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- PDB-2ykd: Structure of the matrix protein from human respiratory syncytial virus -

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Basic information

Entry
Database: PDB / ID: 2ykd
TitleStructure of the matrix protein from human respiratory syncytial virus
ComponentsMATRIX PROTEIN
KeywordsVIRAL PROTEIN / VIRAL MATRIX PROTEIN / PERIPHERAL MEMBRANE PROTEIN / VIRION
Function / homology
Function and homology information


viral tegument / Translation of respiratory syncytial virus mRNAs / virion assembly / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / host cell cytoplasm / structural constituent of virion / viral envelope ...viral tegument / Translation of respiratory syncytial virus mRNAs / virion assembly / RSV-host interactions / Assembly and release of respiratory syncytial virus (RSV) virions / Maturation of hRSV A proteins / Respiratory syncytial virus (RSV) attachment and entry / host cell cytoplasm / structural constituent of virion / viral envelope / host cell nucleus / host cell plasma membrane / membrane
Similarity search - Function
HRSV-S2 matrix protein, N-terminal domain / Pneumovirus matrix protein / Pneumovirus matrix, N-terminal / Pneumovirus matrix protein / Topoisomerase I; domain 3 / Distorted Sandwich / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Matrix protein / Matrix protein
Similarity search - Component
Biological speciesHUMAN RESPIRATORY SYNCYTIAL VIRUS
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.86 Å
AuthorsMcPhee, H.K. / Carlisle, J.L. / Beeby, A. / Money, V.A. / Watson, S.M.D. / Yeo, R.P. / Sanderson, J.M.
CitationJournal: Langmuir / Year: 2011
Title: Influence of Lipids on the Interfacial Disposition of Respiratory Syncytical Virus Matrix Protein.
Authors: Mcphee, H.K. / Carlisle, J.L. / Beeby, A. / Money, V.A. / Watson, S.M.D. / Yeo, R.P. / Sanderson, J.M.
History
DepositionMay 26, 2011Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.3Dec 20, 2023Group: 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

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Assembly

Deposited unit
A: MATRIX PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9803
Polymers28,8611
Non-polymers1182
Water3,495194
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)52.402, 78.902, 65.827
Angle α, β, γ (deg.)90.00, 96.18, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein MATRIX PROTEIN


Mass: 28861.496 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HUMAN RESPIRATORY SYNCYTIAL VIRUS / Strain: A2 / Plasmid: PM254M / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 (CODON PLUS) / References: UniProt: P03419, UniProt: P0DOE7*PLUS
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.32 Å3/Da / Density % sol: 47 % / Description: NONE
Crystal growTemperature: 291 K / pH: 7
Details: MOTHER LIQUOR 45 % TO 65% TACSIMATE PH7, 18 DEGC, PROTEIN AT 1 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54179
DetectorType: MARRESEARCH / Detector: IMAGE PLATE
RadiationMonochromator: NI FLITER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54179 Å / Relative weight: 1
ReflectionResolution: 1.85→25.2 Å / Num. obs: 22370 / % possible obs: 98 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 20.95 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 7.1
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 1.3 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2VQP

2vqp


Resolution: 1.86→25.19 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.928 / SU B: 3.329 / SU ML: 0.101 / Cross valid method: THROUGHOUT / ESU R: 0.148 / ESU R Free: 0.142 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUE 103 IS NOT VISIBLE IN DENSITY
RfactorNum. reflection% reflectionSelection details
Rfree0.22879 1095 4.9 %RANDOM
Rwork0.1796 ---
obs0.1821 21102 99.23 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.769 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20.01 Å2
2--0.17 Å20 Å2
3----0.03 Å2
Refinement stepCycle: LAST / Resolution: 1.86→25.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1996 0 8 194 2198
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0222115
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9812891
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3515279
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.36125.51378
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.78415402
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.259156
X-RAY DIFFRACTIONr_chiral_restr0.1160.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021521
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2130.2893
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.21438
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2970.2164
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.284
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2360.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5841.51366
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.87922188
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.1393850
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.4014.5690
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: 1.861→1.909 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.34 70 -
Rwork0.255 1427 -
obs--91.17 %

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