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- PDB-6cwn: Crystal structure of SpaA-SLH/G109A in complex with 4,6-Pyr-beta-... -

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Basic information

Entry
Database: PDB / ID: 6cwn
TitleCrystal structure of SpaA-SLH/G109A in complex with 4,6-Pyr-beta-D-ManNAcOMe
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 / Chem-6LA / Surface (S-) layer glycoprotein
Function and homology information
Biological speciesPaenibacillus alvei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.53 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 1.3Mar 13, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)20,3404
Polymers19,7981
Non-polymers5423
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area570 Å2
ΔGint-18 kcal/mol
Surface area8710 Å2
MethodPISA
Unit cell
Length a, b, c (Å)93.383, 36.254, 56.896
Angle α, β, γ (deg.)90.000, 103.740, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-456-

HOH

21A-557-

HOH

31A-568-

HOH

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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: Sugar ChemComp-6LA / methyl 2-(acetylamino)-4,6-O-[(1S)-1-carboxyethylidene]-2-deoxy-beta-D-mannopyranoside


Type: D-saccharide / Mass: 305.281 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H19NO8
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.36 Å3/Da / Density % sol: 47.94 % / Mosaicity: 0.95 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop
Details: 0.1 M potassium thiocyanate, pH 6.8, 30% PEG2000 MME

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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: Mar 31, 2016
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: 1.53→50 Å / Num. obs: 27852 / % possible obs: 98.6 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.021 / Rrim(I) all: 0.049 / Χ2: 0.955 / Net I/av σ(I): 28.562 / Net I/σ(I): 23.5 / Num. measured all: 119834
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.53-1.563.40.15511900.9620.0970.1840.85784.8
1.56-1.584.10.14313850.9810.0820.1650.82899.9
1.58-1.6240.12614080.9820.0730.1460.90299.9
1.62-1.654.10.11713850.9850.0670.1350.89799.8
1.65-1.6840.10413950.9860.060.120.91299.6
1.68-1.724.10.09414250.9880.0540.1090.96699.9
1.72-1.774.10.08313610.990.0480.0960.9499.6
1.77-1.8140.07814170.9910.0450.090.99399.9
1.81-1.8740.06913890.9920.040.081.0499.6
1.87-1.933.90.06714140.9930.0390.0781.22499.3
1.93-23.90.0613900.9930.0350.0691.14899.6
2-2.083.80.05713750.9930.0350.0671.19998.6
2.08-2.173.80.05314140.9950.0310.0611.13799.5
2.17-2.293.80.04914010.9950.0290.0571.0699.4
2.29-2.4340.04514010.9960.0260.0520.89299.8
2.43-2.624.40.04714210.9960.0250.0540.95599.9
2.62-2.885.70.0514100.9970.0230.0551.0599.6
2.88-3.35.80.04514220.9970.020.050.91399.3
3.3-4.155.60.0414170.9980.0180.0440.78198.4
4.15-505.30.03614320.9980.0170.040.64696.5

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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 / Resolution: 1.53→50 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.782 / SU ML: 0.03 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.059 / ESU R Free: 0.056
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1513 1386 5 %RANDOM
Rwork0.1126 ---
obs0.1146 26441 99.01 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 92.91 Å2 / Biso mean: 17.079 Å2 / Biso min: 4.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.44 Å20 Å2-0.19 Å2
2---0.45 Å20 Å2
3---0.09 Å2
Refinement stepCycle: final / Resolution: 1.53→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 37 176 1469
Biso mean--22.55 29.6 -
Num. residues----163
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0210.021325
X-RAY DIFFRACTIONr_bond_other_d0.0020.021291
X-RAY DIFFRACTIONr_angle_refined_deg2.0481.9831790
X-RAY DIFFRACTIONr_angle_other_deg0.9993.0082979
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.065164
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.84226.07156
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.87915232
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.808152
X-RAY DIFFRACTIONr_chiral_restr0.1250.2201
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021477
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02281
X-RAY DIFFRACTIONr_mcbond_it2.0951.006656
X-RAY DIFFRACTIONr_mcbond_other1.9020.999655
X-RAY DIFFRACTIONr_mcangle_it2.8081.517820
X-RAY DIFFRACTIONr_rigid_bond_restr5.12232616
X-RAY DIFFRACTIONr_sphericity_free32.057563
X-RAY DIFFRACTIONr_sphericity_bonded10.90452706
LS refinement shellResolution: 1.532→1.572 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.158 102 -
Rwork0.103 1876 -
all-1978 -
obs--95.46 %
Refinement TLS params.Method: refined / Origin x: -10.1228 Å / Origin y: -1.9418 Å / Origin z: 10.3709 Å
111213212223313233
T0.0025 Å2-0.0006 Å20.0031 Å2-0.0198 Å20.0057 Å2--0.0147 Å2
L0.4903 °20.2102 °20.255 °2-0.2199 °20.3051 °2--0.7381 °2
S-0.0041 Å °-0.0395 Å °-0.0057 Å °-0.0106 Å °0.0193 Å °0.0096 Å °-0.0109 Å °0.0466 Å °-0.0151 Å °

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