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- PDB-5d55: Crystal structure of the E. coli Hda pilus minor tip subunit, HdaB -

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Basic information

Entry
Database: PDB / ID: 5d55
TitleCrystal structure of the E. coli Hda pilus minor tip subunit, HdaB
ComponentsHdaB,HdaA (Adhesin), HUS-associated diffuse adherence
KeywordsCELL ADHESION / Biofilm / chaperone-usher / Hda / pilus
Function / homology
Function and homology information


Enterobacteria AfaD invasin / Enterobacteria AfaD invasin protein / Dr adhesin / Dr-adhesin superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
CITRATE ANION / IODIDE ION / HdaB / HdaA (Adhesin), HUS-associated diffuse adherence
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLee, W.-C. / Garnett, J.A. / Matthews, S.J.
CitationJournal: Protein Sci. / Year: 2016
Title: Crystal structure and analysis of HdaB: The enteroaggregative Escherichia coli AAF/IV pilus tip protein.
Authors: Lee, W.C. / Matthews, S. / Garnett, J.A.
History
DepositionAug 10, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HdaB,HdaA (Adhesin), HUS-associated diffuse adherence
B: HdaB,HdaA (Adhesin), HUS-associated diffuse adherence
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,6726
Polymers34,9772
Non-polymers6944
Water4,125229
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-28 kcal/mol
Surface area15620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.294, 112.294, 61.652
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein HdaB,HdaA (Adhesin), HUS-associated diffuse adherence


Mass: 17488.668 Da / Num. of mol.: 2
Fragment: UNP residues 24-142,UNP residues 18-34,UNP residues 24-142,UNP residues 18-34
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: hdaB, hdaA / Production host: Escherichia coli (E. coli) / References: UniProt: B3V224, UniProt: Q08JP6
#2: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H5O7
#3: Chemical ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: I
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / 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: 2.8 Å3/Da / Density % sol: 56.15 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 0.2M Ammonium Citrate, 20% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 1.6531 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 8, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.6531 Å / Relative weight: 1
ReflectionResolution: 2→79.4 Å / Num. obs: 26601 / % possible obs: 98.1 % / Redundancy: 3.6 % / Biso Wilson estimate: 31.636 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 9.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.371 / Mean I/σ(I) obs: 2.7 / % possible all: 95.1

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Processing

Software
NameVersionClassification
REFMAC5.6.0062refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4OR1

4or1


Resolution: 2→79.4 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.927 / SU B: 7.378 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.181 / ESU R Free: 0.169 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24831 2654 10 %RANDOM
Rwork0.20267 ---
obs0.20735 23905 97.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.393 Å2
Baniso -1Baniso -2Baniso -3
1-0.17 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.35 Å2
Refinement stepCycle: 1 / Resolution: 2→79.4 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2187 0 40 229 2456
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212336
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1841.9363184
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1425314
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.7824.08693
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.51915363
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.792158
X-RAY DIFFRACTIONr_chiral_restr0.0770.2352
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021785
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 164 -
Rwork0.325 1628 -
obs--90.37 %
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)
12.55040.8033-0.39611.3457-0.38290.6949-0.0912-0.1678-0.074-0.07980.0444-0.07590.0543-0.03750.04690.0747-0.01770.02510.0276-0.00140.046536.37517.380.254
21.0321.6374-1.8225.3176-5.00786.0827-0.07590.2240.1342-0.20950.31830.1261-0.102-0.3909-0.24250.0855-0.0080.00930.05760.04340.084516.769-3.27922.493
30.93320.6883-0.48633.3197-0.75971.5033-0.06390.06840.0086-0.16380.08540.0772-0.0416-0.1356-0.02140.01780.00210.00520.09550.0420.061114.555-2.87829.833
43.28341.81-3.42842.6192-1.83684.6466-0.03450.0860.0380.13890.10910.0181-0.0265-0.3454-0.07460.02460.0184-0.01080.07330.03070.074337.17215.3517.399
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 119
2X-RAY DIFFRACTION2A120 - 146
3X-RAY DIFFRACTION3B0 - 119
4X-RAY DIFFRACTION4B120 - 146

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