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- PDB-4uj8: Structure of surface layer protein SbsC, domains 6-7 -

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Basic information

Entry
Database: PDB / ID: 4uj8
TitleStructure of surface layer protein SbsC, domains 6-7
ComponentsSURFACE LAYER PROTEIN
KeywordsMEMBRANE PROTEIN / SURFACE LAYER / SELF-ASSEMBLY
Function / homology
Function and homology information


identical protein binding / metal ion 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 / 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: 1.7 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
DepositionApr 8, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 27, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_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.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.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_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
B: SURFACE LAYER PROTEIN
C: SURFACE LAYER PROTEIN
D: SURFACE LAYER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,33220
Polymers98,6904
Non-polymers64116
Water25,7971432
1
A: SURFACE LAYER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8335
Polymers24,6731
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: SURFACE LAYER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8335
Polymers24,6731
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: SURFACE LAYER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8335
Polymers24,6731
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: SURFACE LAYER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,8335
Polymers24,6731
Non-polymers1604
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)50.887, 54.459, 92.243
Angle α, β, γ (deg.)103.59, 105.23, 91.42
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
SURFACE LAYER PROTEIN


Mass: 24672.604 Da / Num. of mol.: 4 / Fragment: RSBSC, UNP RESDIUES 642-882
Source method: isolated from a genetically manipulated source
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.: 16 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1432 / 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: 2.2 Å3/Da / Density % sol: 44.4 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.98
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.7→28.6 Å / Num. obs: 93503 / % possible obs: 91.6 % / Observed criterion σ(I): 2.4 / Redundancy: 1.9 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 8.5
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.29 / Mean I/σ(I) obs: 2.4 / % possible all: 91

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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 4UJ7, 4UIE

4uj7

4uie


Resolution: 1.7→23.001 Å / SU ML: 0.21 / σ(F): 1.99 / Phase error: 24.66 / Stereochemistry target values: MLHL
RfactorNum. reflection% reflection
Rfree0.2316 4671 5 %
Rwork0.1942 --
obs0.196 93436 91.87 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→23.001 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6862 0 16 1432 8310
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0077021
X-RAY DIFFRACTIONf_angle_d1.0539613
X-RAY DIFFRACTIONf_dihedral_angle_d11.6262556
X-RAY DIFFRACTIONf_chiral_restr0.0411282
X-RAY DIFFRACTIONf_plane_restr0.0051242
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.71930.35771370.28832598X-RAY DIFFRACTION82
1.7193-1.73950.34351610.26753065X-RAY DIFFRACTION94
1.7395-1.76070.27651630.25453098X-RAY DIFFRACTION95
1.7607-1.7830.31391570.24752977X-RAY DIFFRACTION94
1.783-1.80650.3091620.24083085X-RAY DIFFRACTION95
1.8065-1.83120.28951600.23223031X-RAY DIFFRACTION94
1.8312-1.85740.26281600.22853031X-RAY DIFFRACTION95
1.8574-1.88510.26981620.23193088X-RAY DIFFRACTION94
1.8851-1.91450.26031500.24342838X-RAY DIFFRACTION90
1.9145-1.94590.26991470.23362828X-RAY DIFFRACTION87
1.9459-1.97940.261570.21552978X-RAY DIFFRACTION93
1.9794-2.01540.23521600.21173039X-RAY DIFFRACTION94
2.0154-2.05410.25071490.21922837X-RAY DIFFRACTION89
2.0541-2.0960.28791380.22462605X-RAY DIFFRACTION80
2.096-2.14160.25511550.2142958X-RAY DIFFRACTION93
2.1416-2.19140.26161600.2123034X-RAY DIFFRACTION94
2.1914-2.24610.23741540.21412926X-RAY DIFFRACTION91
2.2461-2.30680.27281550.21342938X-RAY DIFFRACTION90
2.3068-2.37460.28561590.21253026X-RAY DIFFRACTION94
2.3746-2.45120.24051580.20593008X-RAY DIFFRACTION94
2.4512-2.53870.2671610.21023050X-RAY DIFFRACTION94
2.5387-2.64020.26151580.20213005X-RAY DIFFRACTION94
2.6402-2.76010.22631550.19832947X-RAY DIFFRACTION92
2.7601-2.90540.23081610.19723046X-RAY DIFFRACTION93
2.9054-3.0870.19021560.19282975X-RAY DIFFRACTION93
3.087-3.32470.22441570.18322977X-RAY DIFFRACTION93
3.3247-3.65810.1971580.16282998X-RAY DIFFRACTION93
3.6581-4.18470.16851550.1562950X-RAY DIFFRACTION91
4.1847-5.26190.17291570.13672981X-RAY DIFFRACTION93
5.2619-23.00280.18631490.15092848X-RAY DIFFRACTION88

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