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- PDB-5a0n: N-terminal thioester domain of protein F2 like fibronectin-bindin... -

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Basic information

Entry
Database: PDB / ID: 5a0n
TitleN-terminal thioester domain of protein F2 like fibronectin-binding protein from Streptococcus pneumoniae
ComponentsPROTEIN F2 LIKE FIBRONECTIN-BINDING PROTEIN
KeywordsCELL ADHESION / SURFACE-ASSOCIATED PROTEIN / GRAM-POSITIVE / ADHESIN / INTERNAL THIOESTER / THIOESTER DOMAIN
Function / homologyPrealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulin-like fold / Protein F2 like fibronectin-binding protein
Function and homology information
Biological speciesSTREPTOCOCCUS PNEUMONIAE (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsWalden, M. / Edwards, J.M. / Dziewulska, A.M. / Kan, S.-Y. / Schwarz-Linek, U. / Banfield, M.J.
CitationJournal: Elife / Year: 2015
Title: An internal thioester in a pathogen surface protein mediates covalent host binding.
Authors: Walden, M. / Edwards, J.M. / Dziewulska, A.M. / Bergmann, R. / Saalbach, G. / Kan, S.Y. / Miller, O.K. / Weckener, M. / Jackson, R.J. / Shirran, S.L. / Botting, C.H. / Florence, G.J. / ...Authors: Walden, M. / Edwards, J.M. / Dziewulska, A.M. / Bergmann, R. / Saalbach, G. / Kan, S.Y. / Miller, O.K. / Weckener, M. / Jackson, R.J. / Shirran, S.L. / Botting, C.H. / Florence, G.J. / Rohde, M. / Banfield, M.J. / Schwarz-Linek, U.
History
DepositionApr 21, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Mar 22, 2017Group: Database references
Revision 1.3Oct 30, 2019Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Other
Category: pdbx_database_status / pdbx_unobs_or_zero_occ_atoms ...pdbx_database_status / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn
Item: _pdbx_database_status.status_code_sf
Revision 1.4May 8, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: PROTEIN F2 LIKE FIBRONECTIN-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0963
Polymers25,8091
Non-polymers2872
Water4,216234
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.860, 59.860, 121.660
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2026-

HOH

21A-2027-

HOH

31A-2056-

HOH

41A-2058-

HOH

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Components

#1: Protein PROTEIN F2 LIKE FIBRONECTIN-BINDING PROTEIN


Mass: 25808.996 Da / Num. of mol.: 1 / Fragment: THIOESTER DOMAIN, RESIDUES 42-258
Source method: isolated from a genetically manipulated source
Details: INTERNAL THIOESTER LINKAGE BETWEEN CYS94 AND GLN247
Source: (gene. exp.) STREPTOCOCCUS PNEUMONIAE (bacteria) / Strain: SP14-BS69 / Plasmid: PDEST / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5MCJ6
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#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.: 234 / 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: 2.11 Å3/Da / Density % sol: 41.74 % / Description: NONE
Crystal growpH: 6.5
Details: 0.02 M SODIUM L-GLUTAMATE, 0.02 M DL-ALANINE, 0.02 M GLYCINE, 0.02 M DL-LYSINE, 0.02 M DL-SERINE, 0.1 M MES/IMIDAZOLE PH 6.5, 10% PEG 4000, 20% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Sep 24, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.3→42.67 Å / Num. obs: 51670 / % possible obs: 93.6 % / Observed criterion σ(I): 2 / Redundancy: 23.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 33.8
Reflection shellResolution: 1.3→1.32 Å / Redundancy: 11.9 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 7.4 / % possible all: 62.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
MOSFLMdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.3→53.71 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.968 / SU B: 1.105 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.043 / ESU R Free: 0.042 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1514 2631 5.1 %RANDOM
Rwork0.11926 ---
obs0.12087 48978 93.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.149 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.3→53.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1760 0 18 234 2012
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.021927
X-RAY DIFFRACTIONr_bond_other_d0.0010.021716
X-RAY DIFFRACTIONr_angle_refined_deg1.5051.9332628
X-RAY DIFFRACTIONr_angle_other_deg0.853.0013940
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1845230
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.64724.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.1215301
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.382159
X-RAY DIFFRACTIONr_chiral_restr0.10.2272
X-RAY DIFFRACTIONr_gen_planes_refined0.010.022237
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02498
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5841.076903
X-RAY DIFFRACTIONr_mcbond_other1.5641.074902
X-RAY DIFFRACTIONr_mcangle_it2.0721.6251137
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.7841.3181024
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr2.39133643
X-RAY DIFFRACTIONr_sphericity_free34.003557
X-RAY DIFFRACTIONr_sphericity_bonded11.74253759
LS refinement shellResolution: 1.3→1.334 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.159 135 -
Rwork0.126 2374 -
obs--62.79 %

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