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- PDB-3gea: Donor strand complemented FaeG monomer of F4 variant ad -

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Basic information

Entry
Database: PDB / ID: 3gea
TitleDonor strand complemented FaeG monomer of F4 variant ad
ComponentsK88 fimbrial protein AD
KeywordsCELL ADHESION / immunoglobulin like fold / Fimbrium
Function / homologyFimbrial, major/minor subunit / Fimbrial, major and minor subunit / pilus / cell adhesion / K88 fimbrial protein AD
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.699 Å
AuthorsVan Molle, I. / Moonens, K. / Garcia-Pino, A. / Buts, L. / Bouckaert, J. / De Greve, H.
CitationJournal: J.Mol.Biol. / Year: 2009
Title: Structural and thermodynamic characterization of pre- and postpolymerization states in the F4 fimbrial subunit FaeG
Authors: Van Molle, I. / Moonens, K. / Garcia-Pino, A. / Buts, L. / De Kerpel, M. / Wyns, L. / Bouckaert, J. / De Greve, H.
History
DepositionFeb 25, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.2Jan 29, 2014Group: Database references
Revision 1.3Aug 9, 2017Group: Refinement description / Source and taxonomy / Category: entity_src_gen / software
Revision 1.4Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / 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: K88 fimbrial protein AD
B: K88 fimbrial protein AD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)58,34310
Polymers57,5942
Non-polymers7498
Water9,386521
1
A: K88 fimbrial protein AD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3617
Polymers28,7971
Non-polymers5646
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: K88 fimbrial protein AD
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9813
Polymers28,7971
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)123.965, 123.965, 95.886
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 K88 fimbrial protein AD / FaeGntd/dsc / K88 pilin / K88 antigen


Mass: 28796.998 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Strain: C1360-79 / Gene: faeG / Plasmid: pEXP96 / Production host: Escherichia coli (E. coli) / Strain (production host): C43(DE3) / References: UniProt: P14191
#2: Chemical ChemComp-SO4 / SULFATE ION / K88 pilin / K88 antigen


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE CONFLICT BASED ON REFERENCE 2 OF DATABASE FAEG3_ECOLX (UNIPROTKB/SWISS-PROT P14191). N27S (UNP ...THE CONFLICT BASED ON REFERENCE 2 OF DATABASE FAEG3_ECOLX (UNIPROTKB/SWISS-PROT P14191). N27S (UNP RESIDUE 59) IS CONFLICT OF FAEG3_ECOLX.

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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: 3.69 Å3/Da / Density % sol: 66.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.8M ammonium sulphate, 0.1M Tris pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0723 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: May 9, 2008
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0723 Å / Relative weight: 1
ReflectionResolution: 1.699→28.677 Å / Num. all: 93586 / Num. obs: 93586 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10.5 % / Biso Wilson estimate: 14.79 Å2 / Rmerge(I) obs: 0.115 / Rsym value: 0.115 / Net I/σ(I): 16.5
Reflection shellResolution: 1.699→1.79 Å / Redundancy: 10.3 % / Rmerge(I) obs: 0.664 / Mean I/σ(I) obs: 3.7 / Rsym value: 0.698 / % possible all: 99.3

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3.006data extraction
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2J6G

2j6g


Resolution: 1.699→28.677 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU ML: 0.18 / σ(F): 1.41 / Phase error: 15.07 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1828 4691 5.01 %
Rwork0.1592 --
obs0.1604 93547 99.91 %
all-93586 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.919 Å2 / ksol: 0.378 e/Å3
Displacement parametersBiso mean: 21.097 Å2
Baniso -1Baniso -2Baniso -3
1-0.106 Å20 Å2-0 Å2
2--0.106 Å20 Å2
3----0.212 Å2
Refinement stepCycle: LAST / Resolution: 1.699→28.677 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3883 0 45 521 4449
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0314002
X-RAY DIFFRACTIONf_angle_d2.5375438
X-RAY DIFFRACTIONf_dihedral_angle_d17.4651335
X-RAY DIFFRACTIONf_chiral_restr0.237620
X-RAY DIFFRACTIONf_plane_restr0.013703
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.6988-1.71810.23281540.20492885X-RAY DIFFRACTION98
1.7181-1.73840.2121650.18692903X-RAY DIFFRACTION100
1.7384-1.75950.21011410.17832971X-RAY DIFFRACTION100
1.7595-1.78180.20951670.17152925X-RAY DIFFRACTION100
1.7818-1.80530.19531580.16342912X-RAY DIFFRACTION100
1.8053-1.830.20281440.16232927X-RAY DIFFRACTION100
1.83-1.85610.17591530.16322963X-RAY DIFFRACTION100
1.8561-1.88380.1761740.15142946X-RAY DIFFRACTION100
1.8838-1.91330.17861570.1482931X-RAY DIFFRACTION100
1.9133-1.94460.1841560.14712929X-RAY DIFFRACTION100
1.9446-1.97810.18131410.13992950X-RAY DIFFRACTION100
1.9781-2.01410.1661670.13922941X-RAY DIFFRACTION100
2.0141-2.05280.14851500.14182954X-RAY DIFFRACTION100
2.0528-2.09470.15621590.14142970X-RAY DIFFRACTION100
2.0947-2.14030.15941700.13642903X-RAY DIFFRACTION100
2.1403-2.190.15671680.13552940X-RAY DIFFRACTION100
2.19-2.24480.17141360.13782987X-RAY DIFFRACTION100
2.2448-2.30540.18071360.14082999X-RAY DIFFRACTION100
2.3054-2.37320.15971470.14932955X-RAY DIFFRACTION100
2.3732-2.44980.19051290.15162995X-RAY DIFFRACTION100
2.4498-2.53730.18641590.15272953X-RAY DIFFRACTION100
2.5373-2.63880.16891410.15222966X-RAY DIFFRACTION100
2.6388-2.75880.17511570.15622976X-RAY DIFFRACTION100
2.7588-2.90420.16841470.16032994X-RAY DIFFRACTION100
2.9042-3.08590.17221630.15262955X-RAY DIFFRACTION100
3.0859-3.32390.1861870.16072956X-RAY DIFFRACTION100
3.3239-3.65780.16481560.14663013X-RAY DIFFRACTION100
3.6578-4.18560.15281500.14683006X-RAY DIFFRACTION100
4.1856-5.26810.17051730.14453024X-RAY DIFFRACTION100
5.2681-28.68190.21841860.19083127X-RAY DIFFRACTION100
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)
10.16680.0680.02760.4860.09920.58-0.0018-0.031-0.0052-0.04860.0057-0.0115-0.014-0.0051-0.00490.0548-0.0036-0.01030.0345-0.00070.021857.555922.880914.9631
20.8517-0.9561-0.05371.8503-0.3070.6461-0.0939-0.0758-0.27690.00310.11520.45880.022-0.1109-0.02880.0726-0.00910.00570.06160.03450.198246.366-13.891210.8373
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain A
2X-RAY DIFFRACTION2chain B

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