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- PDB-4bxt: Crystal structure of the human metapneumovirus phosphoprotein tet... -

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Basic information

Entry
Database: PDB / ID: 4bxt
TitleCrystal structure of the human metapneumovirus phosphoprotein tetramerization domain
ComponentsPHOSPHOPROTEIN P
KeywordsVIRAL PROTEIN / TETRAMERIC PARALLEL COILED COIL
Function / homologyPhosphoprotein, pneumoviral / Pneumovirus phosphoprotein / RNA-dependent RNA polymerase activity / Phosphoprotein
Function and homology information
Biological speciesHUMAN METAPNEUMOVIRUS
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.13 Å
AuthorsLeyrat, C. / Renner, M. / Harlos, K. / Grimes, J.M.
CitationJournal: Plos One / Year: 2013
Title: Solution and Crystallographic Structures of the Central Region of the Phosphoprotein from Human Metapneumovirus
Authors: Leyrat, C. / Renner, M. / Harlos, K. / Grimes, J.M.
History
DepositionJul 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)70,1848
Polymers70,1848
Non-polymers00
Water0
1
E: PHOSPHOPROTEIN P
F: PHOSPHOPROTEIN P
G: PHOSPHOPROTEIN P
H: PHOSPHOPROTEIN P


Theoretical massNumber of molelcules
Total (without water)35,0924
Polymers35,0924
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4700 Å2
ΔGint-48.8 kcal/mol
Surface area5820 Å2
MethodPISA
2
A: PHOSPHOPROTEIN P
B: PHOSPHOPROTEIN P
C: PHOSPHOPROTEIN P
D: PHOSPHOPROTEIN P


Theoretical massNumber of molelcules
Total (without water)35,0924
Polymers35,0924
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4530 Å2
ΔGint-46.4 kcal/mol
Surface area6010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.910, 48.520, 64.450
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.941234, 0.205036, -0.2684), (-0.169881, -0.399439, -0.900882), (-0.291923, 0.893537, -0.341134)
Vector: -15.714, 11.369, -20.036)

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Components

#1: Protein
PHOSPHOPROTEIN P


Mass: 8773.052 Da / Num. of mol.: 8 / Fragment: TETRAMERIZATION DOMAIN, RESIDUES 158-237
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN METAPNEUMOVIRUS / Strain: SEROTYPE A1 (NL/1/00) / Plasmid: POPINF / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): ROSETTA2 / References: UniProt: Q91KZ5

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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: 39.7 % / Description: NONE
Crystal growpH: 7.5 / Details: 25 % PEG 3350, 100 MM HEPES PH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.92001
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 22, 2013
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92001 Å / Relative weight: 1
ReflectionResolution: 3.13→66.91 Å / Num. obs: 3602 / % possible obs: 90.3 % / Observed criterion σ(I): 1.5 / Redundancy: 10.5 % / Biso Wilson estimate: 77.44 Å2 / Rmerge(I) obs: 0.35 / Net I/σ(I): 6.4
Reflection shellResolution: 3.13→3.21 Å / Redundancy: 6.1 % / Rmerge(I) obs: 1.35 / Mean I/σ(I) obs: 1.4 / % possible all: 57.1

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: SAXS-FILTERED ROSETTA FOLD-AND-DOCK AB INITIO MODEL

Resolution: 3.13→46.42 Å / Cor.coef. Fo:Fc: 0.8587 / Cor.coef. Fo:Fc free: 0.7759 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.542
RfactorNum. reflection% reflectionSelection details
Rfree0.2523 153 4.28 %RANDOM
Rwork0.2353 ---
obs0.236 3577 89.56 %-
Displacement parametersBiso mean: 53.43 Å2
Baniso -1Baniso -2Baniso -3
1-24.8674 Å20 Å20 Å2
2---25.6698 Å20 Å2
3---0.8024 Å2
Refine analyzeLuzzati coordinate error obs: 0.706 Å
Refinement stepCycle: LAST / Resolution: 3.13→46.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1560 0 0 0 1560
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011552HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.292065HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d625SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes36HARMONIC2
X-RAY DIFFRACTIONt_gen_planes207HARMONIC5
X-RAY DIFFRACTIONt_it1552HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.06
X-RAY DIFFRACTIONt_other_torsion26.79
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion223SEMIHARMONIC5
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_contact1867SEMIHARMONIC4
LS refinement shellResolution: 3.13→3.5 Å / Total num. of bins used: 5
RfactorNum. reflection% reflection
Rfree0.2421 29 4.01 %
Rwork0.25 695 -
all0.2497 724 -
obs--89.56 %
Refinement TLS params.

S11: 0 Å ° / S12: 0 Å ° / S13: 0 Å ° / S21: 0 Å ° / S22: 0 Å ° / S23: 0 Å ° / S31: 0 Å ° / S32: 0 Å ° / S33: 0 Å ° / T11: 0 Å2 / T12: 0 Å2 / T13: 0 Å2 / T22: 0 Å2 / T23: 0 Å2 / T33: 0 Å2 / Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)Origin x (Å)Origin y (Å)Origin z (Å)
10-0.00010.00010.0001-0.00010-11.80333.082-15.3438
20-0.00010.0002000.0001-13.73649.1776-8.8444
30.0001-0.00010000-21.998813.646-14.6572
40.0002-0.00010.00030.00030.00010.0002-20.07686.1739-20.1622
50.00020.00010.00010.0001-0.00010-1.549811.0252-2.2023
60.00020.00020.0003000-8.15854.4436-0.9805
70000.0001-0.00010.0001-2.72020.3146.0718
80.000100.0002000.00013.34168.34725.3746
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C
4X-RAY DIFFRACTION4CHAIN D
5X-RAY DIFFRACTION5CHAIN E
6X-RAY DIFFRACTION6CHAIN F
7X-RAY DIFFRACTION7CHAIN G
8X-RAY DIFFRACTION8CHAIN H

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