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- PDB-6cwm: Crystal structure of SpaA-SLH/G109A -

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Basic information

Entry
Database: PDB / ID: 6cwm
TitleCrystal structure of SpaA-SLH/G109A
ComponentsSurface (S-) layer glycoprotein
KeywordsSUGAR BINDING PROTEIN / Surface layer homology domain / Secondary cell wall polymer / S-layer / SLH / SCWP
Function / homologyS-layer homology domain / S-layer homology (SLH) domain profile. / Copper resistance protein CopC/internalin, immunoglobulin-like / Surface (S-) layer glycoprotein
Function and homology information
Biological speciesPaenibacillus alvei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.15 Å
AuthorsBlackler, R.J. / Evans, S.V.
Funding support Canada, Austria, 3items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada)CGSD3-426678-2012 Canada
Austrian Science FundP22791-B12 Austria
Austrian Science FundP27374-B22 Austria
CitationJournal: Nat Commun / Year: 2018
Title: Structural basis of cell wall anchoring by SLH domains in Paenibacillus alvei.
Authors: Blackler, R.J. / Lopez-Guzman, A. / Hager, F.F. / Janesch, B. / Martinz, G. / Gagnon, S.M.L. / Haji-Ghassemi, O. / Kosma, P. / Messner, P. / Schaffer, C. / Evans, S.V.
History
DepositionMar 30, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2018Provider: repository / Type: Initial release
Revision 1.1Aug 22, 2018Group: Data collection / Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine_hist
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Surface (S-) layer glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,8342
Polymers19,7981
Non-polymers351
Water3,333185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area8900 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.348, 65.668, 73.168
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Surface (S-) layer glycoprotein / SpaA


Mass: 19798.266 Da / Num. of mol.: 1 / Fragment: SLH domains (UNP residues 21-193) / Mutation: G109A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus alvei (bacteria) / Gene: spaA / Plasmid: pET-22b / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1JZ07
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 185 / 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: 2.08 Å3/Da / Density % sol: 40.98 % / Mosaicity: 0.395 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.2 M ammonium acetate, 0.1 M Tris, pH 8.5, 25% w/v PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Jul 19, 2015
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.15→50 Å / Num. obs: 57497 / % possible obs: 96.4 % / Redundancy: 7.3 % / Rmerge(I) obs: 0.043 / Rpim(I) all: 0.018 / Rrim(I) all: 0.047 / Χ2: 0.939 / Net I/av σ(I): 38.406 / Net I/σ(I): 12.8 / Num. measured all: 419434
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.15-1.176.90.74527690.7980.3030.8060.79593.5
1.17-1.197.30.67627590.8560.2660.7270.81994.6
1.19-1.217.40.56828100.9030.2220.6110.85794.8
1.21-1.247.40.48927690.9230.1910.5250.89395
1.24-1.277.40.38527990.9510.1510.4140.91695.4
1.27-1.37.40.32628000.9640.1270.350.90895.6
1.3-1.337.40.2728490.9720.1060.2910.95295.9
1.33-1.367.40.22628430.9780.0880.2430.97296.3
1.36-1.47.40.19128310.9840.0750.2061.01896.3
1.4-1.457.40.15928460.9890.0620.1711.06896.8
1.45-1.57.40.12428980.9920.0490.1331.08996.9
1.5-1.567.40.09728940.9950.0380.1041.01797.3
1.56-1.637.40.07428820.9960.0290.080.9197.6
1.63-1.727.40.06429200.9970.0250.0690.91198
1.72-1.837.40.05929240.9970.0230.0631.07698
1.83-1.977.30.05129450.9980.020.0551.20298.5
1.97-2.167.30.04129710.9990.0160.0440.99398.7
2.16-2.487.30.03529960.9990.0140.0370.83999.1
2.48-3.127.20.03130500.9990.0120.0340.74599.3
3.12-506.40.03229420.9980.0140.0350.7491

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Processing

Software
NameVersionClassification
HKL-2000data scaling
REFMAC5.8.0073refinement
PDB_EXTRACT3.2data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6CWC

6cwc


Resolution: 1.15→50 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.969 / SU B: 0.839 / SU ML: 0.018 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.032 / ESU R Free: 0.033
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.159 2631 4.9 %RANDOM
Rwork0.1309 ---
obs0.1322 51418 90.69 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 79.16 Å2 / Biso mean: 20.294 Å2 / Biso min: 10.38 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--0.17 Å20 Å2
3----0.13 Å2
Refinement stepCycle: final / Resolution: 1.15→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1311 0 1 185 1497
Biso mean--26.38 30.66 -
Num. residues----171
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0240.0191365
X-RAY DIFFRACTIONr_bond_other_d0.0020.021300
X-RAY DIFFRACTIONr_angle_refined_deg2.1581.9461842
X-RAY DIFFRACTIONr_angle_other_deg0.93633010
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3465176
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.74126.06661
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.61715242
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.068152
X-RAY DIFFRACTIONr_chiral_restr0.1310.2199
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.021578
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02302
X-RAY DIFFRACTIONr_mcbond_it1.7471.388698
X-RAY DIFFRACTIONr_mcbond_other1.7181.386697
X-RAY DIFFRACTIONr_mcangle_it1.922.084876
X-RAY DIFFRACTIONr_rigid_bond_restr6.66732665
X-RAY DIFFRACTIONr_sphericity_free25.412547
X-RAY DIFFRACTIONr_sphericity_bonded8.35852780
LS refinement shellResolution: 1.15→1.18 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.23 68 -
Rwork0.226 1455 -
all-1523 -
obs--34.92 %
Refinement TLS params.Method: refined / Origin x: -10.6853 Å / Origin y: -2.9339 Å / Origin z: 11.8142 Å
111213212223313233
T0.0052 Å20.0017 Å20.0031 Å2-0.0087 Å2-0.0047 Å2--0.0157 Å2
L0.3661 °20.0014 °20.1469 °2-0.4871 °20.1635 °2--0.9777 °2
S0.0083 Å °-0.0206 Å °-0.0211 Å °0.0337 Å °0.0039 Å °0.0168 Å °-0.0189 Å °-0.0244 Å °-0.0121 Å °

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