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- PDB-4y9v: Gp54 tailspike of Acinetobacter baumannii bacteriophage AP22 in c... -

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Basic information

Entry
Database: PDB / ID: 4y9v
TitleGp54 tailspike of Acinetobacter baumannii bacteriophage AP22 in complex with A. baumannii capsular saccharide
ComponentsParticle-associated lyase
KeywordsLYASE / AP22 / bacteriophage / capsular polysaccharide / degradation / polysaccharide structure / capsule
Function / homology: / Gp49, pectin lyase-like / : / Tailspike protein-like, Ig-like domain / Tail fiber protein
Function and homology information
Biological speciesAcinetobacter bacteriophage AP22 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 0.9 Å
AuthorsButh, S.A. / Shneider, M.M. / Leiman, P.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
Ecole Polytechnique Federale de Lausanne0577-1 Switzerland
CitationJournal: TO BE PUBLISHED
Title: Structure of Acinetobacter baumannii bacteriophage AP22 polysaccharide degrading lyase in complex with A. baumannii capsular saccharide at 0.9 A resolution
Authors: Buth, S.A. / Shneider, M.M. / Leiman, P.G.
History
DepositionFeb 17, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Feb 1, 2017Provider: repository / Type: Initial release
Revision 1.1Feb 15, 2017Group: Derived calculations
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_alt_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _atom_site_anisotrop.U[1][1] / _atom_site_anisotrop.U[1][2] / _atom_site_anisotrop.U[1][3] / _atom_site_anisotrop.U[2][2] / _atom_site_anisotrop.U[2][3] / _atom_site_anisotrop.U[3][3] / _atom_site_anisotrop.id / _atom_site_anisotrop.pdbx_auth_asym_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_auth_comp_id / _atom_site_anisotrop.pdbx_auth_seq_id / _atom_site_anisotrop.pdbx_label_alt_id / _atom_site_anisotrop.pdbx_label_asym_id / _atom_site_anisotrop.pdbx_label_atom_id / _atom_site_anisotrop.pdbx_label_comp_id / _atom_site_anisotrop.type_symbol / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_conn.ptnr2_symmetry / _struct_conn_type.id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entity_branch_link.leaving_atom_id_1 / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Particle-associated lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,09815
Polymers68,6941
Non-polymers1,40414
Water24,6451368
1
A: Particle-associated lyase
hetero molecules

A: Particle-associated lyase
hetero molecules

A: Particle-associated lyase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,29545
Polymers206,0823
Non-polymers4,21242
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
Buried area25680 Å2
ΔGint-110 kcal/mol
Surface area53670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.634, 92.634, 391.478
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-811-

CL

21A-812-

NA

31A-2297-

HOH

41A-2400-

HOH

51A-3153-

HOH

61A-3231-

HOH

71A-3263-

HOH

81A-3280-

HOH

91A-3326-

HOH

101A-3331-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Particle-associated lyase


Mass: 68694.164 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: GSG is a remnant of the linker connecting the target protein with the expression enhancing leader tag (SlyD domain). A TEV protease cleavage site precedes the GSG sequence.
Source: (gene. exp.) Acinetobacter bacteriophage AP22 (virus)
Plasmid: pTSL (pET23 derivative)
Details (production host): pET23 with cloned SlyD gene, N-terminal His-tag and TEV recognition site
Production host: Escherichia coli B (bacteria) / Strain (production host): 834 / References: UniProt: I2GUG1
#2: Polysaccharide 2-acetamido-2,4-dideoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-alpha-D- ...2-acetamido-2,4-dideoxy-alpha-L-erythro-hex-4-enopyranuronic acid-(1-3)-2-acetamido-2-deoxy-alpha-D-fucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-mannopyranuronic acid


Type: oligosaccharide / Mass: 621.545 Da / Num. of mol.: 1 / Source method: obtained synthetically
DescriptorTypeProgram
WURCS=2.0/3,3,2/[a1122A-1b_1-5_2*NCC/3=O][a2112m-1a_1-5_2*NCC/3=O][a11eEA-1a_1-5_2*NCC/3=O]/1-2-3/a4-b1_b3-c1WURCSPDB2Glycan 1.1.0

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Non-polymers , 5 types, 1381 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1368 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.81 Å3/Da / Density % sol: 49.42 % / Description: rhombohedron
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1 / Details: 6-10% PEG8000, 500mM Li2SO4, 100mM MES pH 6.5 / PH range: 6.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.8 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 5, 2012
RadiationMonochromator: Si(111) monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 0.9→45.9 Å / Num. obs: 466729 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.5 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 13.7
Reflection shellResolution: 0.9→0.96 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.353 / Mean I/σ(I) obs: 3 / % possible all: 86.3

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Processing

Software
NameClassification
Cootmodel building
XDSdata reduction
XSCALEdata scaling
SHELXphasing
SHELXLrefinement
SHELXL-97refinement
RefinementMethod to determine structure: SAD / Resolution: 0.9→45.9 Å / Num. parameters: 55596 / Num. restraintsaints: 75024 / Cross valid method: FREE R-VALUE / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF) BY ?
RfactorNum. reflection% reflectionSelection details
Rfree0.1092 4668 1 %RANDOM
Rwork0.0971 ---
all0.0972 462061 --
obs0.0972 462061 97.9 %-
Refine analyzeNum. disordered residues: 796 / Occupancy sum hydrogen: 4529.46 / Occupancy sum non hydrogen: 5868.42
Refinement stepCycle: LAST / Resolution: 0.9→45.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5409 0 89 1402 6900
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.03
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0335
X-RAY DIFFRACTIONs_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.098
X-RAY DIFFRACTIONs_anti_bump_dis_restr0
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.025
X-RAY DIFFRACTIONs_approx_iso_adps0

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