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- PDB-2z6b: Crystal Structure Analysis of (gp27-gp5)3 conjugated with Fe(III)... -

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Basic information

Entry
Database: PDB / ID: 2z6b
TitleCrystal Structure Analysis of (gp27-gp5)3 conjugated with Fe(III) protoporphyrin
Components
  • Baseplate structural protein Gp27
  • Tail-associated lysozyme
KeywordsHYDROLASE/STRUCTURAL PROTEIN / Protein containing metal complexes / Antimicrobial / Bacteriolytic enzyme / Glycosidase / Hydrolase / Late protein / Virion / HYDROLASE-STRUCTURAL PROTEIN COMPLEX
Function / homology
Function and homology information


symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity ...symbiont entry into host cell via disruption of host cell wall peptidoglycan / virus tail, baseplate / viral tail assembly / symbiont entry into host cell via disruption of host cell envelope / virus tail / symbiont entry into host / peptidoglycan catabolic process / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to bacterium / symbiont entry into host cell / identical protein binding
Similarity search - Function
Bacteriophage T4, Gp27, baseplate hub, domain 3 / Nucleic acid-binding protein domain / Nuclear Transport Factor 2; Chain: A, - #190 / Phage tail proteins - 2 layer sandwich fold - #40 / Phage tail protein beta-alpha-beta fold - #20 / Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 / Gp27, baseplate hub, domain 2 ...Bacteriophage T4, Gp27, baseplate hub, domain 3 / Nucleic acid-binding protein domain / Nuclear Transport Factor 2; Chain: A, - #190 / Phage tail proteins - 2 layer sandwich fold - #40 / Phage tail protein beta-alpha-beta fold - #20 / Bacteriophage T4, Gp27, baseplate hub, C-terminal / Bacteriophage T4, Gp27, baseplate hub, N-terminal / Gp27, baseplate hub, domain 3 / Gp27, baseplate hub, domain 4 / Gp27, baseplate hub, domain 2 / Baseplate structural protein, domain 2 / Baseplate structural protein, domain 1 / Protein Gp5, N-terminal OB-fold domain / Gp5, C-terminal / Pre-baseplate central spike protein Gp5 / Gp5 N-terminal OB domain / Gp5 C-terminal repeat (3 copies) / Phage tail protein beta-alpha-beta fold / Phage tail proteins - 2 layer sandwich fold / 3-Layer(bab) Sandwich / Lysozyme - #40 / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Elongation Factor Tu (Ef-tu); domain 3 / Nuclear Transport Factor 2; Chain: A, / Lysozyme / OB fold (Dihydrolipoamide Acetyltransferase, E2P) / Lysozyme-like domain superfamily / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Roll / Beta Barrel / 2-Layer Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
1-ETHYL-PYRROLIDINE-2,5-DIONE / Pre-baseplate central spike protein Gp5 / Baseplate central spike complex protein gp27
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsKoshiyama, T. / Yokoi, N. / Ueno, T. / Kanamaru, S. / Nagano, S. / Shiro, Y. / Arisaka, F. / Watanabe, Y.
CitationJournal: Small / Year: 2008
Title: Molecular design of heteroprotein assemblies providing a bionanocup as a chemical reactor.
Authors: Koshiyama, T. / Yokoi, N. / Ueno, T. / Kanamaru, S. / Nagano, S. / Shiro, Y. / Arisaka, F. / Watanabe, Y.
History
DepositionJul 28, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
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
Revision 1.3Nov 1, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tail-associated lysozyme
D: Baseplate structural protein Gp27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,8873
Polymers108,7602
Non-polymers1271
Water5,783321
1
A: Tail-associated lysozyme
D: Baseplate structural protein Gp27
hetero molecules

A: Tail-associated lysozyme
D: Baseplate structural protein Gp27
hetero molecules

A: Tail-associated lysozyme
D: Baseplate structural protein Gp27
hetero molecules


Theoretical massNumber of molelcules
Total (without water)326,6629
Polymers326,2806
Non-polymers3813
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area68820 Å2
ΔGint-306.3 kcal/mol
Surface area103830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)138.536, 138.536, 389.121
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number155
Space group name H-MH32
Components on special symmetry positions
IDModelComponents
11A-734-

HOH

21A-765-

HOH

31A-766-

HOH

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Components

#1: Protein Tail-associated lysozyme / Protein Gp5


Mass: 64329.027 Da / Num. of mol.: 1 / Mutation: N7C, S351L
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: 5 / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(de3) / References: UniProt: P16009, lysozyme
#2: Protein Baseplate structural protein Gp27 / Hub protein 27


Mass: 44431.062 Da / Num. of mol.: 1
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: 27 / Plasmid: pET29a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): Bl21(de3) / References: UniProt: P17172
#3: Chemical ChemComp-NEN / 1-ETHYL-PYRROLIDINE-2,5-DIONE


Mass: 127.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H9NO2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / 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: 3.3 Å3/Da / Density % sol: 62.77 %
Crystal growTemperature: 285 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: PEG 8000, Tris, Glycerol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 285K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER / Detector: CCD / Date: Dec 8, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.1→50 Å / Num. obs: 26124 / % possible obs: 99.7 % / Redundancy: 10.9 % / Net I/σ(I): 37.8
Reflection shellResolution: 3.1→3.21 Å / Redundancy: 10.6 % / Mean I/σ(I) obs: 6.8 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
HKL-2000data scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1WTH

1wth


Resolution: 3.11→29.64 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 3537789.97 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.315 1286 5 %RANDOM
Rwork0.243 ---
obs0.243 25739 98 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 88.7714 Å2 / ksol: 0.33135 e/Å3
Displacement parametersBiso mean: 53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.54 Å0.37 Å
Luzzati d res low-5 Å
Luzzati sigma a0.66 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 3.11→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7059 0 9 321 7389
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.5
X-RAY DIFFRACTIONc_improper_angle_d0.86
LS refinement shellResolution: 3.11→3.3 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.414 213 5.2 %
Rwork0.297 3917 -
obs-3917 96 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top
X-RAY DIFFRACTION5LCY02.PARamLCY02.TOP

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