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- PDB-1j8s: PAPG ADHESIN RECEPTOR BINDING DOMAIN-UNBOUND FORM -

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Basic information

Entry
Database: PDB / ID: 1j8s
TitlePAPG ADHESIN RECEPTOR BINDING DOMAIN-UNBOUND FORM
ComponentsPYELONEPHRITIC ADHESIN
KeywordsSTRUCTURAL PROTEIN / PapG adhesin / receptor
Function / homology
Function and homology information


pilus / carbohydrate binding / cell adhesion / extracellular region
Similarity search - Function
Bacterial adhesin receptor binding domain / PapG, chaperone-binding / PapG chaperone-binding domain / PapG, carbohydrate-binding domain / PapG, carbohydrate-binding domain superfamily / PapG carbohydrate binding domain / Fimbrial-type adhesion domain superfamily / Adhesion domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fimbrial adhesin PapGII
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD at the Se edge / Resolution: 2.1 Å
AuthorsDodson, K.W. / Pinkner, J.S. / Rose, T. / Magnusson, G. / Hultgren, S.J. / Waksman, G.
CitationJournal: Cell(Cambridge,Mass.) / Year: 2001
Title: Structural basis of the interaction of the pyelonephritic E. coli adhesin to its human kidney receptor.
Authors: Dodson, K.W. / Pinkner, J.S. / Rose, T. / Magnusson, G. / Hultgren, S.J. / Waksman, G.
History
DepositionMay 22, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PYELONEPHRITIC ADHESIN


Theoretical massNumber of molelcules
Total (without water)22,7681
Polymers22,7681
Non-polymers00
Water2,000111
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)55.130, 78.260, 158.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Cell settingorthorhombic
Space group name H-MI222

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Components

#1: Protein PYELONEPHRITIC ADHESIN / PAPG ADHESIN


Mass: 22768.217 Da / Num. of mol.: 1 / Fragment: PAPG RECEPTOR-BINDING DOMAIN / Source method: isolated from a natural source / Source: (natural) Escherichia coli (E. coli) / References: UniProt: Q47450
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 3.75 Å3/Da / Density % sol: 67.2 %
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
14-5 mg/mlprotein1drop
24 %(w/v)PEG200001reservoir

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM
DetectorDetector: AREA DETECTOR
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.1→27.57 Å / Num. obs: 19087 / % possible obs: 93.3 % / Observed criterion σ(I): 0.5 / Biso Wilson estimate: 21.3 Å2
Reflection shellResolution: 2.1→2.23 Å / Num. unique all: 2813 / % possible all: 95.4

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Processing

SoftwareName: CNS / Version: 1 / Classification: refinement
RefinementMethod to determine structure: MAD at the Se edge / Resolution: 2.1→27.57 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 194646.02 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 1
RfactorNum. reflection% reflectionSelection details
Rfree0.255 1867 9.8 %RANDOM
Rwork0.232 ---
obs0.232 19087 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.3 Å2 / ksol: 0.371 e/Å3
Displacement parametersBiso mean: 29.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.99 Å20 Å20 Å2
2--12.07 Å20 Å2
3----13.06 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.29 Å
Luzzati d res low-6 Å
Luzzati sigma a0.32 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.1→27.57 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1605 0 0 111 1716
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.191.5
X-RAY DIFFRACTIONc_mcangle_it1.792
X-RAY DIFFRACTIONc_scbond_it2.292
X-RAY DIFFRACTIONc_scangle_it3.182.5
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.322 313 11.1 %
Rwork0.324 2500 -
obs--84.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Version: 1 / Classification: refinement
Refinement
*PLUS
σ(F): 1 / % reflection Rfree: 9.8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 29.7 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.322 / % reflection Rfree: 11.1 % / Rfactor Rwork: 0.324

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