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- PDB-5ftx: Structure of surface layer protein SbsC, domains 4-9 -

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Basic information

Entry
Database: PDB / ID: 5ftx
TitleStructure of surface layer protein SbsC, domains 4-9
ComponentsSURFACE LAYER PROTEIN
KeywordsCELL ADHESION / SURFACE LAYER / SELF-ASSEMBLY
Function / homology
Function and homology information


metal ion binding / identical protein binding
Similarity search - Function
S-layer protein SbsC, C-terminal domain / SbsC C-terminal domain / : / SbsC C-terminal domain / S-layer protein SbsC C-terminal domain / Bacterial Ig-like domain / SbsC,spectrin-like repeat / SbsA, Ig-like domain / Bacterial Ig-like domain / Copper resistance protein CopC/internalin, immunoglobulin-like ...S-layer protein SbsC, C-terminal domain / SbsC C-terminal domain / : / SbsC C-terminal domain / S-layer protein SbsC C-terminal domain / Bacterial Ig-like domain / SbsC,spectrin-like repeat / SbsA, Ig-like domain / Bacterial Ig-like domain / Copper resistance protein CopC/internalin, immunoglobulin-like / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Immunoglobulin-like fold
Similarity search - Domain/homology
Surface layer protein
Similarity search - Component
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 4.1 Å
AuthorsDordic, A. / Pavkov-Keller, T. / Eder, M. / Egelseer, E.M. / Davis, K. / Mills, D. / Sleytr, U.B. / Kuehlbrandt, W. / Vonck, J. / Keller, W.
CitationJournal: To be Published
Title: Structure of Surface Layer Protein Sbsc
Authors: Pavkov-Keller, T. / Dordic, A. / Eder, M. / Egelseer, E.M. / Davis, K. / Mills, D. / Sleytr, U.B. / Kuehlbrandt, W. / Vonck, J. / Keller, W.
History
DepositionJan 18, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 22, 2017Provider: repository / Type: Initial release
Revision 2.0Oct 23, 2019Group: Atomic model / Data collection / Other / Category: atom_site / pdbx_database_status
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_database_status.status_code_sf
Revision 2.1Jan 10, 2024Group: 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 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _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

Downloads & links

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Assembly

Deposited unit
A: SURFACE LAYER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,4758
Polymers67,1441
Non-polymers3317
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)100.627, 48.128, 196.136
Angle α, β, γ (deg.)90.00, 96.60, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein SURFACE LAYER PROTEIN / SBSC


Mass: 67143.617 Da / Num. of mol.: 1 / Fragment: RSBSC, UNP RESIDUES 447-1099
Source method: isolated from a genetically manipulated source
Details: STRUCTURE OF SURFACE LAYER PROTEIN SBSC, DOMAINS 4-9
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O68840
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn

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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: 3.5 Å3/Da / Density % sol: 65 % / Description: DATA VERY ANISOTROPIC.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.14
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.14 Å / Relative weight: 1
ReflectionResolution: 3.46→42.5 Å / Num. obs: 11056 / % possible obs: 87.6 % / Observed criterion σ(I): 3.6 / Redundancy: 2.9 % / Biso Wilson estimate: 87.26 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 6
Reflection shellResolution: 3.46→3.66 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.15 / Mean I/σ(I) obs: 3.6 / % possible all: 72.6

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRIES 4UJ6, 4UIC, 4UIE AND 4UJ7

4uj6

4uic

4uie

4uj7


Resolution: 4.1→33.038 Å / SU ML: 0.45 / σ(F): 1.99 / Phase error: 28.84 / Stereochemistry target values: ML
Details: DATA ANISOTROPIC, DATA WERE TRUNCATED TO 4.1 A FOR THE REFINEMENT. FOR SOME DOMAINS, SIDE CHAINS WERE POORLY DEFINED OR NOT VISIBLE.
RfactorNum. reflection% reflection
Rfree0.268 367 5 %
Rwork0.2028 --
obs0.2061 7371 96.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 4.1→33.038 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4703 0 7 0 4710
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074778
X-RAY DIFFRACTIONf_angle_d0.7916533
X-RAY DIFFRACTIONf_dihedral_angle_d12.6471680
X-RAY DIFFRACTIONf_chiral_restr0.043839
X-RAY DIFFRACTIONf_plane_restr0.003829
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
4.1001-4.6920.33961170.2712226X-RAY DIFFRACTION93
4.692-5.90590.28761240.21182354X-RAY DIFFRACTION99
5.9059-33.03890.21541260.16152424X-RAY DIFFRACTION98

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