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- PDB-4p7o: Structure of Escherichia coli PgaB C-terminal domain, P1 crystal form -

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Basic information

Entry
Database: PDB / ID: 4p7o
TitleStructure of Escherichia coli PgaB C-terminal domain, P1 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
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 ...: / 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: 1.48 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
Category: citation / entity_src_gen ...citation / entity_src_gen / pdbx_database_status / pdbx_struct_assembly / pdbx_struct_oper_list / software
Item: _citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag ..._citation.journal_id_CSD / _entity_src_gen.pdbx_alt_source_flag / _pdbx_database_status.pdb_format_compatible / _pdbx_struct_assembly.oligomeric_details / _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 1.5Sep 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
B: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase


Theoretical massNumber of molelcules
Total (without water)84,8842
Polymers84,8842
Non-polymers00
Water14,664814
1
A: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase


Theoretical massNumber of molelcules
Total (without water)42,4421
Polymers42,4421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase


Theoretical massNumber of molelcules
Total (without water)42,4421
Polymers42,4421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.618, 54.016, 86.460
Angle α, β, γ (deg.)101.700, 98.300, 90.190
Int Tables number1
Space group name H-MP1
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.: 2 / 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 814 / 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: 44.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5 / Details: 30% PEG5000 MME, 0.2 M ammonium sulfate, 0.1 M MES

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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: Oct 12, 2012
RadiationMonochromator: Rosenbaum-Rock double crystal sagittal focusing
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.48→50 Å / Num. obs: 126137 / % possible obs: 94.1 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 15.7 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 11.3
Reflection shellResolution: 1.48→1.53 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.299 / Mean I/σ(I) obs: 2.4 / % possible all: 90.4

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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 4P7L

4p7l


Resolution: 1.48→41.864 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 27.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2532 1866 1.72 %
Rwork0.2205 113643 -
obs0.221 115509 92.06 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 80.65 Å2 / Biso mean: 22.8258 Å2 / Biso min: 10.1 Å2
Refinement stepCycle: final / Resolution: 1.48→41.864 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5610 0 0 814 6424
Biso mean---34.18 -
Num. residues----691
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0065763
X-RAY DIFFRACTIONf_angle_d1.0757847
X-RAY DIFFRACTIONf_chiral_restr0.078835
X-RAY DIFFRACTIONf_plane_restr0.0051020
X-RAY DIFFRACTIONf_dihedral_angle_d13.4022089
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 28

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.4747-1.49270.35161260.29237029715581
1.4927-1.51160.31671390.27067831797091
1.5116-1.53150.3471360.31017865800191
1.5315-1.55250.30121420.25297983812592
1.5525-1.57460.29261380.24077948808693
1.5746-1.59820.29141400.23288064820493
1.5982-1.62310.28851440.2248069821393
1.6231-1.64970.24021410.22057981812293
1.6497-1.67820.24591420.21868148829094
1.6782-1.70870.27571380.22168009814794
1.7087-1.74160.25611460.21948232837894
1.7416-1.77710.24761380.2167916805494
1.7771-1.81580.25911410.21348126826794
1.8158-1.8580.27721440.21138093823794
1.858-1.90450.17711280.22947477760586
1.9045-1.9560.41821240.31887038716282
1.956-2.01350.28171470.21478238838595
2.0135-2.07850.29491420.24788085822793
2.0785-2.15280.23331430.2168132827595
2.1528-2.2390.26841210.22776984710582
2.239-2.34090.3221280.27127107723581
2.3409-2.46430.23861440.22038273841796
2.4643-2.61860.31421410.21618288842996
2.6186-2.82080.23611450.21868214835996
2.8208-3.10460.23261450.21588239838496
3.1046-3.55360.25561470.20498298844596
3.5536-4.47630.2171410.18758235837695
4.4763-41.8810.18631510.1988545869699
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)
10.77980.056-0.4480.87350.01061.3358-0.03920.0209-0.02040.05920.03250.03680.0117-0.11550.01910.1704-0.006300.11780.01320.0949-15.1874-10.764866.847
20.22920.1333-0.06790.9612-0.83853.2273-0.0052-0.03340.02660.042-0.01640.0291-0.2134-0.06770.010.1753-0.0017-0.0160.1169-0.00020.12-5.60485.275558.6109
31.91670.1286-1.31282.91580.45033.4510.06050.02250.2883-0.10030.0627-0.3086-0.83590.1153-0.10830.2957-0.0401-0.03040.11670.02380.21686.046715.447447.6037
41.37581.2501-1.74523.9614-4.17834.56410.0372-0.08880.0499-0.0225-0.1331-0.14910.01450.4160.12660.136-0.0127-0.03180.1176-0.00350.12384.81582.790657.9977
50.93520.45970.21291.23720.52121.6204-0.04410.0316-0.0048-0.03560.0150.010.08-0.0040.010.18060.0106-0.00380.09480.01350.0915-2.4342-14.39449.1215
62.4237-0.6505-0.91752.04430.6181.0815-0.08270.0284-0.19630.1229-0.00840.06740.2254-0.05980.05240.2876-0.0143-0.00070.11340.01080.1096-10.8228-25.77657.083
71.126-0.12050.5351.2779-0.21761.2001-0.04760.03450.076-0.06710.03990.0345-0.0594-0.11860.0120.1698-0.0044-0.00790.11710.01040.0924-13.81612.94577.2973
80.371-0.08160.40771.3127-1.20882.70860.02340.0099-0.032-0.0428-0.0284-0.08530.14070.03850.00260.18360.00040.01230.11370.00030.13010.5592-4.191118.5802
90.7679-0.42290.13081.50080.17941.0821-0.0233-0.00270.0779-0.0058-0.0207-0.025-0.1413-0.02330.04930.1912-0.0219-0.00570.09660.00560.0989-4.049419.504723.5204
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 312 through 411 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 412 through 477 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 478 through 499 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 500 through 529 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 530 through 636 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 637 through 669 )A0
7X-RAY DIFFRACTION7chain 'B' and (resid 312 through 411 )B0
8X-RAY DIFFRACTION8chain 'B' and (resid 412 through 529 )B0
9X-RAY DIFFRACTION9chain 'B' and (resid 530 through 669 )B0

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