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- PDB-2x5p: Crystal structure of the Streptococcus pyogenes fibronectin bindi... -

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Basic information

Entry
Database: PDB / ID: 2x5p
TitleCrystal structure of the Streptococcus pyogenes fibronectin binding protein Fbab-B
ComponentsFIBRONECTIN BINDING PROTEIN
KeywordsPROTEIN BINDING
Function / homology
Function and homology information


Fibronectin binding repeat / Collagen-binding surface protein Cna-like, B-type domain / Fibronectin binding repeat / Cna protein B-type domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulins ...Fibronectin binding repeat / Collagen-binding surface protein Cna-like, B-type domain / Fibronectin binding repeat / Cna protein B-type domain / Uncharacterised domain CHP03934, TQXA / Thioester domain / Thioester domain / Prealbumin-like fold domain / Prealbumin-like fold domain / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibronectin binding protein
Similarity search - Component
Biological speciesSTREPTOCOCCUS PYOGENES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionFeb 10, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Aug 10, 2011Group: Data collection / Database references ...Data collection / Database references / Other / Source and taxonomy / Structure summary / Version format compliance
Revision 1.2Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
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 / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIBRONECTIN BINDING PROTEIN


Theoretical massNumber of molelcules
Total (without water)12,8831
Polymers12,8831
Non-polymers00
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.220, 57.220, 64.580
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein FIBRONECTIN BINDING PROTEIN / FBA2


Mass: 12883.226 Da / Num. of mol.: 1 / Fragment: B DOMAIN, RESIDUES 440-557
Source method: isolated from a genetically manipulated source
Details: ISO-PEPTIDE BOND BETWEEN SIDECHAINS OF LYS31 AND ASP117
Source: (gene. exp.) STREPTOCOCCUS PYOGENES (bacteria) / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q8G9G1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.38 Å3/Da / Density % sol: 48.4 % / Description: NONE
Crystal growpH: 8.5
Details: 2.47 - 2.52M AMMONIUM SULFATE, 0.26M MAGNESIUM ACETATE OR 0.21M MAGNESIUM CHLORIDE, 0.1M BICINE PH 8.5 - 9.5. CRYSTAL WAS CRYOPROTECTED DIRECTLY IN THIS SOLUTION SUPPLEMENTED WITH 25% GLYCEROL.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.8
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 17, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.6→1.64 Å / Num. obs: 15019 / % possible obs: 98.2 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22
Reflection shellResolution: 1.6→1.64 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 3.4 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.6.0081refinement
XDSdata reduction
XSCALEdata scaling
SHELXCDESOLVE RESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.6→27.06 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.966 / SU B: 2.714 / SU ML: 0.043 / Cross valid method: THROUGHOUT / ESU R: 0.079 / ESU R Free: 0.067 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.17 789 5 %RANDOM
Rwork0.136 ---
obs0.138 15019 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 16.74 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20.03 Å20 Å2
2--0.05 Å20 Å2
3----0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.6→27.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms779 0 0 103 882
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.022796
X-RAY DIFFRACTIONr_bond_other_d0.0010.02511
X-RAY DIFFRACTIONr_angle_refined_deg1.2351.9431075
X-RAY DIFFRACTIONr_angle_other_deg0.77331262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1895104
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.25225.62532
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3415136
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.974152
X-RAY DIFFRACTIONr_chiral_restr0.0730.2127
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02883
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02150
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_it1.0631.5513
X-RAY DIFFRACTIONr_mcbond_other0.3491.5215
X-RAY DIFFRACTIONr_mcangle_it1.8222825
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.563283
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.0014.5249
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr4.30834285
X-RAY DIFFRACTIONr_sphericity_free8.7625103
X-RAY DIFFRACTIONr_sphericity_bonded4.75751294
LS refinement shellResolution: 1.6→1.64 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.238 56 -
Rwork0.163 1099 -
obs--99.48 %
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)
15.11710.510.51690.39480.20880.72390.0832-0.118-0.2160.0160.0222-0.08040.2432-0.0304-0.10540.0919-0.0114-0.02390.01520.00950.031559.909119.718111.7364
20.91020.13041.12250.08730.32951.8857-0.0011-0.010.02640.03060.00650.00270.10280.0223-0.00550.02340.0076-0.01070.0084-0.00120.020557.158626.24697.5345
37.3168-6.5296-0.1838.9118-2.08532.3668-0.1630.0040.10920.8987-0.1372-2.28480.24390.50390.30030.15830.008-0.01240.15280.03070.161345.161812.556115.063
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A25 - 32
2X-RAY DIFFRACTION1A62 - 68
3X-RAY DIFFRACTION1A110 - 117
4X-RAY DIFFRACTION2A89 - 108
5X-RAY DIFFRACTION2A71 - 79
6X-RAY DIFFRACTION2A41 - 47
7X-RAY DIFFRACTION2A54 - 59
8X-RAY DIFFRACTION3A-2 - 4

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