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- PDB-1n7z: Structure and location of gene product 8 in the bacteriophage T4 ... -

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Basic information

Entry
Database: PDB / ID: 1n7z
TitleStructure and location of gene product 8 in the bacteriophage T4 baseplate
Componentsbaseplate structural protein gp8
KeywordsVIRAL PROTEIN / bacteriophage T4 / baseplate / dimer / beta sandwich
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 / MAD / Resolution: 2 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 1.3Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / 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_conn.pdbx_leaving_atom_flag / _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

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)155,48134
Polymers154,4184
Non-polymers1,06430
Water18,4651025
1
A: baseplate structural protein gp8
B: baseplate structural protein gp8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,74117
Polymers77,2092
Non-polymers53215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7220 Å2
ΔGint-167 kcal/mol
Surface area30020 Å2
MethodPISA
2
C: baseplate structural protein gp8
D: baseplate structural protein gp8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)77,74117
Polymers77,2092
Non-polymers53215
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7290 Å2
ΔGint-168 kcal/mol
Surface area30150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.388, 78.472, 88.227
Angle α, β, γ (deg.)110.96, 97.60, 111.39
Int Tables number1
Space group name H-MP1

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Components

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


Mass: 38604.406 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(+) / Production host: Escherichia coli (E. coli) / Strain (production host): 834 (DE3) / References: UniProt: P19062
#2: Chemical...
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1025 / 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: 2.35 Å3/Da / Density % sol: 47.25 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 7
Details: HEPES, PEG 6000, LiCl, DTT, 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
41.5 M1reservoirLiCl
51 mMdithiothreitol1reservoir
60.1 MHEPES1reservoirpH7.0
716 %PEG60001reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-D / Wavelength: 0.9797, 0.9799,0.9426
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 15, 2001 / Details: Bent cylindrical Si-mirror (Rh coating)
RadiationMonochromator: Si(111) double-crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97971
20.97991
30.94261
ReflectionResolution: 2→50 Å / Num. all: 99719 / Num. obs: 97218 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.9 % / Biso Wilson estimate: 18.1 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 15.1
Reflection shellResolution: 2→2.03 Å / Redundancy: 1.6 % / Rmerge(I) obs: 0.297 / Mean I/σ(I) obs: 4.2 / Num. unique all: 4777 / % possible all: 96.5
Reflection
*PLUS
Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 96.5 % / Redundancy: 1.8 %

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHELXmodel building
CNS1.1refinement
SHELXphasing
RefinementMethod to determine structure: MAD / Resolution: 2→27.08 Å / Rfactor Rfree error: 0.005 / Data cutoff high absF: 1338852.16 / Data cutoff high rms absF: 1338852.16 / 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
Rfree0.24 2410 2.5 %RANDOM
Rwork0.213 ---
all0.213692 99719 --
obs0.213692 97218 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.0041 Å2 / ksol: 0.315156 e/Å3
Displacement parametersBiso mean: 31.4 Å2
Baniso -1Baniso -2Baniso -3
1--6 Å22.05 Å22.84 Å2
2--4.08 Å24.85 Å2
3---1.93 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→27.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10524 0 30 1025 11579
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d25
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.421.5
X-RAY DIFFRACTIONc_mcangle_it2.182
X-RAY DIFFRACTIONc_scbond_it2.132
X-RAY DIFFRACTIONc_scangle_it2.982.5
LS refinement shellResolution: 2→2.09 Å / Rfactor Rfree error: 0.017 / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rfree0.298 308 2.6 %
Rwork0.25 11672 -
obs--96.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 40 Å / Rfactor Rwork: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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