso min: 16.3 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20.45 Å20 Å2
2--0.89 Å20 Å2
3----1.34 Å2
Refinement stepCycle: final / Resolution: 2.05→45.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1411 0 0 11 1422
Biso mean---36.69 -
Num. residues----173
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0191470
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.9581989
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6245177
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.42922.85770
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.49715265
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.9591513
X-RAY DIFFRACTIONr_chiral_restr0.0940.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0211113
Refine LS restraints NCS

Ens-ID: 1 / Number: 98 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.17 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.048→2.102 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.43 40 -
Rwork0.371 785 -
all-825 -
obs--97.98 %

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