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- PDB-1wru: Structure of central hub elucidated by X-ray analysis of gene pro... -

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Basic information

Entry
Database: PDB / ID: 1wru
TitleStructure of central hub elucidated by X-ray analysis of gene product 44; baseplate component of bacteriophage Mu
Components43 kDa tail protein
KeywordsSTRUCTURAL PROTEIN / BACTERIOPHAGE MU / BASEPLATE / GENE PRODUCT 44
Function / homology
Function and homology information


symbiont genome ejection through host cell envelope, contractile tail mechanism / virus tail, baseplate / viral tail assembly / host cell cytoplasm
Similarity search - Function
Baseplate protein-like domain - beta roll fold / Baseplate protein-like domains - 2 layer sandwich fold / Baseplate-like, two-layer sandwich fold / Baseplate protein GpP / Phage tail proteins - horseshoe like beta roll fold / Baseplate protein-like domains / Phage tail baseplate hub (GPD) / Phage tail protein beta-alpha-beta fold / Phage tail proteins - 2 layer sandwich fold / 3-Layer(bab) Sandwich ...Baseplate protein-like domain - beta roll fold / Baseplate protein-like domains - 2 layer sandwich fold / Baseplate-like, two-layer sandwich fold / Baseplate protein GpP / Phage tail proteins - horseshoe like beta roll fold / Baseplate protein-like domains / Phage tail baseplate hub (GPD) / Phage tail protein beta-alpha-beta fold / Phage tail proteins - 2 layer sandwich fold / 3-Layer(bab) Sandwich / Roll / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Baseplate hub protein gp44
Similarity search - Component
Biological speciesEnterobacteria phage Mu (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2.1 Å
AuthorsKondou, Y. / Kitazawa, D. / Takeda, S. / Yamashita, E. / Mizuguchi, M. / Kawano, K. / Tsukihara, T.
CitationJournal: To be Published
Title: Structure of central hub elucidated by X-ray analysis of gene product 44; baseplate component of bacteriophage Mu
Authors: Kondou, Y. / Kitazawa, D. / Takeda, S. / Yamashita, E. / Mizuguchi, M. / Kawano, K. / Tsukihara, T.
History
DepositionOct 27, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 20, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 43 kDa tail protein


Theoretical massNumber of molelcules
Total (without water)41,8401
Polymers41,8401
Non-polymers00
Water3,243180
1
A: 43 kDa tail protein

A: 43 kDa tail protein

A: 43 kDa tail protein


Theoretical massNumber of molelcules
Total (without water)125,5203
Polymers125,5203
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
Buried area7080 Å2
ΔGint-34 kcal/mol
Surface area41250 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)126.562, 126.562, 64.214
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3
DetailsThe biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: -Y+1,X-Y,Z and Y-X+1,-X+1,Z

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Components

#1: Protein 43 kDa tail protein / gpP / gene product 44


Mass: 41840.078 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Mu (virus) / Genus: Mu-like viruses / Gene: 44 / Plasmid: pET17b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: P08558
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 180 / 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: 2.4 Å3/Da / Density % sol: 49.2 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 8
Details: MPD, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å
DetectorType: Bruker DIP-6040 / Detector: CCD / Date: Jul 1, 2003
RadiationMonochromator: MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2.08→40 Å / Num. obs: 23274 / % possible obs: 100 % / Observed criterion σ(F): 0 / Biso Wilson estimate: 54.9 Å2
Reflection shellResolution: 2.08→2.19 Å / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: MIR / Resolution: 2.1→27.7 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 7589999.43 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.249 1105 4.9 %RANDOM
Rwork0.222 ---
obs0.222 22393 100 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 74.5788 Å2 / ksol: 0.32576 e/Å3
Displacement parametersBiso mean: 61.2 Å2
Baniso -1Baniso -2Baniso -3
1--4.17 Å20.69 Å20 Å2
2---4.17 Å20 Å2
3---8.34 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.39 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.38 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.1→27.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 0 180 2697
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.1
X-RAY DIFFRACTIONc_improper_angle_d0.74
X-RAY DIFFRACTIONc_mcbond_it4.681.5
X-RAY DIFFRACTIONc_mcangle_it7.692
X-RAY DIFFRACTIONc_scbond_it6.962
X-RAY DIFFRACTIONc_scangle_it10.842.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.386 198 5.3 %
Rwork0.343 3549 -
obs--100 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER_REP.TOP

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