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- PDB-1usq: Complex of E. Coli DraE adhesin with Chloramphenicol -

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Basic information

Entry
Database: PDB / ID: 1usq
TitleComplex of E. Coli DraE adhesin with Chloramphenicol
ComponentsDR HEMAGGLUTININ STRUCTURAL SUBUNIT
KeywordsADHESIN / DRAE / FIMBRIAL ADHESIN / CHLORAMPHENICOL / 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
CHLORAMPHENICOL / Dr hemagglutinin structural subunit
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionNov 27, 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 / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
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

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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)100,98537
Polymers97,0196
Non-polymers3,96631
Water12,791710
1
A: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules

A: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules

A: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,71621
Polymers48,5103
Non-polymers2,20618
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_655-y+1,x-y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
MethodPQS
2
B: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules

B: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules

B: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,42818
Polymers48,5103
Non-polymers1,91815
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-y+1,x-y+1,z1
crystal symmetry operation3_565-x+y,-x+1,z1
MethodPQS
3
C: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules

C: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules

C: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,42818
Polymers48,5103
Non-polymers1,91815
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
MethodPQS
4
D: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules

D: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules

D: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,53018
Polymers48,5103
Non-polymers2,02015
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_665-x+y+1,-x+1,z1
crystal symmetry operation2_655-y+1,x-y,z1
MethodPQS
5
E: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules

E: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules

E: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,42818
Polymers48,5103
Non-polymers1,91815
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
MethodPQS
6
F: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules

F: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules

F: DR HEMAGGLUTININ STRUCTURAL SUBUNIT
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,42818
Polymers48,5103
Non-polymers1,91815
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_755-y+2,x-y,z1
crystal symmetry operation3_775-x+y+2,-x+2,z1
MethodPQS
Unit cell
Length a, b, c (Å)118.969, 118.969, 57.416
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number143
Space group name H-MP3
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.50111, 0.86537, -0.00541), (-0.86538, -0.5011, 0.00269), (-0.00039, 0.00603, 0.99998)0.06384, 68.71037, -3.67905
2given(-0.37085, -0.92862, -0.01147), (0.92864, -0.37093, 0.00595), (-0.00978, -0.00845, 0.99992)59.50617, 34.36259, -1.05185
3given(-0.99745, 0.07115, -0.00525), (0.07111, 0.99744, 0.00812), (0.00581, 0.00773, -0.99995)116.5445, -4.5186, 29.28418
4given(0.55986, -0.82858, -0.00128), (-0.82858, -0.55987, 0.00236), (-0.00267, -0.00026, -1)-7.10494, 132.77824, 31.45149
5given(0.55521, 0.83167, -0.00822), (0.8317, -0.55513, 0.01046), (0.00414, -0.01265, -0.99991)-63.35427, -26.87984, 33.52893
DetailsTHERE ARE SIX TRIMERS IN THE CRYSTAL CELL , EACH LINKEDINTERNALLY BY 3 INTERMOLECULAR DISULPHIDE BONDS OF THEMONOMER WITH TWO OF ITS THREEFOLD-RELATED COPIES

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Components

#1: Protein
DR HEMAGGLUTININ STRUCTURAL SUBUNIT / ADHESIN / DRAE


Mass: 16169.844 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH CHLORAMPHENICOL / 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.: 14 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 710 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION IN CHAINS A-F, GLY 21 TO ALA 21 ENGINEERED MUTATION IN CHAINS A-F, SER 22 TO ...ENGINEERED MUTATION IN CHAINS A-F, GLY 21 TO ALA 21 ENGINEERED MUTATION IN CHAINS A-F, SER 22 TO GLY 22 ENGINEERED MUTATION IN CHAINS A-F, GLU 39 TO LYS 39
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: 2.42 Å3/Da / Density % sol: 50 % / Description: 20% EGL AS CRYOPROTECTANT
Crystal growpH: 7
Details: 1.7 M AMMONIUM SULPHATE 0.1M TRIS-HCL PH 7.0, 2.8 MM CHLORAMPHENICOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87
DetectorType: ADSC CCD / Detector: CCD / Date: Oct 15, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.9→15 Å / Num. obs: 71543 / % possible obs: 99.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 0.65 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 4.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 1.4 / % possible all: 100

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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: 1.9→15 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
Rfree0.225 3560 5 %RANDOM
Rwork0.191 ---
all0.193 71513 --
obs0.193 71513 99.8 %-
Solvent computationSolvent model: BABINET SCALING / Bsol: 55 Å2 / ksol: 0.47 e/Å3
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6309 0 234 710 7253
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00866642
X-RAY DIFFRACTIONt_angle_deg0.84790523
X-RAY DIFFRACTIONt_dihedral_angle_d17.86337840
X-RAY DIFFRACTIONt_incorr_chiral_ct0
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.0122072
X-RAY DIFFRACTIONt_gen_planes0.029475
X-RAY DIFFRACTIONt_it1.301673620
X-RAY DIFFRACTIONt_nbd0.0693032
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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