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- PDB-7t8n: Crystal structure of the PNAG binding module PgaA-TPR 220-359 -

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Basic information

Entry
Database: PDB / ID: 7t8n
TitleCrystal structure of the PNAG binding module PgaA-TPR 220-359
ComponentsPoly-beta-1,6-N-acetyl-D-glucosamine export protein
KeywordsSTRUCTURAL PROTEIN / PNAG binding module / tetra-trico repeat (TPR) domain / PNAG secretion
Function / homology
Function and homology information


poly-beta-1,6-N-acetyl-D-glucosamine transmembrane transporter activity / polysaccharide transmembrane transporter activity / polysaccharide transport / single-species biofilm formation / cell outer membrane
Similarity search - Function
Poly-beta-1,6 N-acetyl-D-glucosamine export porin PgaA / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Poly-beta-1,6-N-acetyl-D-glucosamine export protein
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.85 Å
AuthorsPfoh, R. / Little, D.J. / Howell, P.L.
Funding support Canada, 1items
OrganizationGrant numberCountry
Canadian Institutes of Health Research (CIHR) Canada
CitationJournal: Plos Pathog. / Year: 2022
Title: The TPR domain of PgaA is a multifunctional scaffold that binds PNAG and modulates PgaB-dependent polymer processing.
Authors: Pfoh, R. / Subramanian, A.S. / Huang, J. / Little, D.J. / Forman, A. / DiFrancesco, B.R. / Balouchestani-Asli, N. / Kitova, E.N. / Klassen, J.S. / Pomes, R. / Nitz, M. / Howell, P.L.
History
DepositionDec 16, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 3, 2022Provider: repository / Type: Initial release
Revision 1.1Aug 17, 2022Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 28, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
AAA: Poly-beta-1,6-N-acetyl-D-glucosamine export protein
BBB: Poly-beta-1,6-N-acetyl-D-glucosamine export protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,6715
Polymers34,5872
Non-polymers843
Water34219
1
AAA: Poly-beta-1,6-N-acetyl-D-glucosamine export protein
BBB: Poly-beta-1,6-N-acetyl-D-glucosamine export protein
hetero molecules

AAA: Poly-beta-1,6-N-acetyl-D-glucosamine export protein
BBB: Poly-beta-1,6-N-acetyl-D-glucosamine export protein
hetero molecules


  • defined by author&software
  • Evidence: gel filtration
  • 69.3 kDa, 4 polymers
Theoretical massNumber of molelcules
Total (without water)69,34210
Polymers69,1734
Non-polymers1686
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_665-x+1,-y+1,z1
Buried area8120 Å2
ΔGint-98 kcal/mol
Surface area26040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.670, 60.670, 185.520
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number171
Space group name H-MP62
Components on special symmetry positions
IDModelComponents
11AAA-401-

MG

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11AAA
21BBB

NCS domain segments:

Ens-ID: 1 / Beg auth comp-ID: THR / Beg label comp-ID: THR / End auth comp-ID: HIS / End label comp-ID: HIS / Auth seq-ID: 224 - 342 / Label seq-ID: 5 - 123

Dom-IDComponent-IDAuth asym-IDLabel asym-ID
11AAAA
22BBBB

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein Poly-beta-1,6-N-acetyl-D-glucosamine export protein / PGA export protein / Poly-beta-1 / 6-GlcNAc export protein


Mass: 17293.357 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: pgaA, ycdS, b1024, JW1010 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P69434
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


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


Mass: 18.015 Da / Num. of mol.: 19 / Source method: isolated from a natural source / Formula: H2O
Compound detailsThe crystallized sequence is: ...The crystallized sequence is: GSHMSAVNNAYDALIIEARKGNTQPALSWFALKSALSNNQIADWLQIALWAGQDKQVITVYNRYRHQQLPARGYAAVAVA YRNLQQWQNSLTLWQKALSLEPQNKDYQRGQILTLADAGHYDTALVKLKQLNSGAPDKANLLAEAYIYKLAGRHQDELRA MTESLPENASTQQYPTEYVQALRNNQLAAAIDDANLTPDIRADIHAELVRLSFMPTRSESERYAIADRALAQYAALEILW HDNPDRTAQYQRIQVDHLGALLTRDRYKDVISHYQRLKKTGQIIPPWGQYWVASAYLKDHQPKKAQSIMTELFYHKETIA PDLSDEELADLFYSHLESEN. As per the authors, the protein must have cleaved and only the C-terminal fragment crystallized. They do not know exactly at which residue the cleavage occurred.
Has ligand of interestN

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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: 2.85 Å3/Da / Density % sol: 61.95 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 15% w/v PEG 8000, 0.1 M Tris pH 7.1, 200 mM MgCl2, and 3% w/v cadaverine

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.85→20.001 Å / Num. obs: 8565 / % possible obs: 99.4 % / Redundancy: 21.6 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 28.8
Reflection shellResolution: 2.85→2.95 Å / Rmerge(I) obs: 0.634 / Num. unique obs: 829

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXDEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.85→20.001 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.878 / SU B: 41.677 / SU ML: 0.344 / Cross valid method: FREE R-VALUE / ESU R Free: 0.414
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2643 499 5.967 %
Rwork0.2347 7863 -
all0.237 --
obs-8362 92.469 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 49.606 Å2
Baniso -1Baniso -2Baniso -3
1--1.598 Å2-0.799 Å2-0 Å2
2---1.598 Å20 Å2
3---5.184 Å2
Refinement stepCycle: LAST / Resolution: 2.85→20.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2125 0 3 19 2147
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0132205
X-RAY DIFFRACTIONr_bond_other_d0.0010.0172034
X-RAY DIFFRACTIONr_angle_refined_deg1.4241.6473000
X-RAY DIFFRACTIONr_angle_other_deg1.2311.5824667
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7955262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.13721.212132
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.09115363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0611519
X-RAY DIFFRACTIONr_chiral_restr0.060.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022499
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02535
X-RAY DIFFRACTIONr_nbd_refined0.2260.2523
X-RAY DIFFRACTIONr_symmetry_nbd_other0.20.21852
X-RAY DIFFRACTIONr_nbtor_refined0.1680.21051
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0840.21038
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.253
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2040.220
X-RAY DIFFRACTIONr_nbd_other0.2910.260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2010.22
X-RAY DIFFRACTIONr_mcbond_it1.3952.6661048
X-RAY DIFFRACTIONr_mcbond_other1.3912.6631047
X-RAY DIFFRACTIONr_mcangle_it2.4753.9871310
X-RAY DIFFRACTIONr_mcangle_other2.4743.9911311
X-RAY DIFFRACTIONr_scbond_it1.1372.7721156
X-RAY DIFFRACTIONr_scbond_other1.1372.7751157
X-RAY DIFFRACTIONr_scangle_it2.0534.1091689
X-RAY DIFFRACTIONr_scangle_other2.0534.1111690
X-RAY DIFFRACTIONr_lrange_it4.79429.9882544
X-RAY DIFFRACTIONr_lrange_other4.79430.0112545
X-RAY DIFFRACTIONr_ncsr_local_group_10.1310.053782
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AAAX-RAY DIFFRACTIONLocal ncs0.131270.05007
12BBBX-RAY DIFFRACTIONLocal ncs0.131270.05007
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.85-2.9220.207110.2772360.2746660.8520.76737.08710.259
2.922-3.0010.341200.3183810.3196240.8570.78864.26280.259
3.001-3.0860.33380.3445880.3436270.7410.80399.84050.258
3.086-3.1780.255360.3195610.3155980.830.84899.83280.231
3.178-3.280.329370.2765420.2795800.8250.87799.82760.207
3.28-3.3920.287340.2655350.2665690.8750.8851000.2
3.392-3.5160.282350.2565140.2575490.8840.8871000.219
3.516-3.6550.311300.2524920.2555220.8770.8991000.196
3.655-3.8110.268320.2264800.2295120.9040.9141000.186
3.811-3.990.309320.2234430.2294750.8820.9191000.186
3.99-4.1970.237230.2154350.2164590.9380.93399.78210.18
4.197-4.4390.309280.1814160.1884440.9080.9521000.156
4.439-4.7290.212250.1793940.1814190.9550.9611000.159
4.729-5.0840.17260.2123600.2093860.9730.9481000.199
5.084-5.5340.32240.2333420.2393660.9220.9371000.209
5.534-6.1290.203150.2153050.2143200.9580.9371000.192
6.129-6.9690.172170.2072800.2052970.9570.9491000.195
6.969-8.2870.247150.1842260.1882410.9620.9651000.189
8.287-10.8270.217130.181950.1822090.9680.97899.52150.182
10.827-20.0010.33580.2641370.2681470.8760.94698.63950.283
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)
11.33530.20581.28020.2438-0.08671.98930.0751-0.16020.0225-0.0637-0.00220.0607-0.1688-0.1733-0.07290.3910.13590.01310.42260.03690.024.42134.28852.696
22.6314-0.3221.71472.2587-0.24243.24720.0972-0.23960.21610.067-0.1340.2208-0.1371-0.1340.03680.21180.04150.08140.3467-0.00330.08162.62534.16382.92
Refinement TLS group
IDRefine-IDRefine TLS-IDSelectionAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1ALLAAA224 - 359
2X-RAY DIFFRACTION2ALLBBB220 - 343

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