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- PDB-2jkj: DraE Adhesin in complex with Chloramphenicol Succinate -

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Basic information

Entry
Database: PDB / ID: 2jkj
TitleDraE Adhesin in complex with Chloramphenicol Succinate
ComponentsDR HEMAGGLUTININ STRUCTURAL SUBUNIT
KeywordsCELL ADHESION / UPEC / DRAE / DAEC / ADHESIN / FIMBRIUM / HAEMAGGLUTININ / CELL PROJECTION / FIMBRIAL ADHESIN / CHLORAMPHENICOL SUCCINATE
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 / THIAMPHENICOL / Dr hemagglutinin structural subunit
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.1Sep 12, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Refinement description / Structure summary / Version format compliance
Revision 1.2Jul 5, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
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 13, 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

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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)101,11129
Polymers97,0196
Non-polymers4,09223
Water2,774154
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)50,05512
Polymers48,5103
Non-polymers1,5469
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 area4800 Å2
ΔGint-31.7 kcal/mol
Surface area23700 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)51,41218
Polymers48,5103
Non-polymers2,90315
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 area4810 Å2
ΔGint-32.5 kcal/mol
Surface area24160 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)50,05512
Polymers48,5103
Non-polymers1,5469
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 area4690 Å2
ΔGint-33.8 kcal/mol
Surface area23800 Å2
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)51,41218
Polymers48,5103
Non-polymers2,90315
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 area4850 Å2
ΔGint-31.8 kcal/mol
Surface area24400 Å2
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)50,05512
Polymers48,5103
Non-polymers1,5469
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_765-x+y+2,-x+1,z1
crystal symmetry operation2_645-y+1,x-y-1,z1
Buried area4750 Å2
ΔGint-34.6 kcal/mol
Surface area23540 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)50,34315
Polymers48,5103
Non-polymers1,83412
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 area4710 Å2
ΔGint-27.6 kcal/mol
Surface area24390 Å2
MethodPQS
Unit cell
Length a, b, c (Å)119.600, 119.600, 57.700
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(-0.48979, -0.87184, 0.00166), (0.87182, -0.48976, 0.00878), (-0.00684, 0.00575, 0.99996)59.33665, 33.84259, 3.20031
2given(-0.40844, 0.91266, -0.01534), (-0.91262, -0.40863, -0.01246), (-0.01764, 0.00891, 0.9998)-7.14714, 68.60696, 1.57366
3given(-0.999, 0.054), (0.054, 0.999, 0.005), (0.005, -1)117.56602, -3.03136, 30.08757
4given(0.5561, -0.83111, 0.00285), (-0.83111, -0.5561, -0.00266), (0.0038, -0.00089, -0.99999)114.95987, 68.82652, 31.15117
5given(0.54413, 0.83899, 0.00501), (0.83896, -0.54404, -0.01259), (-0.00784, 0.01105, -0.99991)58.06283, 37.49632, 33.26504

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Components

#1: Protein
DR HEMAGGLUTININ STRUCTURAL SUBUNIT / DRAE HAEMAGGLUTININ


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
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CLM / CHLORAMPHENICOL


Mass: 323.129 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C11H12Cl2N2O5 / Comment: antibiotic*YM
#4: Chemical ChemComp-TH8 / THIAMPHENICOL


Mass: 356.222 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H15Cl2NO5S / Comment: antibiotic*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.56 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 THIAMPHENICOL SOLUTION

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418
DetectorType: BRUKER / Date: Dec 14, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→25 Å / Num. obs: 43763 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 8.9
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 2.2 / % possible all: 99.9

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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: 2.3→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.278 1641 5 %RANDOM
Rwork0.249 ---
obs0.25 43763 100 %-
Refinement stepCycle: LAST / Resolution: 2.3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6279 0 237 154 6670

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