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- PDB-6cwl: Crystal structure of SpaA-SLH in complex with beta-D-GlcNAc-(1->3... -

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Basic information

Entry
Database: PDB / ID: 6cwl
TitleCrystal structure of SpaA-SLH in complex with beta-D-GlcNAc-(1->3)-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-FHY / Surface (S-) layer glycoprotein
Function and homology information
Biological speciesPaenibacillus alvei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine_hist.d_res_low / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)40,5854
Polymers39,5682
Non-polymers1,0172
Water1,49583
1
A: Surface (S-) layer glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2932
Polymers19,7841
Non-polymers5081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Surface (S-) layer glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,2932
Polymers19,7841
Non-polymers5081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)72.256, 72.256, 126.140
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: SER / End label comp-ID: SER / Refine code: 0 / Auth seq-ID: 28 - 191 / Label seq-ID: 8 - 171

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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


Mass: 19784.240 Da / Num. of mol.: 2 / Fragment: SLH domains (UNP residues 21-193)
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-FHY / (2S,4aR,6R,7S,8R,8aS)-7-(acetylamino)-6-({2-(acetylamino)-3-O-[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]-4,6-O-[(1S)-1-carboxylic acidethylidene]-2-deoxy-beta-D-mannopyranosyl}oxy)-8-{[2-(acetylamino)-2-deoxy-beta-D-glucopyranosyl]oxy}-2-methylhexahydro-2H-pyrano[3,2-d][1,3]dioxine-2-carboxylic acid


Mass: 508.474 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32N2O13
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 83 / 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: 2.54 Å3/Da / Density % sol: 51.54 % / Mosaicity: 0.353 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 mM ammonium sulfate, 50 mM Bis-Tris, pH 6.5, 30% v/v pentaerythritolethoxylate [15/4 EO/OH]

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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: Oct 8, 2014
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: 2.15→40 Å / Num. obs: 21339 / % possible obs: 99.9 % / Redundancy: 13.2 % / Rmerge(I) obs: 0.073 / Rpim(I) all: 0.021 / Rrim(I) all: 0.076 / Χ2: 0.957 / Net I/av σ(I): 34.271 / Net I/σ(I): 11 / Num. measured all: 282615
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.15-2.1913.60.54510680.970.1520.5660.841100
2.19-2.2313.60.52310290.960.1460.5440.852100
2.23-2.2713.60.42810480.9640.120.4450.889100
2.27-2.3213.60.40710550.9730.1140.4230.877100
2.32-2.3713.70.37810450.9740.1060.3920.924100
2.37-2.4213.60.28910500.9840.0810.30.958100
2.42-2.4813.60.23710480.9890.0660.2461.009100
2.48-2.5513.60.21610600.9890.0610.2251.06100
2.55-2.6213.50.19410370.990.0540.2011.041100
2.62-2.7113.60.16110520.9930.0450.1681.056100
2.71-2.8113.60.12910720.9950.0360.1341.034100
2.81-2.9213.50.11510590.9960.0320.1191.004100
2.92-3.0513.50.09810690.9970.0280.1021.016100
3.05-3.2113.30.08910530.9970.0250.0931.086100
3.21-3.4112.90.08110900.9970.0240.0841.183100
3.41-3.6812.50.07210560.9980.0210.0751.159100
3.68-4.0512.70.06210920.9980.0180.0650.978100
4.05-4.6312.80.05510760.9980.0160.0580.823100
4.63-5.8312.70.05111200.9980.0150.0530.688100
5.83-4011.70.04911600.9980.0150.0510.65597.6

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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: 2.15→40 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.88 / SU B: 13.342 / SU ML: 0.168 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.24 / ESU R Free: 0.199
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2552 1132 5.3 %RANDOM
Rwork0.2154 ---
obs0.2175 20168 99.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 87.75 Å2 / Biso mean: 36.463 Å2 / Biso min: 15.44 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20.02 Å20 Å2
2--0.04 Å20 Å2
3----0.14 Å2
Refinement stepCycle: final / Resolution: 2.15→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2380 0 70 98 2548
Biso mean--53.04 39.66 -
Num. residues----310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.022509
X-RAY DIFFRACTIONr_bond_other_d0.0050.022415
X-RAY DIFFRACTIONr_angle_refined_deg1.5811.9853383
X-RAY DIFFRACTIONr_angle_other_deg1.173.0155583
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9085309
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.8525.943106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88515438
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.469154
X-RAY DIFFRACTIONr_chiral_restr0.10.2382
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022791
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02537
X-RAY DIFFRACTIONr_mcbond_it0.6870.9161243
X-RAY DIFFRACTIONr_mcbond_other0.6850.9151242
X-RAY DIFFRACTIONr_mcangle_it1.2131.3631548
Refine LS restraints NCS

Ens-ID: 1 / Number: 8269 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.12 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.151→2.207 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 78 -
Rwork0.253 1475 -
all-1553 -
obs--99.87 %
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)
12.38191.430.4773.88620.58512.6711-0.0343-0.06010.0757-0.0290.01570.2566-0.1966-0.19750.01870.2866-0.086-0.07740.07310.0710.12127.2019-8.360.4859
22.4561-2.4451-0.50484.80150.80676.2610.0321-0.03690.13330.04370.0815-0.239-0.13270.1923-0.11370.30630.1530.01080.0895-0.0160.14646.6462-13.6666-20.621
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 191
2X-RAY DIFFRACTION2B28 - 192

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