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- PDB-2ra1: Crystal structure of the N-terminal part of the bacterial S-layer... -

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Basic information

Entry
Database: PDB / ID: 2ra1
TitleCrystal structure of the N-terminal part of the bacterial S-layer protein SbsC
ComponentsSurface layer protein
KeywordsSUGAR BINDING PROTEIN / triple coiled-coil / s-layer protein / PROTEIN BINDING
Function / homology
Function and homology information


identical protein binding / metal ion binding
Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #770 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #780 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #790 / Immunoglobulin-like - #2120 / 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 / Immunoglobulin-like - #1220 ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #770 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #780 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #790 / Immunoglobulin-like - #2120 / 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 / Immunoglobulin-like - #1220 / Copper resistance protein CopC/internalin, immunoglobulin-like / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2 / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Surface layer protein
Similarity search - Component
Biological speciesGeobacillus stearothermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.406 Å
AuthorsPavkov, T. / Egelseer, E.M. / Tesarz, M. / Sleytr, U.B. / Keller, W.
CitationJournal: Structure / Year: 2008
Title: The structure and binding behavior of the bacterial cell surface layer protein SbsC.
Authors: Pavkov, T. / Egelseer, E.M. / Tesarz, M. / Svergun, D.I. / Sleytr, U.B. / Keller, W.
History
DepositionSep 14, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 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: Surface layer protein


Theoretical massNumber of molelcules
Total (without water)45,0521
Polymers45,0521
Non-polymers00
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.645, 94.877, 59.646
Angle α, β, γ (deg.)90.000, 106.680, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Surface layer protein /


Mass: 45051.746 Da / Num. of mol.: 1 / Fragment: N-terminal domains
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geobacillus stearothermophilus (bacteria)
Gene: sbsC / Plasmid: pET3a / Production host: Escherichia coli (E. coli) / Strain (production host): HMS174(DE3) / References: UniProt: O68840
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / 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: 2.99 Å3/Da / Density % sol: 58.82 %
Crystal growTemperature: 298 K / Method: batch method / pH: 6.5
Details: 6-14% PEG3350, various salts - NaCl, LiCl etc., pH 6.5, batch method, temperature 298K
Temp details: 5.5-7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1.2 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 15, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2 Å / Relative weight: 1
ReflectionResolution: 2.4→99 Å / Num. obs: 20541 / % possible obs: 99.7 % / Rmerge(I) obs: 0.064 / Χ2: 0.829 / Net I/σ(I): 22.1
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
2.4-2.440.19610051.37597.7
2.44-2.490.15510530.708100
2.49-2.530.1389890.672100
2.53-2.590.12610280.623100
2.59-2.640.13610160.906100
2.64-2.70.26810442.022100
2.7-2.770.09110010.555100
2.77-2.850.08810340.52699.9
2.85-2.930.07310370.485100
2.93-3.020.06610140.438100
3.02-3.130.0610470.41100
3.13-3.260.05410150.412100
3.26-3.410.05110150.469100
3.41-3.590.06310420.924100
3.59-3.810.06110481.015100
3.81-4.10.06810241.086100
4.1-4.520.07110201.126100
4.52-5.170.05810280.657100
5.17-6.510.05210580.72100
6.51-990.05310231.06396.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.8 Å15.02 Å
Translation2.8 Å15.02 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACT3data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: N-terminal domains form the structure of rSbsC(31-844)

Resolution: 2.406→20.009 Å / FOM work R set: 0.811 / Stereochemistry target values: ml
RfactorNum. reflection% reflection
Rfree0.24 1036 5.16 %
Rwork0.177 --
obs-20089 97.62 %
Solvent computationBsol: 42.844 Å2 / ksol: 0.333 e/Å3
Displacement parametersBiso max: 109.03 Å2 / Biso mean: 40.03 Å2 / Biso min: 9.77 Å2
Baniso -1Baniso -2Baniso -3
1--4.18 Å2-0 Å2-3.295 Å2
2---7.269 Å20 Å2
3---11.449 Å2
Refinement stepCycle: LAST / Resolution: 2.406→20.009 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3173 0 0 252 3425
Refine LS restraints
Refine-IDTypeDev idealWeight
X-RAY DIFFRACTIONf_angle_d1.1311
X-RAY DIFFRACTIONf_bond_d0.0081
X-RAY DIFFRACTIONf_chiral_restr0.0751
X-RAY DIFFRACTIONf_dihedral_angle_d17.2181
X-RAY DIFFRACTIONf_plane_restr0.0041
X-RAY DIFFRACTIONf_nbd_refined4.1061
LS refinement shell
Resolution (Å)Rfactor RworkNum. reflection RworkRefine-IDTotal num. of bins used% reflection obs (%)
2.406-2.4280.2423X-RAY DIFFRACTION3880
2.428-2.450.216490X-RAY DIFFRACTION3889
2.45-2.4730.219463X-RAY DIFFRACTION3888
2.473-2.4970.209519X-RAY DIFFRACTION3890
2.497-2.5220.212465X-RAY DIFFRACTION3892
2.522-2.5480.194491X-RAY DIFFRACTION3890
2.548-2.5750.198487X-RAY DIFFRACTION3891
2.575-2.6030.211489X-RAY DIFFRACTION3891
2.603-2.6320.207503X-RAY DIFFRACTION3890
2.632-2.6630.188454X-RAY DIFFRACTION3889
2.663-2.6960.201504X-RAY DIFFRACTION3891
2.696-2.730.225500X-RAY DIFFRACTION3892
2.73-2.7660.208502X-RAY DIFFRACTION3892
2.766-2.8030.212508X-RAY DIFFRACTION3895
2.803-2.8430.205488X-RAY DIFFRACTION3892
2.843-2.8860.209518X-RAY DIFFRACTION3894
2.886-2.9310.206505X-RAY DIFFRACTION3895
2.931-2.9790.21504X-RAY DIFFRACTION3892
2.979-3.030.193484X-RAY DIFFRACTION3892
3.03-3.0850.211502X-RAY DIFFRACTION3895
3.085-3.1440.189530X-RAY DIFFRACTION3893
3.144-3.2080.194474X-RAY DIFFRACTION3892
3.208-3.2770.187525X-RAY DIFFRACTION3895
3.277-3.3530.181507X-RAY DIFFRACTION3896
3.353-3.4370.185495X-RAY DIFFRACTION3892
3.437-3.5290.17519X-RAY DIFFRACTION3894
3.529-3.6320.164518X-RAY DIFFRACTION3896
3.632-3.7490.159512X-RAY DIFFRACTION3896
3.749-3.8820.156510X-RAY DIFFRACTION3893
3.882-4.0360.154509X-RAY DIFFRACTION3894
4.036-4.2180.147501X-RAY DIFFRACTION3893
4.218-4.4380.133536X-RAY DIFFRACTION3896
4.438-4.7130.125498X-RAY DIFFRACTION3894
4.713-5.0710.139525X-RAY DIFFRACTION3894
5.071-5.5710.155518X-RAY DIFFRACTION3895
5.571-6.3550.171514X-RAY DIFFRACTION3895
6.355-7.9230.145523X-RAY DIFFRACTION3895
7.923-20.010.13540X-RAY DIFFRACTION3895
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)
10.7421-0.68510.07771.36-0.25520.017-0.0714-0.07290.02560.03790.053-0.2295-0.0545-0.009600.1174-0.00990.00010.13790.03380.180376.6721-58.17751.26
20.513-0.0905-0.30340.3012-0.20230.39030.45970.44510.4934-0.1508-0.1835-0.2032-0.3534-0.25670.01350.26820.15740.02830.23740.12570.267150.9429-28.282135.4641
30.4112-0.238-0.63180.6829-0.46321.12640.1574-0.33740.17480.1635-0.114-0.16090.59560.27470.00020.37660.0569-0.04790.27960.01040.116422.94-8.788126.7294
41.22410.1503-0.84420.14270.08160.8874-0.20670.3101-0.0094-0.04620.097-0.10460.13850.00090.00010.1276-0.03250.00840.1808-0.04070.151117.87163.945658.7025
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsLabel asym-IDLabel seq-ID
1X-RAY DIFFRACTION1chain A and resid 32-198A32 - 198
2X-RAY DIFFRACTION2chain A and resid 199-259A199 - 259
3X-RAY DIFFRACTION3chain A and resid 262-357A262 - 357
4X-RAY DIFFRACTION4chain A and resid 360-443A360 - 443

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