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- PDB-8rwf: Domains 1 and 2 of Bacillus anthracis Sap S-layer in complex with... -

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Basic information

Entry
Database: PDB / ID: 8rwf
TitleDomains 1 and 2 of Bacillus anthracis Sap S-layer in complex with Nb692
Components
  • S-layer protein sap
  • Sap binding Nanobody 692
KeywordsSTRUCTURAL PROTEIN / S-layer / nanobody / anthrax
Function / homology
Function and homology information


S-layer / extracellular region
Similarity search - Function
SbsA, Ig-like domain / Bacterial Ig-like domain / S-layer homology domain / S-layer homology domain / S-layer homology (SLH) domain profile. / Copper resistance protein CopC/internalin, immunoglobulin-like / Bacterial Ig-like domain (group 2) / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain 2 / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Biological speciesBacillus anthracis (anthrax bacterium)
Lama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.11 Å
AuthorsSogues, A. / Remaut, H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 709-2021European Union
CitationJournal: To Be Published / Year: 2024
Title: Molecular dynamics and machine learning stratify motion-dependent activity profiles of S-layer destabilizing nanobodies
Authors: Sogues, A. / Remaut, H.
History
DepositionFeb 4, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: S-layer protein sap
B: S-layer protein sap
C: Sap binding Nanobody 692
D: S-layer protein sap
E: Sap binding Nanobody 692
G: Sap binding Nanobody 692


Theoretical massNumber of molelcules
Total (without water)98,3666
Polymers98,3666
Non-polymers00
Water1,838102
1
A: S-layer protein sap
G: Sap binding Nanobody 692


Theoretical massNumber of molelcules
Total (without water)32,7892
Polymers32,7892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: S-layer protein sap
C: Sap binding Nanobody 692


Theoretical massNumber of molelcules
Total (without water)32,7892
Polymers32,7892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
D: S-layer protein sap
E: Sap binding Nanobody 692


Theoretical massNumber of molelcules
Total (without water)32,7892
Polymers32,7892
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)213.264, 213.264, 53.267
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Space group name HallP4nw2abw
Symmetry operation#1: x,y,z
#2: -y+1/2,x+1/2,z+3/4
#3: y+1/2,-x+1/2,z+1/4
#4: x+1/2,-y+1/2,-z+1/4
#5: -x+1/2,y+1/2,-z+3/4
#6: -x,-y,z+1/2
#7: y,x,-z
#8: -y,-x,-z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1chain "A"
d_2ens_1(chain "B" and (resid 216 through 285 or (resid 286...
d_3ens_1(chain "D" and (resid 216 through 285 or (resid 286...
d_1ens_2(chain "C" and (resid 1 through 18 or (resid 19...
d_2ens_2(chain "E" and (resid 1 through 42 or (resid 43...
d_3ens_2(chain "G" and (resid 1 through 18 or (resid 19...

NCS domain segments:

Component-ID: 1

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_1ens_1SERSERGLYGLYAA216 - 3849 - 177
d_2ens_1SERSERGLYGLYBB216 - 3849 - 177
d_3ens_1SERSERGLYGLYDD216 - 3849 - 177
d_1ens_2GLNGLNSERSERCC1 - 1181 - 118
d_2ens_2GLNGLNSERSEREE1 - 1181 - 118
d_3ens_2GLNGLNSERSERGF1 - 1181 - 118

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.539816683576, -0.841500328795, 0.0217978157569), (-0.841777165408, -0.539725244828, 0.0103857543157), (0.00302521577464, -0.023955307011, -0.999708453168)-49.34417437, -90.6271569876, -2.93585126656
2given(0.196390118649, -0.504671223181, 0.840677035365), (-0.384856713888, 0.74889674046, 0.539480288707), (-0.901840468748, -0.42948879918, -0.0471501888325)-28.5909596121, 12.1355737297, -89.4974760012
3given(0.621875014606, 0.122814864115, -0.773426127928), (-0.771337441571, -0.0745909489712, -0.632040142366), (-0.135314513041, 0.989622503525, 0.0483454555924)11.2728929071, -32.2719279075, -6.54214958609
4given(0.540387524514, -0.841413809381, -0.00203094374468), (-0.841399198126, -0.540359620949, -0.0076726423716), (0.00535842725386, 0.00585503465588, -0.999968502417)-49.5336715189, -90.6522676785, -1.75887844138

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Components

#1: Protein S-layer protein sap / Surface array protein / Surface layer protein


Mass: 19245.465 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: sap, BA_0885, GBAA_0885, BAS0841 / Production host: Escherichia coli (E. coli) / References: UniProt: P49051
#2: Antibody Sap binding Nanobody 692


Mass: 13543.049 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 102 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 3.09 Å3/Da / Density % sol: 60.16 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop
Details: 0.2 M Ammonium chloride, 0.1 M Hepes (pH 7.5) and 25% v/v Glycerol ethoxylate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9179 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: Jan 26, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9179 Å / Relative weight: 1
ReflectionResolution: 3.11→106.63 Å / Num. obs: 22681 / % possible obs: 99.92 % / Redundancy: 26.6 % / Biso Wilson estimate: 46.99 Å2 / Rpim(I) all: 0.265 / Net I/σ(I): 4.5
Reflection shellResolution: 3.22→3.22 Å / Num. unique obs: 2213 / Rpim(I) all: 1.08

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.11→106.63 Å / SU ML: 0.4959 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.1709
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2846 1143 5.04 %
Rwork0.2207 21538 -
obs0.2239 22681 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 44.02 Å2
Refinement stepCycle: LAST / Resolution: 3.11→106.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6451 0 0 102 6553
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00916517
X-RAY DIFFRACTIONf_angle_d1.17118795
X-RAY DIFFRACTIONf_chiral_restr0.06291050
X-RAY DIFFRACTIONf_plane_restr0.0071120
X-RAY DIFFRACTIONf_dihedral_angle_d15.07742391
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.906020139684
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS1.22100278016
ens_2d_2CCX-RAY DIFFRACTIONTorsion NCS0.686320023804
ens_2d_3CCX-RAY DIFFRACTIONTorsion NCS0.765891447816
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.11-3.260.37941170.31882652X-RAY DIFFRACTION99.93
3.26-3.430.37541360.29662629X-RAY DIFFRACTION99.96
3.43-3.640.31751410.25832656X-RAY DIFFRACTION99.79
3.64-3.920.33551430.242649X-RAY DIFFRACTION99.82
3.92-4.320.24991550.2022652X-RAY DIFFRACTION100
4.32-4.940.22471480.17172690X-RAY DIFFRACTION100
4.94-6.230.25791360.19172724X-RAY DIFFRACTION100
6.23-106.630.26151670.18972886X-RAY DIFFRACTION99.93

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