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- PDB-1ut1: DraE adhesin from Escherichia Coli -

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ID or keywords:

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Basic information

Entry
Database: PDB / ID: 1ut1
TitleDraE adhesin from Escherichia Coli
ComponentsDR HEMAGGLUTININ STRUCTURAL SUBUNIT
KeywordsPROTEIN BINDING / ADHESIN / PROTEIN BINDING FIMBRIAL 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
Dr hemagglutinin structural subunit
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 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 1.1Sep 5, 2012Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
B: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
C: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
D: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
E: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
F: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,51148
Polymers96,4976
Non-polymers3,01542
Water15,295849
1
A: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
D: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
E: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,06629
Polymers48,2483
Non-polymers1,81826
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-75.7 kcal/mol
Surface area19120 Å2
MethodPISA
2
B: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
C: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
F: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,44519
Polymers48,2483
Non-polymers1,19716
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7500 Å2
ΔGint-83.8 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.879, 108.507, 119.622
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.99476, -0.00572, 0.10208), (-0.00597, -0.99998, 0.00221), (0.10206, -0.00281, -0.99477)-8.93282, 54.85018, 175.37831
2given(0.99544, 0.01136, 0.09474), (0.0113, -0.99994, 0.00118), (0.09475, -0.00011, -0.9955)-9.05433, 54.42756, 175.65546
3given(0.99481, 0.0044, 0.10161), (0.00489, -0.99998, -0.00459), (0.10159, 0.00506, -0.99481)-8.93156, 54.96851, 175.44121
DetailsTHE MONOMERS ARE ARRANGED IN TWO TRIMERS ADE AND BCF, EACHLINKED INTERNALLY BY 3 INTERMOLECULAR DISULPHIDE BONDS: CYSA 19 - CYS D 51 CYS D 19 - CYS E 51 CYS E 19 - CYS A 51 CYSB 19 - CYS C 51 CYS C 19 - CYS F 51 CYS F 19 - CYS B 51

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Components

#1: Protein
DR HEMAGGLUTININ STRUCTURAL SUBUNIT / DRAA


Mass: 16082.766 Da / Num. of mol.: 6 / Fragment: MATURE PROTEIN, RESIDUES 21-160 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: IH11128 / Description: 6-HIS-TAGGED / Variant: O75\:K5\:H- / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15 / References: UniProt: P24093
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical...
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 30 / Source method: obtained synthetically / Formula: C2H6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 849 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.32 Å3/Da / Density % sol: 48 %
Crystal growpH: 7 / Details: 2.0 M AMMONIUM SULPHATE, 0.1M TRIS-HCL, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.975
DetectorType: ADSC CCD / Detector: CCD / Date: May 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.975 Å / Relative weight: 1
ReflectionResolution: 1.7→54 Å / Num. obs: 94785 / % possible obs: 95.7 % / Redundancy: 4 % / Biso Wilson estimate: 0.76 Å2 / Rmerge(I) obs: 0.048 / Net I/σ(I): 9.6
Reflection shellResolution: 1.7→1.79 Å / Rmerge(I) obs: 0.252 / Mean I/σ(I) obs: 3 / % possible all: 77.2

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Processing

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

1usz


Resolution: 1.7→30 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
Rfree0.207 4743 5 %RANDOM
Rwork0.173 ---
all0.175 94726 --
obs0.175 94726 95.5 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 62 Å2 / ksol: 0.44 e/Å3
Refinement stepCycle: LAST / Resolution: 1.7→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6318 0 180 849 7347
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.01267362
X-RAY DIFFRACTIONt_angle_deg1.04491183
X-RAY DIFFRACTIONt_dihedral_angle_d18.06638660
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0171892
X-RAY DIFFRACTIONt_gen_planes0.0259475
X-RAY DIFFRACTIONt_it1.766673620
X-RAY DIFFRACTIONt_nbd0.3923032
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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