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- PDB-3is0: Crystal structure of functional region of UafA from Staphylococcu... -

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Basic information

Entry
Database: PDB / ID: 3is0
TitleCrystal structure of functional region of UafA from Staphylococcus saprophyticus in the presence of cholesterol
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 ...: / 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 / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsTanaka, Y. / Shouji, Y. / Matsuoka, E. / Kuroda, M. / Tanaka, I. / Yao, M.
CitationJournal: To be Published
Title: Crystal Structure of Functional Region of UafA from Staphylococcus saprophyticus
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 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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)47,7502
Polymers47,6581
Non-polymers921
Water5,459303
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.224, 110.616, 49.773
Angle α, β, γ (deg.)90.00, 106.41, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11X-217-

HOH

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Components

#1: Protein Uro-adherence factor A


Mass: 47658.391 Da / Num. of mol.: 1 / Fragment: functional region, residues 393-811
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus saprophyticus subsp. saprophyticus (bacteria)
Strain: ATCC 15305 / Gene: uafA, SSP0135 / 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


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


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.78 Å3/Da / Density % sol: 55.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 15% PEG 3350, 180mM tri-ammonium citrate, 2mM cholesterol, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 29, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. obs: 51922 / % possible obs: 99.3 % / Redundancy: 3.8 % / Rsym value: 0.053
Reflection shellResolution: 1.75→1.81 Å / Redundancy: 3.3 % / Num. unique all: 4931 / Rsym value: 0.342 / % possible all: 94

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3IS1

3is1


Resolution: 1.75→19.32 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.944 / SU B: 3.914 / SU ML: 0.064 / Cross valid method: THROUGHOUT / ESU R: 0.103 / ESU R Free: 0.101 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The crystal was grown in the solution containing cholesterol. Ambiguous but substantial electron density probably for cholesterol was ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS; The crystal was grown in the solution containing cholesterol. Ambiguous but substantial electron density probably for cholesterol was observed, but the model of cholesterol could not be build. See the details in the paper.
RfactorNum. reflection% reflectionSelection details
Rfree0.21215 3686 7.1 %RANDOM
Rwork0.18281 ---
obs0.18486 48168 99.26 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.508 Å2
Baniso -1Baniso -2Baniso -3
1-0.02 Å20 Å20.01 Å2
2---0.02 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.75→19.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3074 0 6 303 3383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0223149
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3571.9354277
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2815390
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.88424.351154
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.8715492
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.6731516
X-RAY DIFFRACTIONr_chiral_restr0.0960.2478
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022428
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21301
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.22190
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.2246
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2190.252
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.130.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8511.51983
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.39223141
X-RAY DIFFRACTIONr_scbond_it2.24231322
X-RAY DIFFRACTIONr_scangle_it3.5074.51135
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.751→1.796 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 243 -
Rwork0.221 3309 -
obs--92.77 %
Refinement TLS params.

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

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.26910.2873-0.13381.8264-0.35220.34870.0765-0.0572-0.02780.045-0.0729-0.1098-0.0058-0.0067-0.0036-0.0442-0.0327-0.0253-0.0126-0.0003-0.017536.406511.263210.3834
20.90990.22210.10471.66260.17690.50220.0723-0.01110.17180.176-0.17820.15590.1447-0.10580.1059-0.0093-0.09210.0346-0.0233-0.0431-0.029513.075-11.170314.1954
30.8768-1.23460.8322.1782-1.58753.5149-0.0523-0.0664-0.05920.14210.15260.2586-0.0382-0.2273-0.1003-0.00920.03010.041-0.02790.0124-0.027218.611938.01078.2618
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1X394 - 545
2X-RAY DIFFRACTION2X546 - 693
3X-RAY DIFFRACTION3X694 - 705
4X-RAY DIFFRACTION3X717 - 768
5X-RAY DIFFRACTION3X781 - 796
6X-RAY DIFFRACTION3X800 - 809

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