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- PDB-2jkl: DraE Adhesin in complex with Bromamphenicol -

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Basic information

Entry
Database: PDB / ID: 2jkl
TitleDraE Adhesin in complex with Bromamphenicol
ComponentsDR HEMAGGLUTININ STRUCTURAL SUBUNIT
KeywordsCELL ADHESION / BROMAMPHENICOL / CELL PROJECTION / FIMBRIAL ADHESIN / UPEC / DRAE / DAEC / ADHESIN / FIMBRIUM / HAEMAGGLUTININ
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
BROMAMPHENICOL / CHLORAMPHENICOL / Dr hemagglutinin structural subunit
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPettigrew, D.M. / Roversi, P. / Davies, S.G. / Russell, A.J. / Lea, S.M.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2009
Title: A Structural Study of the Interaction between the Dr Haemagglutinin Drae and Derivatives of Chloramphenicol
Authors: Pettigrew, D.M. / Roversi, P. / Davies, S.G. / Russell, A.J. / Lea, S.M.
History
DepositionAug 28, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 16, 2008Provider: repository / Type: Initial release
Revision 1.1May 7, 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 / 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 1.4Nov 6, 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)103,90939
Polymers97,0196
Non-polymers6,89033
Water14,988832
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)51,76621
Polymers48,5103
Non-polymers3,25618
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
Buried area5110 Å2
ΔGint-32.7 kcal/mol
Surface area24140 Å2
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)52,71421
Polymers48,5103
Non-polymers4,20418
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
Buried area5070 Å2
ΔGint-34.3 kcal/mol
Surface area24250 Å2
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)51,47818
Polymers48,5103
Non-polymers2,96815
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
Buried area4900 Å2
ΔGint-34.5 kcal/mol
Surface area23730 Å2
MethodPQS
4
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)51,47818
Polymers48,5103
Non-polymers2,96815
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
Buried area4950 Å2
ΔGint-36 kcal/mol
Surface area23950 Å2
MethodPQS
5
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)53,00224
Polymers48,5103
Non-polymers4,49221
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
Buried area5120 Å2
ΔGint-31.1 kcal/mol
Surface area24020 Å2
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)51,29115
Polymers48,5103
Non-polymers2,78212
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
Buried area4770 Å2
ΔGint-28.6 kcal/mol
Surface area24510 Å2
MethodPQS
Unit cell
Length a, b, c (Å)119.600, 119.600, 57.800
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(-0.4917, -0.87077, 0.00073), (0.87074, -0.49168, 0.00794), (-0.00655, 0.00454, 0.99997)59.44537, 33.96864, 3.3179
2given(-0.40038, 0.91625, -0.01357), (-0.91625, -0.40051, -0.00897), (-0.01366, 0.00884, 0.99987)-7.78679, 68.61376, 1.42409
3given(-0.99835, 0.05734, 0.00247), (0.05735, 0.99834, 0.00523), (-0.00216, 0.00536, -0.99998)117.47514, -3.27306, 30.13104
4given(0.55557, -0.83147, 0.00013), (-0.83147, -0.55557, -0.00096), (0.00087, 0.00043, -1)115.03351, 68.85452, 31.17225
5given(0.54684, 0.83722, 0.00485), (0.83719, -0.54674, -0.01335), (-0.00852, 0.01136, -0.9999)57.97229, 37.75697, 33.32103

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Components

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein
DR HEMAGGLUTININ STRUCTURAL SUBUNIT


Mass: 16169.844 Da / Num. of mol.: 6 / Fragment: ADHESIN SUBUNIT, RESIDUES 23-160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Strain: IH11128 / Cell line: M15 / Variant: O75\:K5\:H / Plasmid: PQE-30 / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24093

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Non-polymers , 5 types, 865 molecules

#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.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-BRX / BROMAMPHENICOL


Mass: 412.031 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C11H12Br2N2O5
#5: Chemical
ChemComp-CLM / CHLORAMPHENICOL


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


Mass: 18.015 Da / Num. of mol.: 832 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.56 Å3/Da / Density % sol: 52 % / Description: NONE
Crystal growDetails: 2M AMMONIUM SULPHATE, 0.1-20 MM CHLORAMPHENICOL SUCCINATE, 0.1 M HEPES PH 7.0 SOAKED IN SATURATED BROMAMPHENICOL SOLUTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.919471
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919471 Å / Relative weight: 1
ReflectionResolution: 1.9→25 Å / Num. obs: 72808 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 6.7 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.2
Reflection shellResolution: 1.9→2 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.24 / Mean I/σ(I) obs: 3 / % possible all: 100

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Processing

Software
NameClassification
BUSTER-TNTrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1USQ

1usq


Resolution: 1.9→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.198 3630 5 %RANDOM
Rwork0.183 ---
obs0.184 72802 100 %-
Refinement stepCycle: LAST / Resolution: 1.9→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6291 0 352 832 7475

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