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- PDB-4p7r: Structure of Escherichia coli PgaB C-terminal domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 4p7r
TitleStructure of Escherichia coli PgaB C-terminal domain in complex with a poly-beta-1,6-N-acetyl-D-glucosamine (PNAG) hexamer
ComponentsPoly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
KeywordsHYDROLASE / beta alpha barrel / carbohydrate binding / glycosyl hydrolase fold / complex
Function / homology
Function and homology information


macromolecule deacylation / cell adhesion involved in biofilm formation / hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds / single-species biofilm formation / Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides / hydrolase activity, hydrolyzing O-glycosyl compounds / cell outer membrane / carbohydrate metabolic process
Similarity search - Function
Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB / Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, C-terminal / Hypothetical glycosyl hydrolase family 13 / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycosidases / TIM Barrel ...Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB / Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase PgaB, C-terminal / Hypothetical glycosyl hydrolase family 13 / NodB homology domain profile. / NodB homology domain / Polysaccharide deacetylase / Glycoside hydrolase/deacetylase, beta/alpha-barrel / Prokaryotic membrane lipoprotein lipid attachment site profile. / Glycosidases / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.8 Å
AuthorsLittle, D.J. / Li, G. / Ing, C. / DiFrancesco, B. / Bamford, N.C. / Robinson, H. / Nitz, M. / Pomes, R. / Howell, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2014
Title: Modification and periplasmic translocation of the biofilm exopolysaccharide poly-beta-1,6-N-acetyl-D-glucosamine.
Authors: Little, D.J. / Li, G. / Ing, C. / DiFrancesco, B.R. / Bamford, N.C. / Robinson, H. / Nitz, M. / Pomes, R. / Howell, P.L.
History
DepositionMar 27, 2014Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 23, 2014Group: Database references
Revision 1.2Oct 1, 2014Group: Database references
Revision 2.0Nov 22, 2017Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / citation ...atom_site / citation / entity / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_oper_list / software / struct_conn / struct_site_gen
Item: _atom_site.label_asym_id / _citation.journal_id_CSD ..._atom_site.label_asym_id / _citation.journal_id_CSD / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_label_asym_id / _struct_site_gen.label_asym_id
Revision 2.1Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 3.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Refinement description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / 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_nonpoly_scheme / pdbx_struct_assembly_gen / refine_hist / struct_asym / struct_conn / 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_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein / _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 3.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4595
Polymers42,4421
Non-polymers1,0174
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint26 kcal/mol
Surface area15540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.232, 77.786, 114.844
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Detailsbiological unit is the same as asym.

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Components

#1: Protein Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase / PgaB / Poly-beta-1 / 6-GlcNAc N-deacetylase


Mass: 42441.867 Da / Num. of mol.: 1 / Fragment: UNP residues 310-672
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: pgaB, ycdR, b1023, JW5142 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
References: UniProt: P75906, Hydrolases; Acting on carbon-nitrogen bonds, other than peptide bonds; In linear amides
#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 830.786 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-6DGlcpNAcb1-6DGlcpNAcb1-6DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,4,3/[a2122h-1b_1-5_2*NCC/3=O]/1-1-1-1/a6-b1_b6-c1_c6-d1WURCSPDB2Glycan 1.1.0
[][b-D-GlcpNAc]{[(6+1)][b-D-GlcpNAc]{[(6+1)][b-D-GlcpNAc]{[(6+1)][b-D-GlcpNAc]{}}}}LINUCSPDB-CARE
#3: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.22 Å3/Da / Density % sol: 44.65 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 18% PEG3350, 0.1 M Bis-Tris, 25 mM PNAG hexamer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.08 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 10, 2013
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 35680 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 10.2 % / Biso Wilson estimate: 25.09 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 48.3
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.557 / Mean I/σ(I) obs: 5.9 / % possible all: 100

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: dev_1615)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4P7L

4p7l


Resolution: 1.8→39.64 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 18.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.192 2000 5.62 %
Rwork0.158 --
obs0.16 35603 99.7 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 32.29 Å2
Refinement stepCycle: final / Resolution: 1.8→39.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2914 0 69 221 3204
Biso mean--65.44 42.12 -
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073062
X-RAY DIFFRACTIONf_angle_d1.1464167
X-RAY DIFFRACTIONf_dihedral_angle_d18.2411130
X-RAY DIFFRACTIONf_chiral_restr0.055451
X-RAY DIFFRACTIONf_plane_restr0.005538
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8034-1.84850.23891360.19252287X-RAY DIFFRACTION96
1.8485-1.89850.24531400.18062361X-RAY DIFFRACTION100
1.8985-1.95440.22821410.17162363X-RAY DIFFRACTION100
1.9544-2.01750.20631420.1612382X-RAY DIFFRACTION100
2.0175-2.08960.19091410.15752368X-RAY DIFFRACTION100
2.0896-2.17320.21961400.16322358X-RAY DIFFRACTION100
2.1732-2.27210.17971430.15742385X-RAY DIFFRACTION100
2.2721-2.39190.18541420.15792402X-RAY DIFFRACTION100
2.3919-2.54170.19821430.16242400X-RAY DIFFRACTION100
2.5417-2.73790.22051420.16482394X-RAY DIFFRACTION100
2.7379-3.01340.17961450.1662430X-RAY DIFFRACTION100
3.0134-3.44920.19821440.15712419X-RAY DIFFRACTION100
3.4492-4.34470.17261470.1412466X-RAY DIFFRACTION100
4.3447-39.64650.18041540.1562588X-RAY DIFFRACTION100
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)
12.3844-1.4085-0.62972.87041.75652.95070.14830.1620.0172-0.1531-0.1046-0.1448-0.0054-0.063-0.03730.20.0025-0.00850.1739-0.00140.214224.618463.526117.4762
21.0437-1.19570.73835.157-1.76213.08050.13430.1902-0.0808-0.3786-0.1157-0.03730.1086-0.0252-0.01940.17080.02060.01440.1891-0.02820.164917.963271.5036113.5722
31.2889-0.6316-0.01673.6195-0.49831.43630.09020.05460.0395-0.1212-0.1353-0.0599-0.0780.00080.04030.1378-0.00470.00580.18310.00640.139613.364886.0129119.1252
42.63190.04311.13443.61921.39638.1585-0.0921-0.16290.43640.1751-0.03290.1203-0.8509-0.12780.14210.27370.02130.00380.2326-0.01710.22216.1254103.1376130.7081
51.33382.18522.45734.54756.69046.24160.068-0.0802-0.06190.139-0.40910.46330.1104-0.40420.42730.2193-0.0093-0.00180.2444-0.02990.25844.637185.2597127.1296
63.0151-1.3350.6172.5546-0.52921.6693-0.1328-0.24530.08830.39250.0733-0.0438-0.0478-0.0730.06710.2071-0.01840.01350.1716-0.00150.1418.085779.6193136.734
74.4684-0.8074-0.10012.84720.77613.95980.0508-0.0077-0.03230.0317-0.0064-0.09550.08840.1714-0.01750.1703-0.0113-0.01560.12360.00850.142827.522568.5498132.8873
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 310 THROUGH 346 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 347 THROUGH 391 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 392 THROUGH 477 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 478 THROUGH 502 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 503 THROUGH 529 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 530 THROUGH 595 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 596 THROUGH 668 )

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