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- PDB-1ezj: CRYSTAL STRUCTURE OF THE MULTIMERIZATION DOMAIN OF THE PHOSPHOPRO... -

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Basic information

Entry
Database: PDB / ID: 1ezj
TitleCRYSTAL STRUCTURE OF THE MULTIMERIZATION DOMAIN OF THE PHOSPHOPROTEIN FROM SENDAI VIRUS
ComponentsNUCLEOCAPSID PHOSPHOPROTEIN
KeywordsViral protein / transferase / Four stranded coiled coil / viral polymerase / Sendai virus / tetramer
Function / homology
Function and homology information


negative stranded viral RNA replication / disordered domain specific binding / host cell cytoplasm / RNA-dependent RNA polymerase activity / DNA-templated transcription / protein-containing complex / RNA binding
Similarity search - Function
Viral phosphoprotein oligmorisation site domain / Helix Hairpins - #340 / Phosphoprotein P, oligomerisation domain 1 / Paramyxovirinae P phosphoprotein C-terminal domain / Paramyxovirinae P phosphoprotein C-terminal region / RNA polymerase, phosphoprotein P, C-terminal XD, paramyxovirinae / Helix Hairpins / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ETHYL MERCURY ION / Phosphoprotein
Similarity search - Component
Biological speciesSendai virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsTarbouriech, N. / Curran, J. / Ruigrok, R.W.H. / Burmeister, W.P.
CitationJournal: Nat.Struct.Biol. / Year: 2000
Title: Tetrameric coiled coil domain of Sendai virus phosphoprotein.
Authors: Tarbouriech, N. / Curran, J. / Ruigrok, R.W. / Burmeister, W.P.
History
DepositionMay 11, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_label_seq_id / _struct_ref_seq_dif.details / _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

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Assembly

Deposited unit
A: NUCLEOCAPSID PHOSPHOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,3863
Polymers13,1161
Non-polymers2702
Water2,630146
1
A: NUCLEOCAPSID PHOSPHOPROTEIN
hetero molecules

A: NUCLEOCAPSID PHOSPHOPROTEIN
hetero molecules

A: NUCLEOCAPSID PHOSPHOPROTEIN
hetero molecules

A: NUCLEOCAPSID PHOSPHOPROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,54212
Polymers52,4634
Non-polymers1,0798
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-x+1,-y,z1
crystal symmetry operation3_545-y+1/2,x-1/2,z1
crystal symmetry operation4_555y+1/2,-x+1/2,z1
Buried area15850 Å2
ΔGint-138 kcal/mol
Surface area23210 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)48.584, 48.584, 100.847
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Components on special symmetry positions
IDModelComponents
11A-1001-

CA

21A-1049-

HOH

31A-1060-

HOH

41A-1067-

HOH

51A-1069-

HOH

61A-1072-

HOH

71A-1073-

HOH

81A-1074-

HOH

91A-1075-

HOH

101A-1092-

HOH

111A-1123-

HOH

121A-1129-

HOH

131A-1133-

HOH

141A-1138-

HOH

DetailsThe biological assembly is a tetramer constructed from chain A and symmetry partners generated by the four-fold axis.

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Components

#1: Protein NUCLEOCAPSID PHOSPHOPROTEIN / RNA POLYMERASE ALPHA SUBUNIT


Mass: 13115.810 Da / Num. of mol.: 1 / Fragment: MULTIMERIZATION DOMAIN (320-433)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sendai virus (strain Harris) / Genus: Respirovirus / Species: Sendai virus / Strain: HARRIS / Plasmid: PT7_7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P04859, RNA-directed RNA polymerase
#2: Chemical ChemComp-EMC / ETHYL MERCURY ION


Mass: 229.651 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H5Hg
#3: Chemical ChemComp-CA / CALCIUM ION


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


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.27 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9
Details: PEG 3000 16%, Sodium chloride 200 mM, Calcium chloride 10 mM, ethylmercurythiosalicilic acid 5 mM, Tris-HCl 100 mM, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 mg/mlprotein1drop
220 mMHEPES1drop
350 mM1dropNaCl
4100 mMTris-HCl1reservoir
5200 mM1reservoirNaCl
610 mM1reservoirCaCl2
715-17 %(w/v)PEG30001reservoir
85 mMEMTS1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.94
DetectorType: MARRESEARCH / Detector: CCD / Date: May 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.94 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. all: 10106 / Num. obs: 9175 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Biso Wilson estimate: 37 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 15
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.386 / Num. unique all: 917 / % possible all: 94.5
Reflection shell
*PLUS
% possible obs: 94.5 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
DENZOdata reduction
CCP4(TRUNCATE)data scaling
RefinementResolution: 1.9→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.293 931 -random
Rwork0.249 ---
all0.255 10106 --
obs0.255 9175 92.1 %-
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms908 0 4 146 1058
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.21
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 15 Å / σ(F): 0 / % reflection Rfree: 10 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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