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- PDB-3vtn: The crystal structure of the C-terminal domain of Mu phage centra... -

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Basic information

Entry
Database: PDB / ID: 3vtn
TitleThe crystal structure of the C-terminal domain of Mu phage central spike - Pt derivative for MAD
ComponentsProtein gp45
KeywordsMETAL BINDING PROTEIN / beta-helix / central spike / Mu phage
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 / metal ion binding
Similarity search - Function
N-terminal domain of TfIIb - #540 / Phage-associated protein Gp45 / : / Bacteriophage Mu Gp45, N-terminal / Phage spike trimer / Phage baseplate assembly protein V/Gp45 / N-terminal domain of TfIIb / Single Sheet / Mainly Beta
Similarity search - Domain/homology
: / : / Baseplate puncturing device gp45
Similarity search - Component
Biological speciesEnterobacteria phage Mu (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.75 Å
AuthorsHarada, K. / Yamashita, E. / Nakagawa, A. / Takeda, S.
CitationJournal: Biochim.Biophys.Acta / Year: 2013
Title: Crystal structure of the C-terminal domain of Mu phage central spike and functions of bound calcium ion
Authors: Harada, K. / Yamashita, E. / Nakagawa, A. / Miyafusa, T. / Tsumoto, K. / Ueno, T. / Toyama, Y. / Takeda, S.
History
DepositionJun 1, 2012Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 6, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Protein gp45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,1633
Polymers10,9121
Non-polymers2512
Water19811
1
A: Protein gp45
hetero molecules

A: Protein gp45
hetero molecules

A: Protein gp45
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,4899
Polymers32,7363
Non-polymers7536
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
Buried area15360 Å2
ΔGint-176 kcal/mol
Surface area9800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.171, 47.171, 72.114
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number150
Space group name H-MP321

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Components

#1: Protein Protein gp45


Mass: 10912.162 Da / Num. of mol.: 1 / Fragment: UNP residues 100-197
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage Mu (virus) / Gene: 45 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9T1V4
#2: Chemical ChemComp-PT / PLATINUM (II) ION


Mass: 195.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Pt
#3: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 11 / 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: 2.12 Å3/Da / Density % sol: 42.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 21% PEG 8000, 0.1M acetate pH 4.5, 0.2M sodium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 1.0717, 1.0721, 1.0539
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Sep 30, 2011
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.07171
21.07211
31.05391
ReflectionResolution: 1.75→36.06 Å / Num. obs: 9825

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Processing

Software
NameVersionClassification
SHARPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MAD / Resolution: 1.75→36.06 Å / Cor.coef. Fo:Fc: 0.913 / Cor.coef. Fo:Fc free: 0.875 / SU B: 2.701 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.137 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30418 467 4.8 %RANDOM
Rwork0.2728 ---
obs0.27436 9223 98.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.963 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→36.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms542 0 2 11 555
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022547
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6761.964736
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.151570
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.28224.54522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.72115105
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.528154
X-RAY DIFFRACTIONr_chiral_restr0.1160.289
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021392
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0931.5350
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.8562572
X-RAY DIFFRACTIONr_scbond_it3.0753197
X-RAY DIFFRACTIONr_scangle_it4.7324.5164
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 37 -
Rwork0.319 656 -
obs--98.02 %

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