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- PDB-4p7q: Structure of Escherichia coli PgaB C-terminal domain in complex w... -

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Basic information

Entry
Database: PDB / ID: 4p7q
TitleStructure of Escherichia coli PgaB C-terminal domain in complex with N-acetylglucosamine
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: 1.651 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 1.3Nov 22, 2017Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description / Source and taxonomy / Structure summary
Category: citation / entity ...citation / entity / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity.pdbx_description ..._citation.journal_id_CSD / _entity.pdbx_description / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_prop.type / _pdbx_struct_assembly_prop.value / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Refinement description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / refine_hist / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.6Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4517
Polymers42,4421
Non-polymers1,0096
Water5,405300
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint18 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.380, 77.958, 115.276
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#3: Sugar
ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE / N-Acetylglucosamine


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 300 / 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: 2.24 Å3/Da / Density % sol: 45.17 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG3350, 0.1 M Bis-Tris, 0.5 M N-acetylglucosamine

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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 5, 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: 1.65→50 Å / Num. obs: 46798 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 14.1 % / Biso Wilson estimate: 23.77 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 64.8
Reflection shellResolution: 1.65→1.71 Å / Redundancy: 13.9 % / Rmerge(I) obs: 0.592 / Mean I/σ(I) obs: 5.2 / % possible all: 98.5

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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: 1.651→37.234 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.01 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 2000 4.3 %Random
Rwork0.1568 44475 --
obs0.1585 46475 99.45 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.75 Å2 / Biso mean: 29.9273 Å2 / Biso min: 13.53 Å2
Refinement stepCycle: final / Resolution: 1.651→37.234 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2925 0 68 300 3293
Biso mean--65.24 40.2 -
Num. residues----359
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063071
X-RAY DIFFRACTIONf_angle_d1.0254177
X-RAY DIFFRACTIONf_chiral_restr0.046451
X-RAY DIFFRACTIONf_plane_restr0.005539
X-RAY DIFFRACTIONf_dihedral_angle_d13.5921118
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6513-1.69260.25511390.19793108324798
1.6926-1.73840.22691410.187231073248100
1.7384-1.78950.22361390.18023097323699
1.7895-1.84730.21071400.16763127326799
1.8473-1.91330.22811410.164731383279100
1.9133-1.98990.22141410.16353142328399
1.9899-2.08050.20421420.16433120326299
2.0805-2.19010.19581410.163531603301100
2.1901-2.32730.18551440.156931973341100
2.3273-2.5070.18241440.163931903334100
2.507-2.75920.20561430.177331883331100
2.7592-3.15830.20661450.163532263371100
3.1583-3.97840.1861460.145532703416100
3.9784-37.24320.17881540.139734053559100
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)
11.6808-2.15730.91043.0873-1.61568.67380.08710.0977-0.0148-0.1305-0.0470.0484-0.00760.2066-0.05530.1234-0.01890.0430.16690.02340.2253-1.43688.59095.6216
21.0147-1.0211-0.22722.93710.28251.48780.13370.1550.0428-0.1821-0.14240.0793-0.0248-0.05320.00130.13780.0078-0.00550.15750.02050.15180.59387.8348-1.0951
30.8489-0.45270.07241.66270.15191.0460.0802-0.0019-0.0726-0.113-0.1303-00.11820.02780.04220.147-0.00560.00140.21570.00390.18659.018166.08856.7664
40.97971.809-2.11935.0705-5.63526.53560.1014-0.08020.02070.1677-0.4088-0.4903-0.01130.39820.34070.1387-0.015-0.02030.23510.03860.249116.371170.387712.2131
52.565-1.4413-0.59272.6120.44651.9027-0.1885-0.1449-0.14650.40460.0750.10040.077-0.00430.10680.1823-0.0228-0.01330.15980.0070.13223.030776.141721.8978
63.7242-1.4585-1.51773.6104-0.61992.51720.01780.1202-0.33770.0333-0.00680.29860.069-0.1897-0.0540.1802-0.0320.00880.1453-0.00680.167-5.834183.010420.2285
75.3686-1.77080.85654.5452-1.07563.3863-0.0878-0.08160.40790.15490.09510.074-0.4095-0.0718-0.03490.1691-0.01560.02950.13150.00990.1626-7.026693.272515.5866
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 310 through 328 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 329 through 391 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 392 through 502 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 503 through 529 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 530 through 595 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 596 through 637 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 638 through 668 )A0

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