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- PDB-3zdo: Tetramerization domain of Measles virus phosphoprotein -

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Basic information

Entry
Database: PDB / ID: 3zdo
TitleTetramerization domain of Measles virus phosphoprotein
ComponentsPHOSPHOPROTEIN
KeywordsVIRAL PROTEIN / COILED-COIL
Function / homology
Function and homology information


viral genome replication / RNA-directed RNA polymerase activity / DNA-templated transcription / RNA binding / metal ion binding
Similarity search - Function
RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / Single alpha-helices involved in coiled-coils or other helix-helix interfaces - #110 / Paramyxovirus structural protein P/V, N-terminal domain / Paramyxovirus structural protein V/P N-terminus / P/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMEASLES VIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.07 Å
AuthorsCommunie, G. / Crepin, T. / Jensen, M.R. / Blackledge, M. / Ruigrok, R.W.H.
CitationJournal: J.Virol. / Year: 2013
Title: Structure of the Tetramerization Domain of Measles Virus Phosphoprotein.
Authors: Communie, G. / Crepin, T. / Maurin, D. / Ringkjobing Jensen, M. / Blackledge, M. / Ruigrok, R.W.
History
DepositionNov 29, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 24, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2013Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PHOSPHOPROTEIN
B: PHOSPHOPROTEIN
C: PHOSPHOPROTEIN
D: PHOSPHOPROTEIN
E: PHOSPHOPROTEIN
F: PHOSPHOPROTEIN
G: PHOSPHOPROTEIN
H: PHOSPHOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,0379
Polymers76,9198
Non-polymers1181
Water1,65792
1
E: PHOSPHOPROTEIN
F: PHOSPHOPROTEIN
G: PHOSPHOPROTEIN
H: PHOSPHOPROTEIN


Theoretical massNumber of molelcules
Total (without water)38,4604
Polymers38,4604
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11680 Å2
ΔGint-106.5 kcal/mol
Surface area13280 Å2
MethodPISA
2
A: PHOSPHOPROTEIN
B: PHOSPHOPROTEIN
C: PHOSPHOPROTEIN
D: PHOSPHOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,5785
Polymers38,4604
Non-polymers1181
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11510 Å2
ΔGint-107.1 kcal/mol
Surface area13150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)27.670, 45.720, 115.830
Angle α, β, γ (deg.)91.42, 93.58, 90.08
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
PHOSPHOPROTEIN


Mass: 9614.888 Da / Num. of mol.: 8 / Fragment: TETRAMERIZATION DOMAIN, RESIDUES 304-377
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MEASLES VIRUS / Strain: EDMONSTON B / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA / References: UniProt: Q83623
#2: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 1.9 Å3/Da / Density % sol: 35.29 % / Description: NONE
Crystal growpH: 5.6 / Details: 100 MM TRI-SODIUM CITRATE PH 5.6, 20% MPD

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 20, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.07→8 Å / Num. obs: 32718 / % possible obs: 94.7 % / Observed criterion σ(I): 1.6 / Redundancy: 2.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.27
Reflection shellResolution: 2.07→2.15 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 1.6 / % possible all: 88.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AB-INITIO MODELS

Resolution: 2.07→8 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.902 / SU B: 5.763 / SU ML: 0.155 / Cross valid method: THROUGHOUT / ESU R: 0.246 / ESU R Free: 0.225 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.28397 1614 5 %RANDOM
Rwork0.20957 ---
obs0.21332 30560 93.17 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.701 Å2
Baniso -1Baniso -2Baniso -3
1--0.21 Å2-0.12 Å2-0.05 Å2
2--0.19 Å2-0.04 Å2
3---0.03 Å2
Refinement stepCycle: LAST / Resolution: 2.07→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3977 0 8 92 4077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0194076
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4531.9915469
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6965515
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.52627.661171
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.2815903
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.429158
X-RAY DIFFRACTIONr_chiral_restr0.1010.2681
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022808
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.07→2.12 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.365 108 -
Rwork0.293 1958 -
obs--84.67 %

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