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- PDB-1n80: Bacteriophage T4 baseplate structural protein gp8 -

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Basic information

Entry
Database: PDB / ID: 1n80
TitleBacteriophage T4 baseplate structural protein gp8
Componentsbaseplate structural protein gp8
KeywordsVIRAL PROTEIN / bacteriophage T4 / baseplate / dimer / beta sandwich / halide binding
Function / homology
Function and homology information


virus tail, baseplate / viral tail assembly
Similarity search - Function
baseplate structural protein gp8, domain 2 / baseplate structural protein gp8, domain 2 / baseplate structural protein gp8, domain 1 / baseplate structural protein gp8, domain 1 / Bacteriophage T4, Gp8 / Bacteriophage T4, Gp8 superfamily / Bacteriophage T4, Gp8 / Beta Complex / Sandwich / Mainly Beta
Similarity search - Domain/homology
Baseplate wedge protein gp8
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsLeiman, P.G. / Shneider, M.M. / Kostyuchenko, V.A. / Chipman, P.R. / Mesyanzhinov, V.V. / Rossmann, M.G.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structure and location of gene product 8 in the bacteriophage T4 baseplate
Authors: Leiman, P.G. / Shneider, M.M. / Kostyuchenko, V.A. / Chipman, P.R. / Mesyanzhinov, V.V. / Rossmann, M.G.
History
DepositionNov 18, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: baseplate structural protein gp8
B: baseplate structural protein gp8
C: baseplate structural protein gp8
D: baseplate structural protein gp8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)153,30136
Polymers152,1674
Non-polymers1,13432
Water8,287460
1
A: baseplate structural protein gp8
B: baseplate structural protein gp8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,65118
Polymers76,0832
Non-polymers56716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7030 Å2
ΔGint-171 kcal/mol
Surface area30540 Å2
MethodPISA
2
C: baseplate structural protein gp8
D: baseplate structural protein gp8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)76,65118
Polymers76,0832
Non-polymers56716
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7160 Å2
ΔGint-177 kcal/mol
Surface area30180 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area16430 Å2
ΔGint-362 kcal/mol
Surface area58480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.869, 66.777, 82.158
Angle α, β, γ (deg.)93.11, 101.28, 90.77
Int Tables number1
Space group name H-MP1
Detailsthe asymmetric unit contains two biologically active identical dimers

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Components

#1: Protein
baseplate structural protein gp8 / Baseplate wedge protein 8


Mass: 38041.668 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Genus: T4-like viruses / Species: Enterobacteria phage T4 sensu lato / Gene: gene 8 / Plasmid: pET-22b(+) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P19062
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 32 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.33 Å3/Da / Density % sol: 46.77 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, PEG 6000, LiCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K
Crystal grow
*PLUS
pH: 7.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mg/mlprotein1drop
210 mMTris-HCl1droppH7.5
31 mMdithiothreitol1drop
41 M1reservoirLiCl
512 mMZwittergent-3-101reservoir
60.1 MHEPES1reservoirpH7.0
716 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 28, 2000 / Details: Bent conical Si-mirror (Rh coating)
RadiationMonochromator: Bent Ge(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. all: 51148 / Num. obs: 49960 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Biso Wilson estimate: 38 Å2 / Rmerge(I) obs: 0.053 / Net I/σ(I): 19.1
Reflection shellResolution: 2.45→2.49 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.176 / Mean I/σ(I) obs: 9.1 / Num. unique all: 2133 / % possible all: 82.4
Reflection
*PLUS
Lowest resolution: 50 Å
Reflection shell
*PLUS
% possible obs: 82.4 % / Redundancy: 2.9 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1N7Z
Resolution: 2.45→39.11 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1056545.54 / Data cutoff high rms absF: 1056545.54 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.284 1286 2.6 %RANDOM
Rwork0.236 ---
all0.237231 51148 --
obs0.236 49960 97.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.1366 Å2 / ksol: 0.342653 e/Å3
Displacement parametersBiso mean: 44.4 Å2
Baniso -1Baniso -2Baniso -3
1--6.19 Å22.37 Å2-0.31 Å2
2---7.94 Å2-0.37 Å2
3---14.13 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.34 Å
Luzzati d res low-5 Å
Luzzati sigma a0.44 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.45→39.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10524 0 32 460 11016
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.481.5
X-RAY DIFFRACTIONc_mcangle_it2.522
X-RAY DIFFRACTIONc_scbond_it1.922
X-RAY DIFFRACTIONc_scangle_it2.762.5
LS refinement shellResolution: 2.45→2.56 Å / Rfactor Rfree error: 0.03 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.39 168 2.7 %
Rwork0.297 5983 -
obs--95.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg24.8
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.91

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