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- PDB-3is1: Crystal structure of functional region of UafA from Staphylococcu... -

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Basic information

Entry
Database: PDB / ID: 3is1
TitleCrystal structure of functional region of UafA from Staphylococcus saprophyticus in C2 form at 2.45 angstrom resolution
ComponentsUro-adherence factor A
KeywordsCELL ADHESION / DEv-IgG fold / Cell wall / Hemagglutinin / Peptidoglycan-anchor / Secreted / Virulence
Function / homology
Function and homology information


cell adhesion / extracellular region
Similarity search - Function
SD-repeat containing protein, B domain / SdrD B-like domain / Immunoglobulin-like - #1290 / Immunoglobulin-like - #1280 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide ...SD-repeat containing protein, B domain / SdrD B-like domain / Immunoglobulin-like - #1290 / Immunoglobulin-like - #1280 / SDR-like Ig domain / Bacterial Ig domain / Fibrogen-binding domain 1 / Adhesion domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Uro-adherence factor A
Similarity search - Component
Biological speciesStaphylococcus saprophyticus subsp. saprophyticus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.45 Å
AuthorsTanaka, Y. / Matsuoka, E. / Shouji, Y. / Kuroda, M. / Tanaka, I. / Yao, M.
CitationJournal: Protein Sci. / Year: 2011
Title: Crystal structure of the functional region of Uro-adherence factor A from Staphylococcus saprophyticus reveals participation of the B domain in ligand binding
Authors: Matsuoka, E. / Tanaka, Y. / Kuroda, M. / Shouji, Y. / Ohta, T. / Tanaka, I. / Yao, M.
History
DepositionAug 24, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Sep 8, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 23, 2013Group: Database references
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
X: Uro-adherence factor A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6032
Polymers49,5111
Non-polymers921
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.585, 110.442, 49.547
Angle α, β, γ (deg.)90.00, 106.49, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-74-

HOH

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Components

#1: Protein Uro-adherence factor A


Mass: 49511.371 Da / Num. of mol.: 1 / Fragment: functional region, residues 376-811
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus saprophyticus subsp. saprophyticus (bacteria)
Strain: ATCC 15305 / Gene: SSP0135, uafA / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q4A0V8
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 113 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 300mM tri-lithium citrate, 20% PEG 3350, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Nov 3, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→50 Å / Num. obs: 18642 / % possible obs: 98.7 % / Redundancy: 4.7 % / Rsym value: 0.061
Reflection shellResolution: 2.45→2.54 Å / Redundancy: 4 % / Num. unique all: 1697 / Rsym value: 0.23 / % possible all: 90.4

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Processing

Software
NameVersionClassification
DMmodel building
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RefinementMethod to determine structure: SAD / Resolution: 2.45→19.83 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.903 / SU B: 16.143 / SU ML: 0.184 / Cross valid method: THROUGHOUT / ESU R: 0.439 / ESU R Free: 0.266 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24574 1328 7.1 %RANDOM
Rwork0.20628 ---
obs0.20905 17271 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 34.804 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20.03 Å2
2---0.02 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.45→19.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3082 0 6 113 3201
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0223153
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.8681.9344281
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7685389
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.09624.387155
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.72415492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.8981516
X-RAY DIFFRACTIONr_chiral_restr0.0570.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.022432
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1620.21260
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3020.22156
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0850.2174
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1620.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.060.215
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.1431.51984
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.25623143
X-RAY DIFFRACTIONr_scbond_it0.29831322
X-RAY DIFFRACTIONr_scangle_it0.5014.51138
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.452→2.515 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 101 -
Rwork0.271 1116 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.20391.748-0.67776.9808-0.4820.97590.2427-0.2841-0.07260.3315-0.1935-0.2081-0.01480.1067-0.0492-0.1473-0.044-0.0532-0.0986-0.0061-0.197236.09511.63210.03
22.37470.4028-0.19924.183-0.35633.43880.0083-0.07610.22720.391-0.19160.38740.1965-0.36010.1833-0.0251-0.1190.0685-0.0931-0.0554-0.081613.036-11.17914.068
34.2322-3.45392.40085.549-4.02117.7923-0.2467-0.211-0.00060.3230.44260.4325-0.1199-0.868-0.1959-0.0149-0.01590.0856-0.0506-0.0341-0.058218.19538.0698.219
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X392 - 545
2X-RAY DIFFRACTION2X546 - 693
3X-RAY DIFFRACTION3X694 - 705
4X-RAY DIFFRACTION3X717 - 768
5X-RAY DIFFRACTION3X780 - 795
6X-RAY DIFFRACTION3X799 - 809

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