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- PDB-6cwh: Crystal structure of SpaA-SLH in complex with 4,6-Pyr-beta-D-ManN... -

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Basic information

Entry
Database: PDB / ID: 6cwh
TitleCrystal structure of SpaA-SLH in complex with 4,6-Pyr-beta-D-ManNAcOMe (P1)
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: 2 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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
C: Surface (S-) layer glycoprotein
D: Surface (S-) layer glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)80,3588
Polymers79,1374
Non-polymers1,2214
Water6,305350
1
A: Surface (S-) layer glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0902
Polymers19,7841
Non-polymers3051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Surface (S-) layer glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0902
Polymers19,7841
Non-polymers3051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Surface (S-) layer glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0902
Polymers19,7841
Non-polymers3051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Surface (S-) layer glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0902
Polymers19,7841
Non-polymers3051
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.215, 72.239, 72.305
Angle α, β, γ (deg.)86.730, 71.290, 71.400
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A8 - 172
2010B8 - 172
1020A9 - 171
2020C9 - 171
1030A8 - 172
2030D8 - 172
1040B9 - 171
2040C9 - 171
1050B8 - 172
2050D8 - 172
1060C9 - 171
2060D9 - 171

NCS ensembles :
ID
1
2
3
4
5
6

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Components

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


Mass: 19784.240 Da / Num. of mol.: 4 / 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: 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.: 4 / Source method: obtained synthetically / Formula: C12H19NO8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 350 / 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: 2.89 Å3/Da / Density % sol: 57.43 % / Mosaicity: 0.93 °
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.2 M sodium malonate, pH 7.0, 20% 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: Oct 9, 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→40 Å / Num. obs: 53737 / % possible obs: 95 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.044 / Rpim(I) all: 0.035 / Rrim(I) all: 0.056 / Χ2: 0.92 / Net I/av σ(I): 19.812 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2-2.032.20.350.9340.2730.4460.91379.8
2.03-2.072.20.3270.9150.2560.4170.94783.8
2.07-2.112.20.2930.9480.230.3740.94387.4
2.11-2.152.20.260.9530.2050.3320.96990.3
2.15-2.22.30.1990.9740.1590.2560.95692.9
2.2-2.252.30.2070.9670.1680.2681.01295.1
2.25-2.312.30.1830.9710.1490.2370.99997.1
2.31-2.372.40.1810.9710.1490.2350.99897.6
2.37-2.442.40.1510.9780.1260.1980.98597.7
2.44-2.522.40.1180.9850.0970.1531.00997.8
2.52-2.612.40.1070.9830.0890.1390.99398
2.61-2.712.40.0880.990.0730.1150.99298.1
2.71-2.842.40.070.9920.0580.0920.96498.3
2.84-2.992.40.0630.9920.0510.0810.96298.4
2.99-3.172.40.050.9950.040.0650.998.6
3.17-3.422.40.0440.9950.0350.0570.88498.4
3.42-3.762.40.0370.9960.0290.0480.85598.4
3.76-4.312.40.0340.9960.0270.0440.74898.8
4.31-5.422.40.0340.9960.0270.0430.70598.6
5.42-402.40.0330.9960.0280.0440.69294

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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→40 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 8.464 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.232 / ESU R Free: 0.196
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2348 2238 5.3 %RANDOM
Rwork0.1855 ---
obs0.1881 39929 74.44 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 102.38 Å2 / Biso mean: 33.738 Å2 / Biso min: 7.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.19 Å20.34 Å20.15 Å2
2--0.2 Å20.04 Å2
3---0.21 Å2
Refinement stepCycle: final / Resolution: 2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5075 0 84 350 5509
Biso mean--24.73 31.71 -
Num. residues----659
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.025279
X-RAY DIFFRACTIONr_bond_other_d0.0070.025074
X-RAY DIFFRACTIONr_angle_refined_deg1.6051.9727123
X-RAY DIFFRACTIONr_angle_other_deg1.2273.00811740
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4985661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.62626.123227
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36615935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.246158
X-RAY DIFFRACTIONr_chiral_restr0.1120.2790
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.025948
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021128
X-RAY DIFFRACTIONr_mcbond_it1.3281.6512644
X-RAY DIFFRACTIONr_mcbond_other1.3271.652643
X-RAY DIFFRACTIONr_mcangle_it2.1422.4633302
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A100520.07
12B100520.07
21A97590.08
22C97590.08
31A99150.08
32D99150.08
41B97050.07
42C97050.07
51B98600.07
52D98600.07
61C99140.05
62D99140.05
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.221 44 -
Rwork0.204 1270 -
all-1314 -
obs--31.92 %
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)
11.3211-0.14030.55011.5626-0.14784.26290.2856-0.2925-0.0730.0432-0.06220.0789-0.0736-0.2988-0.22340.0959-0.06320.03840.07950.01250.0955-0.5948-42.791425.7954
21.44460.2555-0.49051.56-0.12354.43220.27560.25480.06-0.0402-0.06250.07820.1122-0.2619-0.21320.08480.0478-0.03930.06020.01060.095-0.589-68.4517-8.5772
32.8228-0.0185-1.8751.38-0.32573.25870.0930.16260.2283-0.23270.08440.0854-0.48230.1403-0.17740.1978-0.09090.02520.05850.00520.04977.3686-34.7382-9.0913
42.81990.15851.90631.3016-0.22373.47980.1194-0.178-0.22840.23510.07550.05740.5110.0896-0.19490.18860.0736-0.03490.04740.00330.05797.5368-76.53826.3458
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 192
2X-RAY DIFFRACTION2B28 - 192
3X-RAY DIFFRACTION3C29 - 192
4X-RAY DIFFRACTION4D28 - 192

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