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- PDB-3uiz: Crystal structure of SefD_dscA in D2O -

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Basic information

Entry
Database: PDB / ID: 3uiz
TitleCrystal structure of SefD_dscA in D2O
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

Downloads & links

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Assembly

Deposited unit
A: Chimera protein of SefD and SefA
B: Chimera protein of SefD and SefA
C: Chimera protein of SefD and SefA
D: Chimera protein of SefD and SefA
E: Chimera protein of SefD and SefA
F: Chimera protein of SefD and SefA


Theoretical massNumber of molelcules
Total (without water)101,4856
Polymers101,4856
Non-polymers00
Water0
1
A: Chimera protein of SefD and SefA


Theoretical massNumber of molelcules
Total (without water)16,9141
Polymers16,9141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chimera protein of SefD and SefA


Theoretical massNumber of molelcules
Total (without water)16,9141
Polymers16,9141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chimera protein of SefD and SefA


Theoretical massNumber of molelcules
Total (without water)16,9141
Polymers16,9141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chimera protein of SefD and SefA


Theoretical massNumber of molelcules
Total (without water)16,9141
Polymers16,9141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Chimera protein of SefD and SefA


Theoretical massNumber of molelcules
Total (without water)16,9141
Polymers16,9141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Chimera protein of SefD and SefA


Theoretical massNumber of molelcules
Total (without water)16,9141
Polymers16,9141
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
7
A: Chimera protein of SefD and SefA
E: 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
Buried area2050 Å2
ΔGint-13 kcal/mol
Surface area12620 Å2
MethodPISA
8
B: Chimera protein of SefD and SefA
D: 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
Buried area2120 Å2
ΔGint-13 kcal/mol
Surface area12850 Å2
MethodPISA
9
C: Chimera protein of SefD and SefA

F: 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 operation2_544-x+1/2,-y-1,z-1/21
Buried area2130 Å2
ΔGint-11 kcal/mol
Surface area12890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.660, 87.960, 211.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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.: 6
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: 2.42 Å3/Da / Density % sol: 49.09 %
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: 1.5498 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: 1.5498 Å / Relative weight: 1
ReflectionResolution: 3.1→47.15 Å / Num. obs: 18325 / % possible obs: 98.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Biso Wilson estimate: 80.103 Å2 / Rmerge(I) obs: 0.076 / Rsym value: 0.076 / Net I/σ(I): 14.2
Reflection shellResolution: 3.1→3.18 Å / Redundancy: 4.9 % / Rmerge(I) obs: 0.045 / Mean I/σ(I) obs: 3 / Num. unique all: 6336 / Rsym value: 0.45 / % possible all: 97.3

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Processing

Software
NameVersionClassification
Adxvdata processing
MOLREPphasing
REFMAC5.6.0117refinement
xia2data reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3UIY

3uiy


Resolution: 3.1→47.15 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.866 / SU B: 58.992 / SU ML: 0.46 / Isotropic thermal model: TLS / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.554 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.3022 932 5.1 %RANDOM
Rwork0.25918 ---
all0.26127 ---
obs0.26127 17356 98.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 68.622 Å2
Baniso -1Baniso -2Baniso -3
1--1.46 Å20 Å20 Å2
2--5.16 Å20 Å2
3----3.7 Å2
Refinement stepCycle: LAST / Resolution: 3.1→47.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5530 0 0 0 5530
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0195879
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6091.9418000
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.3635785
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.75223.907215
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.8815860
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.2421524
X-RAY DIFFRACTIONr_chiral_restr0.110.2960
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024400
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: 3.1→3.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.39 52 -
Rwork0.307 1113 -
obs-1290 96.84 %
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)
14.20980.0994-1.45840.7426-0.25961.9168-0.1821-0.192-0.12570.0790.0650.10760.177-0.30470.11710.210.0006-0.04690.3285-0.02290.25020.2658-32.790649.5669
22.0511-0.9318-0.61441.78731.17393.9701-0.2179-0.2148-0.02520.40870.180.27350.003-0.19120.03790.31930.10630.03580.22970.05080.201412.1503-27.806586.7605
31.31120.3123-0.8892.1208-1.20413.77990.0202-0.1472-0.25780.1397-0.1634-0.05060.24740.01160.14330.3235-0.0573-0.0450.23720.010.22220.944-49.568215.9385
43.3221-0.0642-1.78181.10780.48483.2038-0.05760.1827-0.2081-0.07660.0689-0.13710.12280.3164-0.01130.20770.0098-0.04850.3669-0.02950.245326.7996-32.7549.3016
51.96360.8687-0.85281.4656-0.56786.4895-0.17480.23950.0092-0.58380.2282-0.3583-1.34120.6213-0.05340.6483-0.24960.16150.2483-0.07940.178814.9847-27.4812.9695
61.3541-0.0585-0.17920.22990.15546.57870.34740.1919-0.486-0.2856-0.18680.06961.64520.5831-0.16061.00020.3948-0.27470.2241-0.10780.200125.1579-50.380884.2872
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 143
2X-RAY DIFFRACTION2B2 - 143
3X-RAY DIFFRACTION3C3 - 143
4X-RAY DIFFRACTION4D3 - 143
5X-RAY DIFFRACTION5E3 - 143
6X-RAY DIFFRACTION6F4 - 143

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