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- PDB-4ku0: Enterobacteria phage T4 gp5.4 PAAR repeat protein in complex with... -

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Basic information

Entry
Database: PDB / ID: 4ku0
TitleEnterobacteria phage T4 gp5.4 PAAR repeat protein in complex with T4 gp5 beta-helix fragment
Components
  • Tail-associated lysozyme
  • Uncharacterized 10.2 kDa protein in segC-Gp6 intergenic region
KeywordsHYDROLASE/PROTEIN BINDING / PAAR-repeat motif / membrane piercing / type VI secretion system / T6SS / cell puncturing device / beta-helix / gp5-gp27 protein complex / HYDROLASE-PROTEIN BINDING complex
Function / homology
Function and homology information


peptidoglycan beta-N-acetylmuramidase 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 ...peptidoglycan beta-N-acetylmuramidase 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 / metal ion binding
Similarity search - Function
Tumour Suppressor Smad4 - #60 / 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) / PAAR motif / PAAR motif / Tumour Suppressor Smad4 / T4-type lysozyme ...Tumour Suppressor Smad4 - #60 / 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) / PAAR motif / PAAR motif / Tumour Suppressor Smad4 / T4-type lysozyme / Glycoside hydrolase, family 24 / Lysozyme domain superfamily / Phage lysozyme / Lysozyme-like domain superfamily / Sandwich / Mainly Beta
Similarity search - Domain/homology
9-OCTADECENOIC ACID / : / PALMITIC ACID / STEARIC ACID / Pre-baseplate central spike protein Gp5 / Baseplate puncturing device gp5.4
Similarity search - Component
Biological speciesEnterobacteria phage T4 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsButh, S.A. / Leiman, P.G. / Shneider, M.M.
CitationJournal: To be Published
Title: Crystall structute of the business end of the T4 cell-puncturing device
Authors: Buth, S.A. / Leiman, P.G. / Shneider, M.M.
History
DepositionMay 21, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software
Revision 1.2Nov 8, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _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: Tail-associated lysozyme
B: Tail-associated lysozyme
C: Tail-associated lysozyme
D: Uncharacterized 10.2 kDa protein in segC-Gp6 intergenic region
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,84714
Polymers39,6734
Non-polymers1,17510
Water10,106561
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area25770 Å2
ΔGint-67 kcal/mol
Surface area13960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.302, 49.327, 84.057
Angle α, β, γ (deg.)90.00, 96.19, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 4 molecules ABCD

#1: Protein Tail-associated lysozyme / Protein Gp5 / Gp5C


Mass: 9856.678 Da / Num. of mol.: 3 / Fragment: residues 484-575
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 5 / Plasmid: pEEva2, a pET23a derivative / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P16009, lysozyme
#2: Protein Uncharacterized 10.2 kDa protein in segC-Gp6 intergenic region / gp5.4


Mass: 10102.467 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Enterobacteria phage T4 (virus) / Gene: 5.4, y08B / Plasmid: pEEva2, a pET23a derivative / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P39234

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Non-polymers , 8 types, 571 molecules

#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ELA / 9-OCTADECENOIC ACID


Mass: 282.461 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H34O2
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-STE / STEARIC ACID


Mass: 284.477 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H36O2
#7: Chemical ChemComp-PLM / PALMITIC ACID


Mass: 256.424 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H32O2
#8: Chemical ChemComp-FE / FE (III) ION


Mass: 55.845 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe
#9: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 561 / 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: 2.41 Å3/Da / Density % sol: 48.87 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 23-25% PEG 3350, 100mM Tris pH=8.5, 40-100mM MgCl2, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2012 / Details: dynamically bendable mirror
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→46 Å / Num. all: 129006 / Num. obs: 124490 / % possible obs: 96.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 6.13 % / Biso Wilson estimate: 18.103 Å2 / Rmerge(I) obs: 0.0532 / Net I/σ(I): 12.12
Reflection shellResolution: 1.15→1.22 Å / Redundancy: 4.12 % / Mean I/σ(I) obs: 2.27 / Num. unique all: 21326 / % possible all: 81.3

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Processing

Software
NameClassification
PHASERphasing
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JJ2

4jj2


Resolution: 1.15→46 Å / Num. parameters: 31827 / Num. restraintsaints: 40407 / Cross valid method: THROUGHOUT / σ(F): 4 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.171 4516 3.63 %RANDOM
all0.1367 129006 --
obs0.1265 124490 96.2 %-
Refine analyzeNum. disordered residues: 23 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 3356.94
Refinement stepCycle: LAST / Resolution: 1.15→46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2719 0 77 561 3357
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.0134
X-RAY DIFFRACTIONs_angle_d0.0296
X-RAY DIFFRACTIONs_similar_dist0.0278
X-RAY DIFFRACTIONs_from_restr_planes0.0052
X-RAY DIFFRACTIONs_zero_chiral_vol0.0747
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.0946
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.0271
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.0473
X-RAY DIFFRACTIONs_approx_iso_adps0.1483

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