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- PDB-6htl: Measles Phosphoprotein Coiled-Coil Domain IPKI Variant -

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Basic information

Entry
Database: PDB / ID: 6htl
TitleMeasles Phosphoprotein Coiled-Coil Domain IPKI Variant
ComponentsPhosphoprotein
KeywordsVIRAL PROTEIN / Coiled-Coil / Alpha Helix / Tetramer / 3-10 Helix
Function / homology
Function and homology information


viral genome replication / RNA-dependent RNA polymerase activity / DNA-templated transcription / RNA binding
Similarity search - Function
RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / 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 - #110 / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMeasles morbillivirus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsSchramm, A. / Longhi, S.
CitationJournal: Sci Adv / Year: 2019
Title: Regulation of measles virus gene expression by P protein coiled-coil properties.
Authors: Bloyet, L.M. / Schramm, A. / Lazert, C. / Raynal, B. / Hologne, M. / Walker, O. / Longhi, S. / Gerlier, D.
History
DepositionOct 4, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 5, 2019Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)8,9662
Polymers8,9261
Non-polymers401
Water75742
1
A: Phosphoprotein
hetero molecules

A: Phosphoprotein
hetero molecules

A: Phosphoprotein
hetero molecules

A: Phosphoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,8658
Polymers35,7044
Non-polymers1604
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
crystal symmetry operation3_555-y,x,z1
crystal symmetry operation4_555y,-x,z1
Buried area11590 Å2
ΔGint-134 kcal/mol
Surface area13570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.450, 33.450, 275.620
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Phosphoprotein


Mass: 8926.093 Da / Num. of mol.: 1 / Mutation: L339I, L340P, L341K, L342I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Measles morbillivirus / Plasmid: pDest14 / Production host: Escherichia coli (E. coli) / References: UniProt: Q83623
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.65 Å3/Da / Density % sol: 53.5 % / Description: elongated
Crystal growTemperature: 300 K / Method: vapor diffusion, sitting drop / Details: PEG 4000, Calcium Chloride, Trizma / PH range: 8 - 9

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97911 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97911 Å / Relative weight: 1
ReflectionResolution: 2.2→45.94 Å / Num. obs: 4440 / % possible obs: 99.2 % / Redundancy: 22.3 % / Biso Wilson estimate: 35 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.07 / Rpim(I) all: 0.016 / Rrim(I) all: 0.072 / Net I/σ(I): 15.8
Reflection shellResolution: 2.2→2.26 Å / Redundancy: 13.8 % / Rmerge(I) obs: 2.11 / Mean I/σ(I) obs: 1 / Num. unique obs: 287 / CC1/2: 0.956 / Rpim(I) all: 0.592 / Rrim(I) all: 2.202 / % possible all: 92.1

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
BUSTER2.10.3refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZD0

3zd0


Resolution: 2.3→45.94 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.885 / SU R Cruickshank DPI: 0.31 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.39 / SU Rfree Blow DPI: 0.26 / SU Rfree Cruickshank DPI: 0.239
Details: Even if collection were carried out at 2.2 angstrom resoltuion, the anisotropic nature of the data had a harmfull impact on model refinement especially when the 2.2 - 2.3 shell was included. ...Details: Even if collection were carried out at 2.2 angstrom resoltuion, the anisotropic nature of the data had a harmfull impact on model refinement especially when the 2.2 - 2.3 shell was included. Refinement was carried out at 2.3 angstrom as maximum resolution.
RfactorNum. reflection% reflectionSelection details
Rfree0.285 198 5.01 %RANDOM
Rwork0.252 ---
obs0.254 3952 99.9 %-
Displacement parametersBiso max: 112.32 Å2 / Biso mean: 30.44 Å2 / Biso min: 3 Å2
Baniso -1Baniso -2Baniso -3
1--1.7824 Å20 Å20 Å2
2---1.7824 Å20 Å2
3---3.5648 Å2
Refine analyzeLuzzati coordinate error obs: 0.45 Å
Refinement stepCycle: final / Resolution: 2.3→45.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms484 0 1 42 527
Biso mean--29.24 34.63 -
Num. residues----64
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d181SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes82HARMONIC5
X-RAY DIFFRACTIONt_it487HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion72SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact653SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d487HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg654HARMONIC21.13
X-RAY DIFFRACTIONt_omega_torsion2.24
X-RAY DIFFRACTIONt_other_torsion21.27
LS refinement shellResolution: 2.3→2.39 Å / Rfactor Rfree error: 0 / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3728 22 5 %
Rwork0.3559 418 -
all0.3569 440 -
obs--99.32 %

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