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- PDB-2axw: Structure of DraD invasin from uropathogenic Escherichia coli -

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Basic information

Entry
Database: PDB / ID: 2axw
TitleStructure of DraD invasin from uropathogenic Escherichia coli
ComponentsDraD invasin
KeywordsCELL INVASION / HOMODIMER / BETA-SANDWICH / IMMUNOGLOBULIN-LIKE FOLD / SWAPPED C-TERMINAL STRANDS
Function / homology
Function and homology information


Enterobacteria AfaD invasin / Enterobacteria AfaD invasin protein / Dr adhesin / Dr-adhesin superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.05 Å
AuthorsJedrzejczak, R. / Dauter, Z. / Dauter, M. / Piatek, R. / Zalewska, B. / Mroz, M. / Bury, K. / Nowicki, B. / Kur, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2006
Title: Structure of DraD invasin from uropathogenic Escherichia coli: a dimer with swapped beta-tails.
Authors: Jedrzejczak, R. / Dauter, Z. / Dauter, M. / Piatek, R. / Zalewska, B. / Mroz, M. / Bury, K. / Nowicki, B. / Kur, J.
History
DepositionSep 6, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 1, 2005Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DraD invasin
B: DraD invasin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5544
Polymers29,4272
Non-polymers1282
Water5,242291
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4270 Å2
ΔGint-24 kcal/mol
Surface area14560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)33.590, 61.820, 112.200
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein DraD invasin


Mass: 14713.293 Da / Num. of mol.: 2 / Fragment: DraD invasin
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: draD / Plasmid: pInvDsyg-C-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q7BG36, UniProt: Q47038*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 291 / 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: 1.91 Å3/Da / Density % sol: 35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: NaCl, Hepes, glycerol, PEG-2000 MME, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 5, 2005 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL CUT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→30 Å / Num. all: 109502 / Num. obs: 108822 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5.6 % / Biso Wilson estimate: 9.1 Å2 / Rmerge(I) obs: 0.066 / Net I/σ(I): 21.4
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.388 / Mean I/σ(I) obs: 2.9 / Num. unique all: 10677 / % possible all: 97.6

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.05→29.49 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.974 / SU B: 0.311 / SU ML: 0.016 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.027 / ESU R Free: 0.027 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16768 2183 2 %RANDOM
Rwork0.15069 ---
all0.15104 108805 --
obs0.15104 106622 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 12.984 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2---0.23 Å20 Å2
3----0.42 Å2
Refinement stepCycle: LAST / Resolution: 1.05→29.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2070 0 7 291 2368
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212167
X-RAY DIFFRACTIONr_bond_other_d0.0020.021919
X-RAY DIFFRACTIONr_angle_refined_deg1.6671.9132916
X-RAY DIFFRACTIONr_angle_other_deg0.86334445
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.025266
X-RAY DIFFRACTIONr_chiral_restr0.1260.2295
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022488
X-RAY DIFFRACTIONr_gen_planes_other0.0090.02478
X-RAY DIFFRACTIONr_nbd_refined0.1980.2315
X-RAY DIFFRACTIONr_nbd_other0.2690.22218
X-RAY DIFFRACTIONr_nbtor_other0.0890.21439
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1840.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.27
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3370.2127
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1610.228
X-RAY DIFFRACTIONr_mcbond_it2.35331318
X-RAY DIFFRACTIONr_mcangle_it3.58852096
X-RAY DIFFRACTIONr_scbond_it3.6076849
X-RAY DIFFRACTIONr_scangle_it5.3268820
X-RAY DIFFRACTIONr_rigid_bond_restr1.83222167
X-RAY DIFFRACTIONr_sphericity_free5.42292
X-RAY DIFFRACTIONr_sphericity_bonded4.35222120
LS refinement shellResolution: 1.05→1.077 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.213 149
Rwork0.204 7645

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