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- PDB-4uie: Crystal structure of the S-layer protein SbsC, domains 7, 8 and 9 -

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Basic information

Entry
Database: PDB / ID: 4uie
TitleCrystal structure of the S-layer protein SbsC, domains 7, 8 and 9
ComponentsSURFACE LAYER PROTEIN
KeywordsSUGAR BINDING PROTEIN / S-LAYER
Function / homology
Function and homology information


identical protein binding / metal ion binding
Bacterial Ig-like, group 2 / Immunoglobulin-like fold / SbsA, Ig-like domain / S-layer protein SbsC, C-terminal domain / SbsC C-terminal domain / Bacterial Ig-like domain / SbsC C-terminal domain / S-layer protein SbsC C-terminal domain
Surface layer protein
Biological speciesGEOBACILLUS STEAROTHERMOPHILUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SIRAS / Resolution: 3.1 Å
AuthorsPavkov-Keller, T. / Dordic, A. / Egelseer, E.M. / Sleytr, U.B. / Keller, W.
CitationJournal: To be Published
Title: Crystal 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.
Validation Report
SummaryFull reportAbout validation report
History
DepositionMar 27, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 17, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SURFACE LAYER PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,7204
Polymers35,2991
Non-polymers4213
Water1,02757
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)69.831, 69.831, 196.018
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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


Mass: 35299.309 Da / Num. of mol.: 1 / Fragment: DOMAINS 7,8 AND 9, RESIDUES 754-1099
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-OS / OSMIUM ION


Mass: 190.230 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Os / Osmium
#3: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca / Calcium
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 3.9 Å3/Da / Density % sol: 68.4 %
Description: 3 DIFFERENT CRYSTAL FORMS WERE AVAILABLE - P41211, P21212 AND P3121. THIS CRYSTAL IS THE ONLY ONE FOR THE FORM P3121 AND WAS PREPARED AS OS-DERIVATIVE. THE STRUCTURE WAS SOLVED BY SIRAS USING NATIVE AND AU- DERIVATIVE DATA OF ANISOTROPIC CRYSTAL FORM P41211. THIS INITIAL PHASES WERE USED AS STARTING POINT FOR DMMULTI. THE BEST ELECTRON DENSITY MAP WAS OBTAINED FROM THE DATA FROM P3121 CRYSTAL. THIS WAS ALSO THE ONLY FORM WHERE DOMAIN 9 WAS NICELY ORDERED AND THE SEQUENCE COULD BE PLACED IN THE ELECTRON DENSITY. 2 OS ATOMS THAT ARE PRESENT IN THE STRUCTURE SHOULD COME FROM THE SOAKING. NEVERTHELESS, THE STRUCTURE COULD NOT BE SOLVED BY SAD USING ONLY THIS DATA. CA ATOM PRESENT IN DOMAIN 7 IS ALSO PRESENT IN NATIVE STRUCTURES FROM OTHER FORMS. TWO OTHER FORMS WERE NOT FURTHER REFINED AND DEPOSITED WHILE DOMAIN 9 IS PARTIALLY DISORDERED.
Crystal growDetails: CA. 5MG/ML PROTEIN CONC. 2-2.4M SODIUM MALONATE PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9486
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 27, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9486 Å / Relative weight: 1
ReflectionResolution: 3.1→20 Å / Num. obs: 9719 / % possible obs: 91 % / Observed criterion σ(I): 2 / Redundancy: 4.9 % / Rmerge(I) obs: 0.18 / Net I/σ(I): 7.2
Reflection shellResolution: 3.1→3.15 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2.1 / % possible all: 83.6

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
PHENIXphasing
DMphasing
REFMAC5.8.0107refinement
RefinementMethod to determine structure: SIRAS
Starting model: NONE

Resolution: 3.1→19.75 Å / Cor.coef. Fo:Fc: 0.901 / Cor.coef. Fo:Fc free: 0.831 / SU B: 20.708 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.485 / 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. 3 DIFFERENT CRYSTAL FORMS WERE AVAILABLE - P41211, P21212 AND P3121. THIS CRYSTAL IS THE ONLY ONE FOR THE FORM P3121. ONLY IN THIS FORM DOMAIN 9 WAS NICELY ORDERED AND THE SEQUENCE COULD BE PLACED IN ELECTRON DENSITY.
RfactorNum. reflection% reflectionSelection details
Rfree0.2897 487 4.9 %RANDOM
Rwork0.21638 ---
Obs0.21993 9372 92.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 42.394 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0.13 Å20 Å2
2---0.26 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 3.1→19.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2440 0 3 57 2500
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0070.022479
r_bond_other_d
r_angle_refined_deg1.2051.9673378
r_angle_other_deg
r_dihedral_angle_1_deg5.8895342
r_dihedral_angle_2_deg40.18227.2580
r_dihedral_angle_3_deg16.55215404
r_dihedral_angle_4_deg16.891153
r_chiral_restr0.0710.2438
r_gen_planes_refined0.0040.0211788
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it0.9814.2321371
r_mcbond_other
r_mcangle_it1.7526.3431710
r_mcangle_other
r_scbond_it0.8524.2971107
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 3.1→3.178 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.351 47 -
Rwork0.267 651 -
Obs--91.36 %

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