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- PDB-5bu6: Structure of BpsB deaceylase domain from Bordetella bronchiseptica -

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Basic information

Entry
Database: PDB / ID: 5bu6
TitleStructure of BpsB deaceylase domain from Bordetella bronchiseptica
ComponentsBpsB (PgaB), Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
KeywordsHYDROLASE / deacetylase / family 4 carbohydrate esterase
Function / homologyGlycoside hydrolase/deacetylase / TIM Barrel / Alpha-Beta Barrel / Alpha Beta / NICKEL (II) ION / THIOCYANATE ION / :
Function and homology information
Biological speciesBordetella bronchiseptica RB50 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.951 Å
AuthorsLittle, D.J. / Bamford, N.C. / Howell, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)43998 Canada
CitationJournal: J.Biol.Chem. / Year: 2015
Title: The Protein BpsB Is a Poly-beta-1,6-N-acetyl-d-glucosamine Deacetylase Required for Biofilm Formation in Bordetella bronchiseptica.
Authors: Little, D.J. / Milek, S. / Bamford, N.C. / Ganguly, T. / DiFrancesco, B.R. / Nitz, M. / Deora, R. / Howell, P.L.
History
DepositionJun 3, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 29, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2015Group: Database references
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_audit_support / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _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.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _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_label_seq_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BpsB (PgaB), Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
B: BpsB (PgaB), Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,50413
Polymers61,8582
Non-polymers64611
Water2,252125
1
A: BpsB (PgaB), Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3999
Polymers30,9291
Non-polymers4708
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: BpsB (PgaB), Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1044
Polymers30,9291
Non-polymers1753
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: BpsB (PgaB), Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
hetero molecules

B: BpsB (PgaB), Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,50413
Polymers61,8582
Non-polymers64611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area2880 Å2
ΔGint-81 kcal/mol
Surface area24270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.947, 77.785, 76.861
Angle α, β, γ (deg.)90.00, 108.00, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein BpsB (PgaB), Poly-beta-1,6-N-acetyl-D-glucosamine N-deacetylase


Mass: 30928.957 Da / Num. of mol.: 2 / Fragment: UNP residues 35-307 / Mutation: C48S, K128A, K129A, D235H, E239H
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bordetella bronchiseptica RB50 (bacteria)
Strain: RB50 / Gene: hmsF, BN113_1689, BB1768 / Plasmid: pET28A / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: A0A0E1QQI1, EC: 3.5.1.33
#2: Chemical
ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ni
#3: Chemical
ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / 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: 2.2 Å3/Da / Density % sol: 44 % / Description: Small thin needles
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 2000 MME, 0.1 M potassium thiocyanate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jan 16, 2014
Details: DCM with cryo-cooled 1st crystal sagittally bent 2nd crystal followed by vertically focusing mirror
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 39033 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 39.02 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 33
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 3.2 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIXdev_1760refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
Coot0.7.1model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4F9D

4f9d


Resolution: 1.951→45.6 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.99 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2076 1998 5.19 %Random seletion
Rwork0.1694 ---
obs0.1713 38470 98.25 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 54 Å2
Refinement stepCycle: LAST / Resolution: 1.951→45.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4136 0 24 125 4285
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074257
X-RAY DIFFRACTIONf_angle_d1.0585808
X-RAY DIFFRACTIONf_dihedral_angle_d13.641546
X-RAY DIFFRACTIONf_chiral_restr0.044650
X-RAY DIFFRACTIONf_plane_restr0.006767
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9511-1.99990.2641330.22592436X-RAY DIFFRACTION93
1.9999-2.05390.22781410.20782581X-RAY DIFFRACTION98
2.0539-2.11440.24751450.20192597X-RAY DIFFRACTION98
2.1144-2.18260.2471380.19562610X-RAY DIFFRACTION98
2.1826-2.26060.26011420.19692582X-RAY DIFFRACTION98
2.2606-2.35110.2291410.19542594X-RAY DIFFRACTION99
2.3511-2.45810.24081440.18962613X-RAY DIFFRACTION99
2.4581-2.58770.24341470.19572625X-RAY DIFFRACTION99
2.5877-2.74980.2391390.20192618X-RAY DIFFRACTION99
2.7498-2.96210.28631410.20542650X-RAY DIFFRACTION99
2.9621-3.26010.20631470.18722602X-RAY DIFFRACTION99
3.2601-3.73170.22591470.16792635X-RAY DIFFRACTION99
3.7317-4.70080.16941480.13912645X-RAY DIFFRACTION99
4.7008-45.6120.16981450.14362684X-RAY DIFFRACTION98
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)
14.49081.5024-0.5117.97943.00911.7703-0.048-0.25070.59620.0954-0.31140.6326-0.57-0.26240.27290.51610.0274-0.03970.5331-0.08110.3114110.3299-13.2542156.4765
22.0132-0.17270.35343.0456-1.16453.37730.0263-0.0776-0.01860.0608-0.094-0.0622-0.11560.11630.09620.2466-0.01360.00430.2528-0.04570.2832117.1937-15.7115144.6873
35.7303-1.40320.88963.7869-0.29123.14760.21570.27780.46180.30610.31840.2251-0.433-0.9435-0.49190.45170.12990.05440.83820.19151.104587.8272-8.8703139.5016
42.8610.0222-0.09132.2102-1.16053.7462-0.0507-0.1117-0.1208-0.0326-0.00490.34510.1897-0.43670.03670.2777-0.001-0.00450.2568-0.02970.3091104.5127-21.1721143.0683
58.5116-4.8221.72472.9379-1.63426.18710.17950.57870.7624-0.3642-0.2681-1.0514-0.33610.56510.23470.5176-0.0544-0.01860.53830.01460.4737101.24620.1754167.9185
64.1909-1.4187-0.91775.46620.28954.6873-0.25870.2531-0.7436-0.24010.2372-0.4790.47920.2736-0.02640.50030.00480.0610.8284-0.01640.816109.7257-11.4263172.1638
72.66630.3539-0.3963.1209-1.16454.2194-0.0067-0.01630.09720.0843-0.0441-0.3634-0.09510.36750.04730.26130.0243-0.00170.3446-0.04160.281899.3684-6.9833183.2807
81.8920.60240.57443.3634-0.02212.0909-0.08510.3361-0.079-0.24250.05890.08030.1416-0.0060.01570.30720.0220.02490.356-0.01260.26987.4883-14.6537175.1877
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 35 through 72 )
2X-RAY DIFFRACTION2chain 'A' and (resid 73 through 190 )
3X-RAY DIFFRACTION3chain 'A' and (resid 191 through 218 )
4X-RAY DIFFRACTION4chain 'A' and (resid 219 through 298 )
5X-RAY DIFFRACTION5chain 'B' and (resid 35 through 50 )
6X-RAY DIFFRACTION6chain 'B' and (resid 51 through 83 )
7X-RAY DIFFRACTION7chain 'B' and (resid 84 through 190 )
8X-RAY DIFFRACTION8chain 'B' and (resid 191 through 298 )

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