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- PDB-5bx9: Structure of PslG from Pseudomonas aeruginosa -

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Basic information

Entry
Database: PDB / ID: 5bx9
TitleStructure of PslG from Pseudomonas aeruginosa
ComponentsPslG
KeywordsHYDROLASE / GH39 / glycosidase / 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 / : / PslG
Function and homology information
Biological speciesPseudomonas aeruginosa (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.001 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 1.5Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_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

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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)48,11410
Polymers47,3811
Non-polymers7339
Water6,972387
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)83.169, 83.169, 163.396
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

#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
#2: Chemical
ChemComp-CD / CADMIUM ION


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


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


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 387 / 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: 2.98 Å3/Da / Density % sol: 59 % / Description: small rods
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 5% PEG 3350, 1 mM CdCl2, 0.1 M HEPES pH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2013
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 39575 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 30.3 % / Biso Wilson estimate: 20.52 Å2 / Rmerge(I) obs: 0.139 / Net I/σ(I): 36.8
Reflection shellResolution: 2→2.07 Å / Redundancy: 28.7 % / Rmerge(I) obs: 0.656 / Mean I/σ(I) obs: 6.1 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIXdev_1760refinement
HKL-2000data reduction
HKL-2000data scaling
Cootmodel building
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.001→47.729 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 16.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.188 2000 5.07 %Random selection
Rwork0.1489 ---
obs0.1509 39485 99.95 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.001→47.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3341 0 21 387 3749
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073457
X-RAY DIFFRACTIONf_angle_d1.0234705
X-RAY DIFFRACTIONf_dihedral_angle_d13.4541272
X-RAY DIFFRACTIONf_chiral_restr0.045496
X-RAY DIFFRACTIONf_plane_restr0.006612
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0013-2.05140.21851390.16762605X-RAY DIFFRACTION99
2.0514-2.10680.21371410.15482633X-RAY DIFFRACTION100
2.1068-2.16880.19191390.14712623X-RAY DIFFRACTION100
2.1688-2.23880.19281410.14222646X-RAY DIFFRACTION100
2.2388-2.31880.16771410.14142632X-RAY DIFFRACTION100
2.3188-2.41170.18031410.14342633X-RAY DIFFRACTION100
2.4117-2.52140.19491420.15132668X-RAY DIFFRACTION100
2.5214-2.65440.20741410.15642649X-RAY DIFFRACTION100
2.6544-2.82060.22251410.15852652X-RAY DIFFRACTION100
2.8206-3.03840.23331430.17122679X-RAY DIFFRACTION100
3.0384-3.34410.20721440.1672696X-RAY DIFFRACTION100
3.3441-3.82780.17721450.15082707X-RAY DIFFRACTION100
3.8278-4.82190.14811460.12392751X-RAY DIFFRACTION100
4.8219-47.7430.171560.14232911X-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)
11.5891-0.5097-0.20182.7514-0.32791.53610.0317-0.0023-0.08640.0309-0.0606-0.19130.01310.07150.04720.0567-0.02780.01530.14550.00810.10723.049632.7397-7.608
22.31121.187-0.55692.97030.16611.80920.1277-0.13820.23530.0811-0.12850.1287-0.2339-0.0364-0.00770.1404-0.0126-0.00070.1576-0.03390.10573.841253.40040.1254
33.48291.0187-0.71251.22930.42770.54190.24420.11150.628-0.23140.04810.2371-0.64150.1652-0.25770.399-0.05330.04790.1339-0.01170.194512.742657.329-10.5617
41.2944-0.3867-0.42741.62160.59081.32610.098-0.04380.1307-0.15790.0595-0.2152-0.270.3068-0.08940.1464-0.08930.02460.2139-0.01110.160919.451149.8704-10.0326
51.59730.73930.22291.40020.62651.03020.0403-0.0666-0.114-0.130.0005-0.1793-0.02350.1665-0.03190.11560.00530.02570.1480.02080.101713.535.7048-18.3636
64.468-0.58530.94962.1084-0.00452.27980.04840.1971-0.0097-0.2021-0.1453-0.02650.00160.06480.07740.1045-0.01190.01290.09390.0070.07523.935634.7947-15.6744
70.88340.3101-0.20372.8510.04521.31610.038-0.0716-0.00840.0065-0.11550.11430.0116-0.06680.05970.0507-0.0078-0.01270.1260.00180.1062-3.245431.1585-8.1732
83.92571.742-0.86996.5529-1.29613.8071-0.0121-0.06-0.18750.0082-0.09460.18050.3913-0.16180.08690.1185-0.07420.00220.1984-0.01730.1801-11.597515.2314-10.3583
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 106 )
3X-RAY DIFFRACTION3chain 'A' and (resid 107 through 131 )
4X-RAY DIFFRACTION4chain 'A' and (resid 132 through 217 )
5X-RAY DIFFRACTION5chain 'A' and (resid 218 through 252 )
6X-RAY DIFFRACTION6chain 'A' and (resid 253 through 310 )
7X-RAY DIFFRACTION7chain 'A' and (resid 311 through 394 )
8X-RAY DIFFRACTION8chain 'A' and (resid 395 through 442 )

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