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- PDB-5bxa: Structure of PslG from Pseudomonas aeruginosa in complex with mannose -

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Basic information

Entry
Database: PDB / ID: 5bxa
TitleStructure of PslG from Pseudomonas aeruginosa in complex with mannose
ComponentsPslG
KeywordsHYDROLASE / glycosidase / carbohydrate binding / alpha beta barrel
Function / homologyextracellular polysaccharide biosynthetic process / single-species biofilm formation / Cellulase (glycosyl hydrolase family 5) / hydrolase activity, hydrolyzing O-glycosyl compounds / Glycoside hydrolase superfamily / : / alpha-D-mannopyranose / PslG
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsBaker, P. / Little, D.J. / Howell, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR)43998 Canada
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Characterization of the Pseudomonas aeruginosa Glycoside Hydrolase PslG Reveals That Its Levels Are Critical for Psl Polysaccharide Biosynthesis and Biofilm Formation.
Authors: Baker, P. / Whitfield, G.B. / Hill, P.J. / Little, D.J. / Pestrak, M.J. / Robinson, H. / Wozniak, D.J. / Howell, P.L.
History
DepositionJun 8, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 7, 2015Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2015Group: Database references
Revision 1.2Dec 2, 2015Group: Database references
Revision 1.3Nov 1, 2017Group: Author supporting evidence / Database references / Derived calculations
Category: citation / pdbx_struct_assembly_auth_evidence / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _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 / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_symmetry
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: PslG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,64911
Polymers47,3811
Non-polymers1,26810
Water6,395355
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)83.655, 83.655, 163.366
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Detailsauthors have indicated that monomer was identified by gel filtration chromatography

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Components

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Protein / Sugars , 2 types, 5 molecules A

#1: Protein PslG


Mass: 47380.715 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas aeruginosa (bacteria) / Strain: ATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228 / Gene: pslG, PA2237 / Plasmid: pET28A / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9I1N2
#3: Sugar
ChemComp-MAN / alpha-D-mannopyranose / alpha-D-mannose / D-mannose / mannose


Type: D-saccharide, alpha linking / Mass: 180.156 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DManpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-mannopyranoseCOMMON NAMEGMML 1.0
a-D-ManpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
ManSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 361 molecules

#2: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


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


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.02 Å3/Da / Density % sol: 59 % / Description: small rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 5% PEG 3350, 2 mM CdCl2, 0.1 M HEPES pH 7.0, 3 M mannose in protein solution

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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
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: 1.9→50 Å / Num. obs: 46642 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 12.1 % / Biso Wilson estimate: 24.4 Å2 / Rmerge(I) obs: 0.107 / Net I/σ(I): 36.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 12.5 % / Rmerge(I) obs: 0.639 / Mean I/σ(I) obs: 4.8 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1760refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5BX9

5bx9


Resolution: 1.9→47.91 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 17.87 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.187 2000 4.3 %Random selection
Rwork0.1549 ---
obs0.1563 46542 99.94 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→47.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 57 355 3753
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073490
X-RAY DIFFRACTIONf_angle_d1.0534757
X-RAY DIFFRACTIONf_dihedral_angle_d13.2471311
X-RAY DIFFRACTIONf_chiral_restr0.044515
X-RAY DIFFRACTIONf_plane_restr0.005610
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8992-1.94670.26791390.20633110X-RAY DIFFRACTION99
1.9467-1.99930.1971410.17513116X-RAY DIFFRACTION100
1.9993-2.05810.20961390.17453126X-RAY DIFFRACTION100
2.0581-2.12460.2271410.16243132X-RAY DIFFRACTION100
2.1246-2.20050.18761420.15993141X-RAY DIFFRACTION100
2.2005-2.28860.18891390.15663123X-RAY DIFFRACTION100
2.2886-2.39270.18241430.15863156X-RAY DIFFRACTION100
2.3927-2.51890.21631420.1583174X-RAY DIFFRACTION100
2.5189-2.67670.21121420.17013158X-RAY DIFFRACTION100
2.6767-2.88330.19161430.16933187X-RAY DIFFRACTION100
2.8833-3.17340.23321430.17413182X-RAY DIFFRACTION100
3.1734-3.63250.19251440.15163222X-RAY DIFFRACTION100
3.6325-4.5760.1351480.12073273X-RAY DIFFRACTION100
4.576-47.92480.16361540.15063442X-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)
11.4341-0.1430.18642.6559-0.40211.38220.00430.0684-0.09670.0541-0.0437-0.10220.0169-0.0240.0230.068-0.02540.01360.1336-0.00660.104-38.8471-9.0199-7.4473
23.25611.8924-0.70015.25910.14671.95140.00650.08440.14240.1066-0.02460.2222-0.1009-0.3810.00720.15630.0274-0.0240.1879-0.02470.0877-41.12317.0574-0.7464
31.740.1446-0.71981.86250.88512.16480.12660.04150.238-0.2486-0.0119-0.1112-0.51260.0789-0.08420.2212-0.03090.00620.13390.00340.1763-27.142314.2331-7.3741
43.76581.1871.54653.14532.24185.19550.03370.0867-0.0385-0.12330.1376-0.18620.02230.4228-0.14770.10660.00070.00880.12560.00260.1868-20.24582.843-10.5194
51.18590.90430.82331.51430.85182.0347-0.01440.0328-0.0027-0.09810.016-0.0777-0.03740.1046-0.00730.14310.01460.02040.13730.00780.1419-28.5027-6.1061-18.2901
66.0735-1.19811.90972.71630.1632.58990.02420.32740.1505-0.2322-0.0986-0.1715-0.03370.12250.07290.1178-0.03520.03210.11340.04160.0862-34.8949-5.7645-16.2847
71.01120.1910.01432.79590.36861.6503-0.00430.0330.0407-0.0681-0.07210.1521-0.1311-0.07810.08180.0821-0.0131-0.00930.1487-0.010.1358-45.4594-7.4031-9.7458
82.97461.397-0.03943.6327-0.3513.25270.0452-0.0644-0.1960.0424-0.03770.0470.2445-0.2138-0.00660.1078-0.01430.01080.1191-0.01010.1706-48.6659-25.3776-8.6915
94.43883.8903-1.57917.122-0.83714.33780.0877-0.136-0.11060.1829-0.15570.11330.3203-0.20520.02710.1157-0.0562-0.0140.21-0.01690.1858-54.6423-24.6571-9.2428
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 29 through 57 )
2X-RAY DIFFRACTION2chain 'A' and (resid 58 through 85 )
3X-RAY DIFFRACTION3chain 'A' and (resid 86 through 177 )
4X-RAY DIFFRACTION4chain 'A' and (resid 178 through 217 )
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 252 )
6X-RAY DIFFRACTION6chain 'A' and (resid 253 through 292 )
7X-RAY DIFFRACTION7chain 'A' and (resid 293 through 377 )
8X-RAY DIFFRACTION8chain 'A' and (resid 378 through 413 )
9X-RAY DIFFRACTION9chain 'A' and (resid 414 through 442 )

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