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- PDB-5dfk: Crystal Structure of the Escherichia coli Common Pilus Chaperone, EcpB -

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Basic information

Entry
Database: PDB / ID: 5dfk
TitleCrystal Structure of the Escherichia coli Common Pilus Chaperone, EcpB
ComponentsProbable fimbrial chaperone EcpB
KeywordsSTRUCTURAL PROTEIN / chaperone usher / pilus / pili / biofilm / adhesion / biogenesis / E. coli / virulence
Function / homologyEcpB, C-terminal / EcpB C-terminal domain / PapD-like superfamily / Immunoglobulin-like fold / Probable fimbrial chaperone EcpB / Probable fimbrial chaperone EcpB
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 2.4 Å
AuthorsGarnett, J.A. / Diallo, M. / Matthews, S.J.
CitationJournal: Plos Pathog. / Year: 2015
Title: Structural Insight into Archaic and Alternative Chaperone-Usher Pathways Reveals a Novel Mechanism of Pilus Biogenesis.
Authors: Pakharukova, N. / Garnett, J.A. / Tuittila, M. / Paavilainen, S. / Diallo, M. / Xu, Y. / Matthews, S.J. / Zavialov, A.V.
History
DepositionAug 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Nov 4, 2015Provider: repository / Type: Initial release
Revision 1.1Dec 2, 2015Group: Database references
Revision 1.2Nov 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _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: Probable fimbrial chaperone EcpB


Theoretical massNumber of molelcules
Total (without water)24,2611
Polymers24,2611
Non-polymers00
Water1,31573
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.650, 62.650, 121.140
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Probable fimbrial chaperone EcpB


Mass: 24261.309 Da / Num. of mol.: 1 / Fragment: UNP residues 21-222
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ecpB, matC, ECS88_0289 / Production host: Escherichia coli CFT073 (bacteria) / References: UniProt: B7MCA3, UniProt: P77188*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 73 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.19 Å3/Da / Density % sol: 43.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 15% (v/v) glycerol, 15% (w/v) PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97949 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97949 Å / Relative weight: 1
ReflectionResolution: 2.4→54.26 Å / Num. obs: 11265 / % possible obs: 99.9 % / Redundancy: 19.2 % / Biso Wilson estimate: 32.306 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 44.4
Reflection shellResolution: 2.4→2.46 Å / Redundancy: 19.4 % / Rmerge(I) obs: 0.492 / Mean I/σ(I) obs: 6.6 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
SCALAdata scaling
SHARPphasing
RefinementMethod to determine structure: SIRAS / Resolution: 2.4→54.26 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.925 / SU B: 13.018 / SU ML: 0.157 / Cross valid method: THROUGHOUT / ESU R: 0.282 / ESU R Free: 0.217 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23774 537 4.8 %RANDOM
Rwork0.2051 ---
obs0.20669 10708 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.69 Å2
Baniso -1Baniso -2Baniso -3
1-0.51 Å20.25 Å20 Å2
2--0.51 Å20 Å2
3----1.64 Å2
Refinement stepCycle: 1 / Resolution: 2.4→54.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1417 0 0 73 1490
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0191445
X-RAY DIFFRACTIONr_bond_other_d0.0010.021355
X-RAY DIFFRACTIONr_angle_refined_deg1.3071.9661963
X-RAY DIFFRACTIONr_angle_other_deg0.73533101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3735183
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.55723.7564
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.51415230
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5971511
X-RAY DIFFRACTIONr_chiral_restr0.0780.2222
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211656
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02333
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_it1.1572.441738
X-RAY DIFFRACTIONr_mcbond_other1.1572.442737
X-RAY DIFFRACTIONr_mcangle_it2.0193.651919
X-RAY DIFFRACTIONr_mcangle_other2.0183.65920
X-RAY DIFFRACTIONr_scbond_it1.2212.506707
X-RAY DIFFRACTIONr_scbond_other1.222.506707
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.0933.7161044
X-RAY DIFFRACTIONr_long_range_B_refined5.21319.2851514
X-RAY DIFFRACTIONr_long_range_B_other5.09518.9671493
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.4→2.462 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 29 -
Rwork0.272 770 -
obs--99.5 %
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)
11.50120.38730.06921.50240.14871.63140.02490.069-0.1492-0.04150.0869-0.32130.27960.2412-0.11180.18260.0261-0.02770.241-0.03320.0985-25.64218.529-21.367
23.94150.52910.07690.6636-0.15241.43230.0047-0.0798-0.24950.0163-0.0111-0.04770.16850.05060.00640.22480.0155-0.02410.2153-0.00770.1124-10.24830.301-4.744
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 144
2X-RAY DIFFRACTION2A145 - 217

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