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- PDB-7sv4: Crystal structure of SpaA-SLH in complex with 4,6-Pyr-beta-D-ManN... -

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Basic information

Entry
Database: PDB / ID: 7sv4
TitleCrystal structure of SpaA-SLH in complex with 4,6-Pyr-beta-D-ManNAc-(1->4)-beta-D-GlcNAc-(1->3)-4,6-Pyr-beta-D-ManNAcOMe
ComponentsSurface (S-) layer glycoprotein
KeywordsSUGAR BINDING PROTEIN / S-layer / SLH domain / Secondary cell wall polymer
Function / homologyS-layer homology domain / S-layer homology (SLH) domain profile. / Copper resistance protein CopC/internalin, immunoglobulin-like / Chem-D4I / Surface (S-) layer glycoprotein
Function and homology information
Biological speciesPaenibacillus alvei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.06 Å
AuthorsLegg, M.S.G. / Evans, S.V.
Funding support Austria, 3items
OrganizationGrant numberCountry
Natural Sciences and Engineering Research Council (NSERC, Canada) Austria
Austrian Science FundP27374-B22 Austria
Austrian Science FundP32521-B22 Austria
CitationJournal: J.Biol.Chem. / Year: 2022
Title: The S-layer homology domains of Paenibacillus alvei surface protein SpaA bind to cell wall polysaccharide through the terminal monosaccharide residue.
Authors: Legg, M.S.G. / Hager-Mair, F.F. / Krauter, S. / Gagnon, S.M.L. / Lopez-Guzman, A. / Lim, C. / Blaukopf, M. / Kosma, P. / Schaffer, C. / Evans, S.V.
History
DepositionNov 18, 2021Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 9, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 6, 2022Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)20,6583
Polymers19,7841
Non-polymers8742
Water2,468137
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)34.694, 67.302, 72.749
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: 19784.240 Da / Num. of mol.: 1 / Fragment: SLH domains (UNP residues 21-193)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paenibacillus alvei (bacteria) / Gene: spaA / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: C1JZ07
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-D4I / methyl 2-acetamido-4,6-O-[(1S)-1-carboxyethylidene]-2-deoxy-beta-D-mannopyranosyl-(1->4)-2-acetamido-2-deoxy-beta-D-glucopyranosyl-(1->3)-2-acetamido-4,6-O-[(1S)-1-carboxyethylidene]-2-deoxy-beta-D-mannopyranoside


Mass: 781.713 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H47N3O20 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 137 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.15 Å3/Da / Density % sol: 42.7 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M Magnesium Chloride, 0.1 M Bis-Tris pH 5.5, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Mar 15, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.06→20 Å / Num. obs: 11130 / % possible obs: 98.4 % / Redundancy: 10.2 % / Rmerge(I) obs: 0.143 / Rpim(I) all: 0.043 / Rrim(I) all: 0.15 / Χ2: 0.804 / Net I/σ(I): 13.5 / Num. measured all: 113668
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.06-2.133.30.5919950.1370.2950.6691.13190.1
2.13-2.225.20.33910600.8820.1590.3781.06196.3
2.22-2.328.10.33211080.9240.1230.3560.89298.9
2.32-2.4410.30.30610950.9390.10.3230.91699.7
2.44-2.5910.70.26811050.9610.0860.2830.90999.4
2.59-2.7911.50.22811100.9470.0710.240.82599.3
2.79-3.0711.70.17611180.9870.0540.1840.8799.6
3.07-3.5212.70.12711550.9930.0370.1330.717100
3.52-4.4214.30.12211500.9920.0340.1270.657100
4.42-2012.90.10212340.9950.0290.1070.634100

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6CWM

6cwm


Resolution: 2.06→19.88 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.158 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.257 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2394 589 5.5 %RANDOM
Rwork0.2047 ---
obs0.2066 10218 97.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 66.71 Å2 / Biso mean: 23.747 Å2 / Biso min: 6.72 Å2
Baniso -1Baniso -2Baniso -3
1--0.05 Å20 Å20 Å2
2--1.27 Å20 Å2
3----1.22 Å2
Refinement stepCycle: final / Resolution: 2.06→19.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1284 0 66 138 1488
Biso mean--36.66 32.81 -
Num. residues----170
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0131383
X-RAY DIFFRACTIONr_bond_other_d0.0020.0181268
X-RAY DIFFRACTIONr_angle_refined_deg1.231.7021873
X-RAY DIFFRACTIONr_angle_other_deg1.2931.6592955
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1815171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.39425.42459
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.66415224
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.89152
X-RAY DIFFRACTIONr_chiral_restr0.0390.2191
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.021515
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02265
LS refinement shellResolution: 2.06→2.113 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 32 -
Rwork0.254 683 -
all-715 -
obs--91.2 %

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