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- PDB-7sv5: Crystal structure of SpaA-SLH/G109A in complex with 4,6-Pyr-beta-... -

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Basic information

Entry
Database: PDB / ID: 7sv5
TitleCrystal structure of SpaA-SLH/G109A in complex with 4,6-Pyr-beta-D-ManNAc-(1->4)-beta-D-GlcNAcOMe
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-D2Y / Surface (S-) layer glycoprotein
Function and homology information
Biological speciesPaenibacillus alvei (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 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
B: Surface (S-) layer glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7986
Polymers39,5972
Non-polymers1,2014
Water5,459303
1
A: Surface (S-) layer glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3993
Polymers19,7981
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Surface (S-) layer glycoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,3993
Polymers19,7981
Non-polymers6012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)111.847, 45.320, 87.490
Angle α, β, γ (deg.)90.000, 129.470, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-515-

HOH

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Components

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


Mass: 19798.266 Da / Num. of mol.: 2 / 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 / 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.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-D2Y / methyl 2-acetamido-4-O-{2-acetamido-4,6-O-[(1S)-1-carboxyethylidene]-2-deoxy-beta-D-mannopyranosyl}-2-deoxy-beta-D-glucopyranoside


Mass: 508.474 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H32N2O13 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 303 / 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: 2.16 Å3/Da / Density % sol: 43.09 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1 M HEPES pH 7.5, 25% (w/v) PEG 1000

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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: Jun 1, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.72→20 Å / Num. obs: 32683 / % possible obs: 90.3 % / Redundancy: 6.7 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.029 / Rrim(I) all: 0.077 / Χ2: 0.677 / Net I/σ(I): 12.4 / Num. measured all: 217438
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.72-1.783.60.53929700.6990.3010.6220.93482.6
1.78-1.855.60.46334210.9180.2010.5070.98895.8
1.85-1.946.90.42835870.740.1790.4660.69299.3
1.94-2.047.30.19336120.9740.0750.2080.725100
2.04-2.177.60.15835820.8670.0620.170.484100
2.17-2.337.90.10336140.9930.0390.110.479100
2.33-2.5780.07835990.9970.0290.0831.051100
2.57-2.9460.07330760.9930.0310.0790.50384.4
2.94-3.75.20.04314980.9920.0190.0480.2541.1
3.7-2070.03737240.9980.0150.040.54499.9

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Processing

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

6cwn


Resolution: 1.72→19.86 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.531 / SU ML: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.125 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1953 1665 5.1 %RANDOM
Rwork0.1777 ---
obs0.1786 30968 90.04 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 53.94 Å2 / Biso mean: 20.215 Å2 / Biso min: 12.39 Å2
Baniso -1Baniso -2Baniso -3
1-0.39 Å20 Å2-0.04 Å2
2--0.81 Å20 Å2
3----0.48 Å2
Refinement stepCycle: final / Resolution: 1.72→19.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2517 0 82 303 2902
Biso mean--19.45 31.59 -
Num. residues----329
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0030.0132651
X-RAY DIFFRACTIONr_bond_other_d0.0020.0182473
X-RAY DIFFRACTIONr_angle_refined_deg1.2071.6843583
X-RAY DIFFRACTIONr_angle_other_deg1.2631.6375760
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2695329
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.47325.478115
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.70315449
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.737154
X-RAY DIFFRACTIONr_chiral_restr0.0510.2364
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.022912
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02512
LS refinement shellResolution: 1.72→1.765 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 132 -
Rwork0.292 2012 -
all-2144 -
obs--80.54 %

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