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- PDB-3ct1: Crystal and cryoEM structural studies of a cell wall degrading en... -

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Basic information

Entry
Database: PDB / ID: 3ct1
TitleCrystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail
ComponentsMorphogenesis protein 1
KeywordsHYDROLASE / Cell wall / phi29 / infection / Late protein
Function / homology
Function and homology information


virus tail, tip / virus tail fiber assembly / symbiont entry into host cell via disruption of host cell wall peptidoglycan / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, acting on glycosyl bonds / Hydrolases; Acting on peptide bonds (peptidases) / cell wall organization / metallopeptidase activity ...virus tail, tip / virus tail fiber assembly / symbiont entry into host cell via disruption of host cell wall peptidoglycan / symbiont genome ejection through host cell envelope, short tail mechanism / symbiont entry into host cell via disruption of host cell envelope / Hydrolases; Glycosylases; Glycosidases, i.e. enzymes that hydrolyse O- and S-glycosyl compounds / hydrolase activity, acting on glycosyl bonds / Hydrolases; Acting on peptide bonds (peptidases) / cell wall organization / metallopeptidase activity / killing of cells of another organism / defense response to bacterium / proteolysis / metal ion binding
Similarity search - Function
Phage tail lysozyme / Phage tail lysozyme / Duplicated hybrid motif / Lysozyme - #10 / Lysozyme / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
triacetyl-beta-chitotriose / Morphogenesis protein 1
Similarity search - Component
Biological speciesBacteriophage phi-29 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.51 Å
AuthorsXiang, Y. / Rossmann, M.G.
CitationJournal: Proc Natl Acad Sci U S A / Year: 2008
Title: Crystal and cryoEM structural studies of a cell wall degrading enzyme in the bacteriophage phi29 tail.
Authors: Ye Xiang / Marc C Morais / Daniel N Cohen / Valorie D Bowman / Dwight L Anderson / Michael G Rossmann /
Abstract: The small bacteriophage phi29 must penetrate the approximately 250-A thick external peptidoglycan cell wall and cell membrane of the Gram-positive Bacillus subtilis, before ejecting its dsDNA genome ...The small bacteriophage phi29 must penetrate the approximately 250-A thick external peptidoglycan cell wall and cell membrane of the Gram-positive Bacillus subtilis, before ejecting its dsDNA genome through its tail into the bacterial cytoplasm. The tail of bacteriophage phi29 is noncontractile and approximately 380 A long. A 1.8-A resolution crystal structure of gene product 13 (gp13) shows that this tail protein has spatially well separated N- and C-terminal domains, whose structures resemble lysozyme-like enzymes and metallo-endopeptidases, respectively. CryoEM reconstructions of the WT bacteriophage and mutant bacteriophages missing some or most of gp13 shows that this enzyme is located at the distal end of the phi29 tail knob. This finding suggests that gp13 functions as a tail-associated, peptidoglycan-degrading enzyme able to cleave both the polysaccharide backbone and peptide cross-links of the peptidoglycan cell wall. Comparisons of the gp13(-) mutants with the phi29 mature and emptied phage structures suggest the sequence of events that occur during the penetration of the tail through the peptidoglycan layer.
History
DepositionApr 11, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Feb 21, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Morphogenesis protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,0682
Polymers18,4411
Non-polymers6281
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)30.800, 69.388, 71.208
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Morphogenesis protein 1 / / Late protein GP13


Mass: 18440.746 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacteriophage phi-29 (virus) / Gene: 13 / Plasmid: PTYB1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21DE3 CODON PLUS RP / References: UniProt: P15132
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose / triacetyl-beta-chitotriose


Type: oligosaccharide, Oligosaccharide / Class: Inhibitor / Mass: 627.594 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: triacetyl-beta-chitotriose
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,3,2/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTORS STATE THAT RESIDUE 89 SHOULD BE ASN ACCORDING TO THEIR SEQUENCING RESULTS OF THE GENE.

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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: 2.06 Å3/Da / Density % sol: 40.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8
Details: 20% PEG4000, 100mM Tris-HCl, 10% glycerol, 10mM NAG5, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 14-BM-C / Wavelength: 0.9 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Details: MIRRORS
RadiationMonochromator: Ge 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1.5→35.6 Å / Num. obs: 23681 / % possible obs: 96.4 % / Rmerge(I) obs: 0.06 / Rsym value: 6 / Net I/σ(I): 24.5
Reflection shellResolution: 1.5→1.55 Å / Rmerge(I) obs: 0.373 / Mean I/σ(I) obs: 4.4 / Rsym value: 37.3 / % possible all: 99.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.51→35.6 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.165 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22177 1160 4.9 %RANDOM
Rwork0.19214 ---
obs0.19357 22521 95.25 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.585 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.32 Å20 Å2
3---0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.51→35.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1296 0 43 126 1465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221385
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5271.9711888
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.85162
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.27925.58868
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15715232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.68155
X-RAY DIFFRACTIONr_chiral_restr0.0950.2203
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021052
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2110.2661
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3170.2963
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.2109
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1780.218
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2710.29
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8531.5824
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.20821290
X-RAY DIFFRACTIONr_scbond_it2.0493672
X-RAY DIFFRACTIONr_scangle_it2.6824.5596
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.51→1.546 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 84 -
Rwork0.239 1423 -
obs--82.48 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.73020.69870.11212.9510.05290.8991-0.06770.02640.05790.25470.09210.0152-0.0583-0.0052-0.0244-0.13970.0183-0.0054-0.13540.0038-0.14781.51824.527618.5228
220.71514.015613.297627.63735.392514.2175-0.57371.12070.7565-1.28450.67930.0869-0.79070.0289-0.1057-0.0203-0.0652-0.04470.0460.093-0.0499-0.289532.40037.6164
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 1591 - 159
2X-RAY DIFFRACTION2AB201 - 2031 - 3

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