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- PDB-1ut2: AfaE-3 adhesin from Escherichia Coli -

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Basic information

Entry
Database: PDB / ID: 1ut2
TitleAfaE-3 adhesin from Escherichia Coli
ComponentsAFIMBRIAL ADHESIN AFA-III
KeywordsADHESIN / AFAE-3 / AFIMBRIAL ADHESIN / UPEC / DAEC
Function / homology
Function and homology information


Adhesin, Dr-family / Adhesin, Dr family, signal peptide / Dr-family adhesin / Dr family adhesin / Dr adhesin / Dr-adhesin superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Afimbrial adhesin AFA-III
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.3 Å
AuthorsAnderson, K.L. / Billington, J. / Pettigrew, D. / Cota, E. / Roversi, P. / Simpson, P. / Chen, H.A. / Urvil, P. / Dumerle, L. / Barlow, P. ...Anderson, K.L. / Billington, J. / Pettigrew, D. / Cota, E. / Roversi, P. / Simpson, P. / Chen, H.A. / Urvil, P. / Dumerle, L. / Barlow, P. / Medof, E. / Smith, R.A.G. / Nowicki, B. / Le Bouguenec, C. / Lea, S.M. / Matthews, S.
Citation
Journal: J.Biol.Chem. / Year: 2004
Title: High Resolution Studies of the Afa/Dr Adhesin Drae and its Interaction with Chloramphenicol
Authors: Pettigrew, D. / Anderson, K.L. / Billington, J. / Cota, E. / Simpson, P. / Urvil, P. / Rabuzin, F. / Roversi, P. / Nowicki, B. / Du Merle, L. / Le Bouguenec, C. / Matthews, S. / Lea, S.M.
#1: Journal: Mol.Cell / Year: 2004
Title: An Atomic Resolution Model for Assmebly, Architecture,and Function of the Dr Adhesins
Authors: Anderson, K.L. / Billington, J. / Pettigrew, D. / Cota, E. / Simpson, P. / Roversi, P. / Chen, H.A. / Urvil, P. / Du Merle, L. / Barlow, P.N. / Medof, M.E. / Smith, R.A.G. / Nowicki, B. / Le ...Authors: Anderson, K.L. / Billington, J. / Pettigrew, D. / Cota, E. / Simpson, P. / Roversi, P. / Chen, H.A. / Urvil, P. / Du Merle, L. / Barlow, P.N. / Medof, M.E. / Smith, R.A.G. / Nowicki, B. / Le Bouguenec, C. / Lea, S.M. / Matthews, S.
History
DepositionDec 2, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 31, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AFIMBRIAL ADHESIN AFA-III
B: AFIMBRIAL ADHESIN AFA-III
C: AFIMBRIAL ADHESIN AFA-III
D: AFIMBRIAL ADHESIN AFA-III
E: AFIMBRIAL ADHESIN AFA-III
F: AFIMBRIAL ADHESIN AFA-III
G: AFIMBRIAL ADHESIN AFA-III
H: AFIMBRIAL ADHESIN AFA-III
I: AFIMBRIAL ADHESIN AFA-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,97012
Polymers145,6819
Non-polymers2883
Water48627
1
A: AFIMBRIAL ADHESIN AFA-III
B: AFIMBRIAL ADHESIN AFA-III
C: AFIMBRIAL ADHESIN AFA-III


Theoretical massNumber of molelcules
Total (without water)48,5603
Polymers48,5603
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
D: AFIMBRIAL ADHESIN AFA-III
E: AFIMBRIAL ADHESIN AFA-III
I: AFIMBRIAL ADHESIN AFA-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7535
Polymers48,5603
Non-polymers1922
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
F: AFIMBRIAL ADHESIN AFA-III
G: AFIMBRIAL ADHESIN AFA-III
H: AFIMBRIAL ADHESIN AFA-III
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6574
Polymers48,5603
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)113.295, 113.295, 164.125
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.50291, -0.86381, -0.03017), (0.86427, -0.503, -0.00487), (-0.01097, -0.02852, 0.99953)119.25115, 73.45293, 2.11582
2given(-0.49767, 0.86619, 0.04512), (-0.86659, -0.49875, 0.01652), (0.03681, -0.03088, 0.99884)-4.80212, 138.94499, 1.00065
3given(-0.99734, 0.06351, -0.03565), (-0.06364, -0.99797, 0.0025), (-0.03542, 0.00476, 0.99936)131.77222, 115.14204, 5.47299
4given(0.44378, -0.8961, -0.0084), (0.8931, 0.44148, 0.08645), (-0.07376, -0.04586, 0.99622)30.37418, -33.02155, 10.30572
5given(-0.39513, 0.91833, -0.0234), (0.91859, 0.39521, -0.00135), (0.00801, -0.02203, -0.99973)-10.21558, 13.76989, 59.81935
6given(0.99085, -0.12371, -0.05403), (-0.12662, -0.99047, -0.05414), (-0.04682, 0.06049, -0.99707)16.43862, 144.32909, 55.11076
7given(-0.60896, -0.7932, -0.00174), (-0.7919, 0.60783, 0.05873), (-0.04553, 0.03714, -0.99827)112.12747, 53.27749, 56.40563
8given(0.53559, 0.82809, 0.16554), (-0.83028, 0.55217, -0.07585), (-0.15421, -0.09682, 0.98328)-47.23882, 130.50336, 21.80345
DetailsTHE MONOMERS ARE ARRANGED IN THREE TRIMERS LINKEDINTERNALLY BY INTERMOLECULAR DISULPHIDE BONDS. TRIMER ABC: LINK A|19 C|51 B|19 A|51 C| 19 B|51 SSBONDTRIMER DEI: LINK D|19 E|51 E| 19 I|51 I|19 D|51 SSBONDTRIMER GFH: LINK F| 19 G|51 G|19 H|51 H|19 F|51 SSBOND

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Components

#1: Protein
AFIMBRIAL ADHESIN AFA-III / AFA-III / AFAE3


Mass: 16186.830 Da / Num. of mol.: 9 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: A30 / Description: N-TERMINUS 6-HIS-TAGGED / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: Q57254
#2: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 27 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAIN A-I GLY 21 TO ALA 21 ENGINEERED MUTATION IN CHAIN A-I SER 22 TO GLY 22 ...ENGINEERED MUTATION IN CHAIN A-I GLY 21 TO ALA 21 ENGINEERED MUTATION IN CHAIN A-I SER 22 TO GLY 22 BELONGS TO THE AFA-I/AFA-III/DRAA/DAAE FAMILY OF ADHESINS.

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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: 2.09 Å3/Da / Density % sol: 44 %
Crystal growpH: 7
Details: 0.2 M MAGNESIUM SULPHATE 20% PEG 4000, 0.1M TRIS-HCL PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9786
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 3.3→63.3 Å / Num. obs: 18872 / % possible obs: 99.9 % / Redundancy: 4 % / Biso Wilson estimate: 5.5 Å2 / Rmerge(I) obs: 0.194 / Net I/σ(I): 3.2
Reflection shellResolution: 3.3→3.48 Å / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 2 / % possible all: 99.9

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
XFITphasing
TNT5Erefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ID 1USZ

1usz


Resolution: 3.3→63.3 Å / Isotropic thermal model: TNT BCORREL / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: TNT CSDX_PROTGEO / Details: MAXIMUM LIKELIHOOD BUSTER-TNT REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.266 968 5 %RANDOM
Rwork0.226 ---
all0.228 18845 --
obs0.228 18845 99.9 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 11 Å2 / ksol: 0.33 e/Å3
Refinement stepCycle: LAST / Resolution: 3.3→63.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9455 0 15 27 9497
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00497122
X-RAY DIFFRACTIONt_angle_deg0.59132093
X-RAY DIFFRACTIONt_dihedral_angle_d21.456740
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0052702
X-RAY DIFFRACTIONt_gen_planes0.007140910
X-RAY DIFFRACTIONt_it0.604971220
X-RAY DIFFRACTIONt_nbd0.0351945
X-RAY DIFFRACTIONt_omega_torsion
X-RAY DIFFRACTIONt_other_torsion
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact

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