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- PDB-3bbz: Structure of the nucleocapsid-binding domain from the mumps virus... -

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Basic information

Entry
Database: PDB / ID: 3bbz
TitleStructure of the nucleocapsid-binding domain from the mumps virus phosphoprotein
ComponentsP protein
KeywordsVIRAL PROTEIN / REPLICATION / molten globule
Function / homologyP/V phosphoprotein, paramyxoviral / Paramyxovirus P/V phosphoprotein C-terminal / Ubiquitin-associated (UBA) domain / Helicase, Ruva Protein; domain 3 / Orthogonal Bundle / Mainly Alpha / BROMIDE ION / FORMIC ACID / Phosphoprotein
Function and homology information
Biological speciesMumps virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.1 Å
AuthorsKingston, R.L. / Gay, L.S. / Baase, W.S. / Matthews, B.W.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: Structure of the nucleocapsid-binding domain from the mumps virus polymerase; an example of protein folding induced by crystallization
Authors: Kingston, R.L. / Gay, L.S. / Baase, W.S. / Matthews, B.W.
History
DepositionNov 11, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: P protein
B: P protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,34710
Polymers10,9112
Non-polymers4368
Water93752
1
A: P protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6735
Polymers5,4551
Non-polymers2184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: P protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)5,6735
Polymers5,4551
Non-polymers2184
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: P protein
hetero molecules

B: P protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,34710
Polymers10,9112
Non-polymers4368
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_845-x+3,y-1/2,-z+1/21
Buried area2500 Å2
ΔGint-9 kcal/mol
Surface area5750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)23.992, 55.485, 60.019
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein/peptide P protein / phosphoprotein


Mass: 5455.335 Da / Num. of mol.: 2 / Fragment: nucleocapsid-binding domain, UNP residues 343-391 / Mutation: C356S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mumps virus / Strain: Jeryl-Lynn vaccine / Plasmid: pET41A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-Star (DE3) / References: UniProt: Q9J4L6
#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Br
#3: Chemical
ChemComp-FMT / FORMIC ACID


Mass: 46.025 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: CH2O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.83 Å3/Da / Density % sol: 32.81 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 9.7
Details: 0.2M Alanine/KOH pH 9.7, 3.6-4.6M Ammonium formate, VAPOR DIFFUSION, SITTING DROP, temperature 277K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONALS 8.2.110.92
SYNCHROTRONSSRL BL9-120.954,0.979
Detector
TypeIDDetectorDate
ADSC QUANTUM 3151CCDDec 2, 2004
ADSC QUANTUM 3152CCDJun 27, 2006
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Double Crystal Si(111)SINGLE WAVELENGTHMx-ray1
2Double Crystal Si(111)MADMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.921
20.9541
30.9791
ReflectionResolution: 2.1→41.27 Å / Num. all: 4915 / Num. obs: 4915 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 8.4 % / Biso Wilson estimate: 13 Å2 / Rmerge(I) obs: 0.14 / Rsym value: 0.14 / Net I/σ(I): 5.8
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 8.7 % / Rmerge(I) obs: 0.343 / Mean I/σ(I) obs: 2.4 / Num. unique all: 484 / % possible all: 98.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MLPHAREphasing
RefinementMethod to determine structure: MAD / Resolution: 2.1→40.74 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.931 / SU B: 5.771 / SU ML: 0.154 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.318 / ESU R Free: 0.219 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2411 238 4.9 %RANDOM
Rwork0.18994 ---
all0.19254 4915 --
obs0.19254 4677 97.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.779 Å2
Baniso -1Baniso -2Baniso -3
1--0.14 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.45 Å2
Refinement stepCycle: LAST / Resolution: 2.1→40.74 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms751 0 2 70 823
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.022766
X-RAY DIFFRACTIONr_angle_refined_deg1.6061.9781013
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.487596
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55925.62532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.51515165
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.897156
X-RAY DIFFRACTIONr_chiral_restr0.1040.2121
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02528
X-RAY DIFFRACTIONr_nbd_refined0.2180.2310
X-RAY DIFFRACTIONr_nbtor_refined0.290.2516
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2090.239
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.20.267
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1090.215
X-RAY DIFFRACTIONr_mcbond_it1.3621.5522
X-RAY DIFFRACTIONr_mcangle_it1.9542778
X-RAY DIFFRACTIONr_scbond_it2.9663279
X-RAY DIFFRACTIONr_scangle_it4.3944.5234
LS refinement shellHighest resolution: 2.1 Å / Num. reflection Rwork: 345 / Total num. of bins used: 20

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