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- PDB-4p7l: Structure of Escherichia coli PgaB C-terminal domain, P212121 cry... -

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Basic information

Entry
Database: PDB / ID: 4p7l
TitleStructure of Escherichia coli PgaB C-terminal domain, P212121 crystal form
ComponentsPoly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
KeywordsHYDROLASE / beta alpha barrel / carbohydrate binding / glycosyl hydrolase fold
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 / hydrolase activity
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 / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. ...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 / Glycosidases / Prokaryotic membrane lipoprotein lipid attachment site profile. / 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 K12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.802 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 1.3Sep 13, 2017Group: Author supporting evidence / Database references ...Author supporting evidence / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_audit_support / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_prop / pdbx_struct_oper_list / struct_keywords
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _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 / _struct_keywords.text
Revision 1.4Nov 22, 2017Group: Refinement description / Category: software
Revision 1.5Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.6Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.pdbx_number_atoms_nucleic_acid / _refine_hist.pdbx_number_atoms_protein

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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)42,5393
Polymers42,4421
Non-polymers982
Water5,026279
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area320 Å2
ΔGint-5 kcal/mol
Surface area14840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.764, 78.213, 97.924
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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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: C-terminal domain (UNP residues 310-672)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K12 (bacteria) / Strain: K12 / Gene: pgaB, ycdR, b1023, JW5142 / Plasmid: pET28A / Production host: Escherichia coli BL21 (bacteria) / 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


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 279 / 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: 1.88 Å3/Da / Density % sol: 34.72 % / Description: Long rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 18% PEG3350, 0.1 M Bis-Tris

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2012
RadiationMonochromator: 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: 30391 / % possible obs: 97.5 % / Observed criterion σ(I): -3 / Redundancy: 13.5 % / Biso Wilson estimate: 17.73 Å2 / Rmerge(I) obs: 0.104 / Net I/σ(I): 26.8
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 12.7 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 5.1 / % possible all: 96.4

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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 4F9D

4f9d


Resolution: 1.802→48.962 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 16.76 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1893 1973 6.73 %Random
Rwork0.1419 52026 --
obs0.1451 29644 97.48 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 76.19 Å2 / Biso mean: 21.5705 Å2 / Biso min: 6.93 Å2
Refinement stepCycle: final / Resolution: 1.802→48.962 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2875 0 5 279 3159
Biso mean--25.81 32.93 -
Num. residues----357
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0072955
X-RAY DIFFRACTIONf_angle_d1.0194024
X-RAY DIFFRACTIONf_chiral_restr0.049429
X-RAY DIFFRACTIONf_plane_restr0.005529
X-RAY DIFFRACTIONf_dihedral_angle_d13.8671072
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.802-1.82510.25361320.19291778191091
1.8251-1.84910.27291380.19261908204696
1.8491-1.87440.21181370.17581871200895
1.8744-1.90120.2081370.16221909204695
1.9012-1.92960.23761370.16641928206599
1.9296-1.95980.22771370.15871873201095
1.9598-1.99190.25461380.14191913205195
1.9919-2.02620.16411350.13721938207399
2.0262-2.06310.18061390.14171913205295
2.0631-2.10280.18381340.14351890202496
2.1028-2.14570.20991400.142819372077100
2.1457-2.19230.19441370.1421893203094
2.1923-2.24330.17191430.13181945208899
2.2433-2.29940.19241400.13311919205997
2.2994-2.36160.18871380.1361947208598
2.3616-2.43110.19071420.14681932207498
2.4311-2.50960.18631410.14751930207198
2.5096-2.59930.19191410.14341980212198
2.5993-2.70330.17761370.15281938207599
2.7033-2.82630.15921400.14911918205898
2.8263-2.97530.1971460.14071972211899
2.9753-3.16170.20371470.14719722119100
3.1617-3.40580.18611410.14061951209299
3.4058-3.74840.2021380.13181949208799
3.7484-4.29050.16521370.12061988212599
4.2905-5.40450.16121410.122619632104100
5.4045-48.98010.1821410.154619712112100
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)
11.62321.30070.19063.001-0.92224.18130.0513-0.0932-0.02710.0584-0.04750.05590.0012-0.0094-0.01240.03160.0044-0.01450.07610.01740.10641.4885-14.4652-2.5157
20.8420.0079-0.01791.9911-0.13370.70130.0424-0.01980.0867-0.0006-0.0765-0.0961-0.09630.03040.03680.0722-0.0007-0.00450.10620.00820.075913.08346.2333-7.2674
31.76960.88070.28261.92-0.44361.9323-0.00250.09820.0162-0.20730.08760.11650.0632-0.1666-0.06410.11970.0128-0.01080.101-0.00770.08480.8861-5.7288-20.1487
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 310 through 346 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 347 through 553 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 554 through 666 )A0

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