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- PDB-2w5p: DraE Adhesin in complex with Chloramphenicol Succinate (monoclini... -

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Basic information

Entry
Database: PDB / ID: 2w5p
TitleDraE Adhesin in complex with Chloramphenicol Succinate (monoclinic 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 / 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
DepositionDec 11, 2008Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 2, 2009Provider: 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 ...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 1.4Oct 9, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0679
Polymers48,5103
Non-polymers1,5586
Water6,215345
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4590 Å2
ΔGint-41.4 kcal/mol
Surface area23000 Å2
MethodPQS
Unit cell
Length a, b, c (Å)118.941, 68.553, 62.061
Angle α, β, γ (deg.)90.00, 111.17, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein DR HEMAGGLUTININ STRUCTURAL SUBUNIT / DRAE HAEMAGGLUTININ


Mass: 16169.844 Da / Num. of mol.: 3 / Fragment: ADHESIN SUBUNIT, RESIDUES 23-160 / Mutation: YES
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-CL8 / CHLORAMPHENICOL SUCCINATE


Mass: 423.202 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C15H16Cl2N2O8 / Comment: antibiotic*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 345 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, GLU 39 TO LYS ENGINEERED RESIDUE IN CHAIN B, GLU 39 TO LYS ...ENGINEERED RESIDUE IN CHAIN A, GLU 39 TO LYS ENGINEERED RESIDUE IN CHAIN B, GLU 39 TO LYS ENGINEERED RESIDUE IN CHAIN C, GLU 39 TO LYS
Has protein modificationY
Sequence detailsE18K

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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: 2.28 Å3/Da / Density % sol: 46.2 % / Description: NONE
Crystal growpH: 7
Details: (NH4)2SO4 2M, 10 MM CHLORAMPHENICOL SUCCINATE, 0.1 M NAHEPES PH 7.0

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Dec 5, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.9→59 Å / Num. obs: 34784 / % possible obs: 96.8 % / Observed criterion σ(I): 0 / Redundancy: 4.1 % / Biso Wilson estimate: 1 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 6
Reflection shellResolution: 1.9→2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / % possible all: 78

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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→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. STRUCTURE REFINED WITH NO NCS ALTHOUGH IT CONTAINS THREE COPIES OF THE SAME PROTEIN. THE NCS WAS NOT ENFORCED
RfactorNum. reflection% reflectionSelection details
Rfree0.237 1747 5 %RANDOM
Rwork0.193 ---
obs0.195 34784 99 %-
Displacement parametersBiso mean: 26 Å2
Baniso -1Baniso -3Baniso -2
1-2.4 Å2-0.45 Å2-
2---1.2 Å2
3---3.5 Å2-
Refinement stepCycle: LAST / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3164 0 33 345 3542
LS refinement shellResolution: 1.9→2 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.237 271 5 %
Rwork0.193 4957 -
all0.195 5228 -
obs--78.1 %

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