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- PDB-3qs2: Crystal structure of the biofilm forming subunit of the E. coli c... -

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Basic information

Entry
Database: PDB / ID: 3qs2
TitleCrystal structure of the biofilm forming subunit of the E. coli common pilus: full length domain swapped dimer of EcpA
ComponentsFimbrillin matB homolog
KeywordsCELL ADHESION / pilin / Ig-like fold / biofilms / adhesion / Immunoglobulin-like fold / major pilin domain involved in biofilms / intermolecular and hydrophobic abiotic surface binding / extracellular membrane
Function / homology
Function and homology information


Fimbrial protein EcpA / Fimbrial protein EcpA / Fimbrillin subunit EcpA superfamily / Fimbrillin MatB / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
IODIDE ION / Common pilus major fimbrillin subunit EcpA
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.78 Å
AuthorsGarnett, J.A. / Matthews, S.J.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2012
Title: Structural insights into the biogenesis and biofilm formation by the Escherichia coli common pilus.
Authors: Garnett, J.A. / Martinez-Santos, V.I. / Saldana, Z. / Pape, T. / Hawthorne, W. / Chan, J. / Simpson, P.J. / Cota, E. / Puente, J.L. / Giron, J.A. / Matthews, S.
History
DepositionFeb 19, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 7, 2012Group: Database references
Revision 1.2Mar 21, 2012Group: Database references
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fimbrillin matB homolog
B: Fimbrillin matB homolog
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,15023
Polymers39,4852
Non-polymers2,66521
Water8,287460
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-25 kcal/mol
Surface area15400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.860, 72.080, 108.320
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Fimbrillin matB homolog


Mass: 19742.523 Da / Num. of mol.: 2 / Fragment: Full length processed EcpA, rsidues 23-195
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: CFT073 / Gene: matB / Plasmid: pET46 Ek/LIC / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8CWB9
#2: Chemical...
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 460 / 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: 2.32 Å3/Da / Density % sol: 46.9 %
Crystal growTemperature: 293 K / pH: 3.2
Details: 15% PEG 3350, 100 mM phosphate/citrate, 200 mM NaI, pH 3.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 1.54
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 24, 2010 / Details: MIRRORS
RadiationMonochromator: SI (111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.78→60.01 Å / Num. obs: 35831 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 26.5 % / Rsym value: 0.35 / Net I/σ(I): 3.7
Reflection shellResolution: 1.78→1.88 Å / Redundancy: 26.4 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.11 / % possible all: 100

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHARPphasing
REFMAC5.6.0104refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.78→60.01 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.932 / SU B: 3.96 / SU ML: 0.073 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / ESU R Free: 0.125 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3576 10 %RANDOM
Rwork0.179 ---
obs0.183 35831 100 %-
all-32195 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20 Å2
2---0.46 Å20 Å2
3---0.44 Å2
Refinement stepCycle: LAST / Resolution: 1.78→60.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2502 0 21 460 2983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222630
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9333630
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9845378
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.27226.21195
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41415387
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.491154
X-RAY DIFFRACTIONr_chiral_restr0.0980.2457
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021986
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.78→1.83 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 218 -
Rwork0.271 2184 -
obs--100 %
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)
10.40980.0480.00311.55320.61860.69930.0079-0.04830.0356-0.058-0.03890.0179-0.0191-0.04190.03090.00330.0026-0.00250.0378-0.02870.023613.417866.197611.5867
20.90270.0255-0.01930.93-0.32370.81920.02740.00160.0423-0.0124-0.03190.0157-0.07650.07250.00450.0262-0.0066-0.0020.04540.00740.026235.008172.612613.1023
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 173
2X-RAY DIFFRACTION2B1 - 173

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