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- PDB-4uid: Crystal structure of the S-layer protein SbsC domains 4 and 5 -

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Basic information

Entry
Database: PDB / ID: 4uid
TitleCrystal structure of the S-layer protein SbsC domains 4 and 5
ComponentsSURFACE LAYER PROTEIN
KeywordsSUGAR BINDING PROTEIN / S-LAYER / SBSC / G. STEAROTHERMOPHILUS
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: 2.8 Å
AuthorsPavkov-Keller, T. / Dordic, A. / Egelseer, E.M. / Sleytr, U.B. / Keller, W.
CitationJournal: To be Published
Title: Structure of the S-Layer Protein Sbsc
Authors: Pavkov-Keller, T. / Dordic, A. / Eder, M. / Davies, K. / Mills, D. / Egelseer, E.M. / Sleytr, U.B. / Kuehlbrandt, W. / Vonck, J. / Keller, W.
History
DepositionMar 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1May 1, 2024Group: Data collection / Database references ...Data collection / Database references / 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SURFACE LAYER PROTEIN
B: SURFACE LAYER PROTEIN


Theoretical massNumber of molelcules
Total (without water)43,2842
Polymers43,2842
Non-polymers00
Water1,06359
1
A: SURFACE LAYER PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,6421
Polymers21,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: SURFACE LAYER PROTEIN


Theoretical massNumber of molelcules
Total (without water)21,6421
Polymers21,6421
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)110.367, 110.367, 87.143
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein SURFACE LAYER PROTEIN / S-LAYER SBSC


Mass: 21642.205 Da / Num. of mol.: 2 / Fragment: DOMAINS 4 AND 5, RESIDUES 443-650
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) GEOBACILLUS STEAROTHERMOPHILUS (bacteria)
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O68840
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 3.5 Å3/Da / Density % sol: 63 % / Description: NONE
Crystal growDetails: 5.5 MG/ML IN 50MM TRIS/HCL PH 7.2 INDEX CONDITION NO.40 (0.01M CITRIC ACID PH 3.5, 3.0%(W/V) PEG 3350)

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 29, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→25 Å / Num. obs: 14641 / % possible obs: 89 % / Observed criterion σ(I): 2.8 / Redundancy: 6.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0107refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: POLYALA OF RSBSC AA31-844 STRUCTURE

Resolution: 2.8→24.93 Å / Cor.coef. Fo:Fc: 0.914 / Cor.coef. Fo:Fc free: 0.875 / SU B: 15.101 / SU ML: 0.298 / Cross valid method: THROUGHOUT / ESU R: 0.782 / ESU R Free: 0.378 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY. HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. CHAIN B CONTAINS DISORDERED REGIONS IN DOMAIN 4
RfactorNum. reflection% reflectionSelection details
Rfree0.28636 684 5 %RANDOM
Rwork0.223 ---
obs0.2262 13044 99.63 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.26 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2---0.11 Å20 Å2
3---0.23 Å2
Refinement stepCycle: LAST / Resolution: 2.8→24.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2739 0 0 59 2798
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022767
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.5591.9683768
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.035370
X-RAY DIFFRACTIONr_dihedral_angle_2_deg43.58127.80291
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.45415472
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.090.2488
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211967
X-RAY DIFFRACTIONr_gen_planes_other
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_it2.2613.9181495
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.7385.8591860
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8654.2111271
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_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.872 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.303 48 -
Rwork0.254 938 -
obs--100 %

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