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- PDB-2jkn: DraE Adhesin in complex with Chloramphenicol Succinate (trigonal form) -

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Basic information

Entry
Database: PDB / ID: 2jkn
TitleDraE Adhesin in complex with Chloramphenicol Succinate (trigonal form)
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 SUCCINATE / Dr hemagglutinin structural subunit
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsPettigrew, D.M. / Roversi, P. / Davies, S.G. / Russell, A.J. / Lea, S.M.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / 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
Revision 1.2Jun 6, 2018Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_assembly ...citation / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.title / _pdbx_struct_assembly.details / _pdbx_struct_assembly.method_details / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[1] / _pdbx_struct_oper_list.vector[2]
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
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)101,45636
Polymers97,0196
Non-polymers4,43730
Water12,647702
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)50,72818
Polymers48,5103
Non-polymers2,21815
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
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)50,72818
Polymers48,5103
Non-polymers2,21815
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
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)50,72818
Polymers48,5103
Non-polymers2,21815
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-y,x-y,z1
crystal symmetry operation3_555-x+y,-x,z1
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)50,72818
Polymers48,5103
Non-polymers2,21815
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
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)50,72818
Polymers48,5103
Non-polymers2,21815
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
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)50,72818
Polymers48,5103
Non-polymers2,21815
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
Unit cell
Length a, b, c (Å)119.300, 119.300, 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(-0.50233, -0.86468, 8.0E-5), (0.86465, -0.50231, 0.00793), (-0.00682, 0.00405, 0.99997)59.67759, 34.59671, 3.4219
2given(-0.37444, 0.92716, -0.01272), (-0.92713, -0.37458, -0.01124), (-0.01519, 0.00758, 0.99986)-9.62355, 68.18225, 1.49265
3given(-0.99737, 0.07248, 0.00152), (0.07248, 0.99736, 0.00531), (-0.00114, 0.0054, -0.99998)116.60059, -4.08717, 29.99885
4given(0.55633, -0.83096, 0.00119), (-0.83095, -0.55633, -0.00394), (0.00394, 0.00121, -0.99999)114.65899, 68.62978, 30.97505
5given(0.55439, 0.83223, 0.00579), (0.83224, -0.55432, -0.01054), (-0.00557, 0.01066, -0.99993)57.56631, 38.22191, 33.23239

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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.: 12 / Source method: obtained synthetically / Formula: SO4
#3: Chemical
ChemComp-CL8 / CHLORAMPHENICOL SUCCINATE


Mass: 423.202 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C15H16Cl2N2O8 / Comment: antibiotic*YM
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 702 / Source method: isolated from a natural source / Formula: H2O

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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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 26, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. obs: 60758 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 4.6
Reflection shellResolution: 1.9→2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 2.1 / % possible all: 97.7

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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→30 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.212 3550 5 %RANDOM
Rwork0.191 ---
obs0.192 71074 98.2 %-
Refinement stepCycle: LAST / Resolution: 1.9→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6309 0 270 702 7281

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