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- PDB-3uiy: Crystal structure of SefD_dscA in H2O -

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Basic information

Entry
Database: PDB / ID: 3uiy
TitleCrystal structure of SefD_dscA in H2O
ComponentsChimera protein of SefD and SefA
KeywordsSTRUCTURAL PROTEIN / deuterium / pilin / Immunoglobulin / Immunoglobulin like fold / Chaperone-usher minor pilin domain / Extracellular membrane surface
Function / homology
Function and homology information


Fimbrial protein SefA / SEF14-like adhesin / Enterobacteria AfaD invasin / Enterobacteria AfaD invasin protein / Dr adhesin / Dr-adhesin superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fimbrial protein / SefD
Similarity search - Component
Biological speciesSalmonella enterica subsp. enterica serovar Enteritidis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsGarnett, J.A. / Wei-chao, L. / Liu, B. / Matthews, S.J.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Promoting crystallisation of the Salmonella enteritidis fimbriae 14 pilin SefD using deuterium oxide.
Authors: Liu, B. / Garnett, J.A. / Lee, W.C. / Lin, J. / Salgado, P. / Taylor, J. / Xu, Y. / Lambert, S. / Cota, E. / Matthews, S.
History
DepositionNov 7, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 9, 2013Group: Database references
Revision 1.2Jul 26, 2017Group: Data collection / Refinement description / Source and taxonomy
Category: diffrn_detector / entity_src_gen / software / Item: _diffrn_detector.detector
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.classification / _software.name
Revision 1.4Sep 13, 2023Group: 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 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chimera protein of SefD and SefA


Theoretical massNumber of molelcules
Total (without water)16,9141
Polymers16,9141
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Chimera protein of SefD and SefA

A: Chimera protein of SefD and SefA


Theoretical massNumber of molelcules
Total (without water)33,8282
Polymers33,8282
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_554y,x,-z-1/31
Buried area2090 Å2
ΔGint-13 kcal/mol
Surface area12650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.480, 52.480, 218.030
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522
DetailsAuthor stated that the biological unit of SefD is a monomer. It is dimeric in the crystal structure (and purifies as a dimer) due to sheet interactions stabilized by residues 141-143. However, these residues are non-native (encoded by the vector) and as such it is monomeric in its native form

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Components

#1: Protein Chimera protein of SefD and SefA


Mass: 16914.174 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Salmonella enterica subsp. enterica serovar Enteritidis (bacteria)
Gene: sefD / Plasmid: pQE-30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: Q53997, UniProt: P12061

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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: 2.56 Å3/Da / Density % sol: 51.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 4 M ammonium acetate, 0.1 M sodium acetate, pH 4.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.9778 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 14, 2011
RadiationMonochromator: Double Crystal Monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9778 Å / Relative weight: 1
ReflectionResolution: 3.1→45.45 Å / Num. obs: 3659 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.2 % / Biso Wilson estimate: 71.841 Å2 / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 15.2
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.443 / Mean I/σ(I) obs: 3.2 / Num. unique all: 250 / Rsym value: 0.443 / % possible all: 99.5

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Processing

Software
NameVersionClassification
Adxvdata processing
PHASERphasing
REFMAC5.6.0117refinement
xia2data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AXW

2axw


Resolution: 3.1→45.45 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.81 / SU B: 43.435 / SU ML: 0.33 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.556 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.33151 154 4.3 %RANDOM
Rwork0.26793 ---
all0.27027 ---
obs0.27027 3450 97.88 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 64.71 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.15 Å20 Å2
2--0.31 Å20 Å2
3----0.46 Å2
Refinement stepCycle: LAST / Resolution: 3.1→45.45 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms935 0 0 0 935
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.019980
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8111.941334
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.2585131
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.28723.88936
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15515142
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.084154
X-RAY DIFFRACTIONr_chiral_restr0.1180.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.02735
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: 3.103→3.183 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.228 8 -
Rwork0.3 180 -
obs-1155 98.95 %
Refinement TLS params.Method: refined / Origin x: -13.1952 Å / Origin y: -5.39 Å / Origin z: -54.2472 Å
111213212223313233
T0.0937 Å2-0.01 Å20.0414 Å2-0.4142 Å20.0596 Å2--0.2229 Å2
L4.2482 °2-0.997 °22.4346 °2-1.7736 °20.6834 °2--3.1118 °2
S-0.096 Å °0.3733 Å °0.3251 Å °-0.1078 Å °-0.1517 Å °0.1332 Å °-0.0747 Å °-0.1012 Å °0.2477 Å °

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