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- PDB-4y25: Bacterial polysaccharide outer membrane secretin -

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Basic information

Entry
Database: PDB / ID: 4y25
TitleBacterial polysaccharide outer membrane secretin
ComponentsPoly-beta-1,6-N-acetyl-D-glucosamine export protein
KeywordsMEMBRANE PROTEIN / bacterial polysaccharide / outer membrane seretin / beta-barrel / biofilm
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 (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.821 Å
AuthorsWang, Y. / AndolePannuri, A. / Ni, D. / Zhou, H. / Cao, X. / Lu, X. / Romeo, T. / Huang, Y.
Funding support China, United States, 5items
OrganizationGrant numberCountry
National Natural Science Foundation of China31470743 and 31170698 China
Ministry of Science and Technology of P.R.China 973 Project2013CB910603 and 2012CB917302 China
Chinese Academy of SciencesXDB08020302 China
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM059969 and GM066794 United States
University of Florida CHRIS projectFLA-MCS-004949 United States
CitationJournal: J.Biol.Chem. / Year: 2016
Title: Structural Basis for Translocation of a Biofilm-supporting Exopolysaccharide across the Bacterial Outer Membrane
Authors: Wang, Y. / Andole Pannuri, A. / Ni, D. / Zhou, H. / Cao, X. / Lu, X. / Romeo, T. / Huang, Y.
History
DepositionFeb 9, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 16, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 1, 2016Group: Database references
Revision 1.2Oct 18, 2017Group: 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 1.3Mar 23, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Poly-beta-1,6-N-acetyl-D-glucosamine export protein


Theoretical massNumber of molelcules
Total (without water)36,3911
Polymers36,3911
Non-polymers00
Water0
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16590 Å2
Unit cell
Length a, b, c (Å)143.972, 143.972, 90.560
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

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


Mass: 36390.879 Da / Num. of mol.: 1 / Fragment: UNP residues 511-807
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (strain K12) (bacteria)
Strain: K12 / Gene: pgaA, ycdS, b1024, JW1010 / Plasmid: pBAD22 / Production host: Escherichia coli (E. coli) / Strain (production host): sf100 / References: UniProt: P69434

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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: 3.73 Å3/Da / Density % sol: 67.03 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1M NaOAc, pH 4.5, 31% MPD, 0.4M NaCl, 0.3M NDSB-195
PH range: 4.0 - 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 1, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 13051 / % possible obs: 94.4 % / Redundancy: 10.9 % / Rsym value: 0.069 / Net I/σ(I): 28.9
Reflection shellResolution: 2.82→2.92 Å / Redundancy: 10.5 % / Mean I/σ(I) obs: 1.9 / % possible all: 91.8

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Processing

Software
NameVersionClassification
HKL-2000data processing
PHENIX(phenix.refine: 1.8.4_1496)phasing
PHENIX(phenix.refine: 1.8.4_1496)model building
PHENIX(phenix.refine: 1.8.4_1496)refinement
Cootmodel building
Cootrefinement
RefinementMethod to determine structure: SAD / Resolution: 2.821→33.448 Å / SU ML: 0.39 / Cross valid method: NONE / σ(F): 1.34 / Phase error: 28.91 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2831 1305 10 %Random selection
Rwork0.232 ---
obs0.2372 13046 94.52 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.821→33.448 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2402 0 0 0 2402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052479
X-RAY DIFFRACTIONf_angle_d0.9333371
X-RAY DIFFRACTIONf_dihedral_angle_d14.148876
X-RAY DIFFRACTIONf_chiral_restr0.038328
X-RAY DIFFRACTIONf_plane_restr0.005442
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.8209-2.93380.37371380.29571240X-RAY DIFFRACTION92
2.9338-3.06730.32071420.26911276X-RAY DIFFRACTION96
3.0673-3.22890.34191440.27261300X-RAY DIFFRACTION96
3.2289-3.4310.29441440.23731304X-RAY DIFFRACTION96
3.431-3.69560.26961470.23821316X-RAY DIFFRACTION96
3.6956-4.06690.31551440.24681304X-RAY DIFFRACTION96
4.0669-4.6540.23581480.2081323X-RAY DIFFRACTION95
4.654-5.85850.28851480.21741332X-RAY DIFFRACTION95
5.8585-33.45030.2771500.23141346X-RAY DIFFRACTION90
Refinement TLS params.Method: refined / Origin x: -185.7285 Å / Origin y: 288.4982 Å / Origin z: 191.0296 Å
111213212223313233
T0.5686 Å20.0765 Å20.1495 Å2-0.7685 Å20.2389 Å2--0.7572 Å2
L1.1268 °20.7486 °2-0.7249 °2-1.4726 °2-0.3282 °2--0.7861 °2
S-0.1832 Å °0.4245 Å °-0.2214 Å °-0.1974 Å °-0.0786 Å °-0.4734 Å °-0.0296 Å °0.1299 Å °0.2392 Å °
Refinement TLS groupSelection details: all

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