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- PDB-8rw9: Domains 1 and 2 of Bacillus anthracis Sap S-layer in complex with... -

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Basic information

Entry
Database: PDB / ID: 8rw9
TitleDomains 1 and 2 of Bacillus anthracis Sap S-layer in complex with Nb694
Components
  • Nanobody694
  • S-layer protein sap
KeywordsSTRUCTURAL PROTEIN / S-layer / anthracis / nanobodies
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) / Bacterial Ig-like domain 2 / Invasin/intimin cell-adhesion fragments / Bacterial Ig-like domain, group 2
Similarity search - Domain/homology
Biological speciesLama glama (llama)
Bacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsSogues, A. / Remaut, H.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Molecular Biology Organization (EMBO)ALTF 709-2021European Union
CitationJournal: Pnas Nexus / Year: 2024
Title: Molecular dynamics and machine learning stratify motion-dependent activity profiles of S-layer destabilizing nanobodies.
Authors: Cecil, A.J. / Sogues, A. / Gurumurthi, M. / Lane, K.S. / Remaut, H. / Pak, A.J.
History
DepositionFeb 2, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2024Provider: repository / Type: Initial release
Revision 1.1Dec 25, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nanobody694
B: Nanobody694
C: Nanobody694
D: Nanobody694
E: S-layer protein sap
F: S-layer protein sap
G: S-layer protein sap
H: S-layer protein sap


Theoretical massNumber of molelcules
Total (without water)134,4948
Polymers134,4948
Non-polymers00
Water16,087893
1
A: Nanobody694

F: S-layer protein sap


Theoretical massNumber of molelcules
Total (without water)33,6242
Polymers33,6242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_445x-1,y-1,z1
2
B: Nanobody694

G: S-layer protein sap


Theoretical massNumber of molelcules
Total (without water)33,6242
Polymers33,6242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_565x,y+1,z1
3
C: Nanobody694

H: S-layer protein sap


Theoretical massNumber of molelcules
Total (without water)33,6242
Polymers33,6242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_454x-1,y,z-11
4
D: Nanobody694

E: S-layer protein sap


Theoretical massNumber of molelcules
Total (without water)33,6242
Polymers33,6242
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Unit cell
Length a, b, c (Å)33.410, 113.970, 122.700
Angle α, β, γ (deg.)90.710, 96.010, 97.050
Int Tables number1
Space group name H-MP1
Space group name HallP1
Symmetry operation#1: x,y,z
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
d_1ens_1(chain "A" and resid 1 through 123)
d_2ens_1(chain "B" and resid 1 through 123)
d_3ens_1(chain "C" and (resid 1 through 115 or (resid 116...
d_4ens_1chain "D"
d_1ens_2(chain "E" and (resid 216 through 260 or (resid 261...
d_2ens_2(chain "F" and (resid 216 through 217 or (resid 218...
d_3ens_2(chain "G" and (resid 216 through 312 or (resid 313...
d_4ens_2(chain "H" and (resid 216 through 217 or (resid 218...

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
d_11ens_1GLNGLNSERSERAA1 - 1231 - 123
d_21ens_1GLNGLNSERSERBB1 - 1231 - 123
d_31ens_1GLNGLNSERSERCC1 - 1231 - 123
d_41ens_1GLNGLNSERSERDD1 - 1231 - 123
d_11ens_2SERSERLYSLYSEE216 - 3669 - 159
d_12ens_2GLYGLYSERSEREE369 - 381162 - 174
d_21ens_2SERSERSERSERFF216 - 3819 - 174
d_31ens_2SERSERLYSLYSGG216 - 3669 - 159
d_32ens_2GLYGLYSERSERGG369 - 381162 - 174
d_41ens_2SERSERLYSLYSHH216 - 3669 - 159
d_42ens_2GLYGLYSERSERHH369 - 381162 - 174

NCS ensembles :
ID
ens_1
ens_2

NCS oper:
IDCodeMatrixVector
1given(0.997774231779, -0.0404476833317, -0.0530147838963), (-0.0404774554862, -0.999180320562, 0.000512444704576), (-0.0529920559692, 0.00163459943384, -0.998593596058)3.68753300981, 97.2270024711, 67.789522241
2given(-0.975000520177, 0.186393274873, 0.120960872752), (0.123907879386, 0.00419868312776, 0.992284842415), (0.184447345009, 0.982466242749, -0.0271893136549)-10.5521446557, 18.7108271926, -17.5780867923
3given(-0.991537938729, 0.0920374158713, 0.0915512432502), (-0.0935926499585, -0.0181051345838, -0.995445940258), (-0.0899607244005, -0.995590939182, 0.0265659534723)-5.41526555849, 79.1533113639, 85.8821356246
4given(-0.99990810647, -0.01353224748, 0.000810489634417), (-0.00142184771906, 0.0452295663616, -0.998975607648), (0.0134817270545, -0.998884960646, -0.0452446508523)51.4810294784, 196.603973787, 82.1802489141
5given(-0.99977648515, 0.0188784982506, -0.00951746005436), (-0.0102955584457, -0.0415564643751, 0.999083110529), (0.0184656767647, 0.998957788183, 0.0417415405703)46.8811752818, -99.4981777709, -14.9881681608
6given(0.988549820064, -0.0377268985459, -0.146102479027), (-0.0379508853845, -0.999278817662, 0.00125493869862), (-0.146044457445, 0.00430414901125, -0.989268664596)-3.07076487941, 95.8355025091, 193.193828319

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Components

#1: Antibody
Nanobody694


Mass: 14528.984 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Production host: Escherichia coli (E. coli)
#2: Protein
S-layer protein sap / Surface array protein / Surface layer protein


Mass: 19094.625 Da / Num. of mol.: 4
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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 893 / Source method: isolated from a natural source / Formula: H2O
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: 3.43 Å3/Da / Density % sol: 64.11 %
Crystal growTemperature: 293.15 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: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.9786 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Dec 16, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9786 Å / Relative weight: 1
ReflectionResolution: 1.99→42 Å / Num. obs: 118902 / % possible obs: 97.5 % / Redundancy: 3.6 % / Biso Wilson estimate: 48.37 Å2 / Rpim(I) all: 0.03 / Net I/σ(I): 9.5
Reflection shellResolution: 1.99→42 Å / Num. unique obs: 10826 / Rpim(I) all: 1.53

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Processing

Software
NameVersionClassification
PHENIX1.21_5207refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→42 Å / SU ML: 0.3766 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 32.941
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2492 5944 5 %
Rwork0.2092 112958 -
obs0.2112 118902 96.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 55.35 Å2
Refinement stepCycle: LAST / Resolution: 1.99→42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8773 0 0 893 9666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00778904
X-RAY DIFFRACTIONf_angle_d1.04612065
X-RAY DIFFRACTIONf_chiral_restr0.0631427
X-RAY DIFFRACTIONf_plane_restr0.00661519
X-RAY DIFFRACTIONf_dihedral_angle_d17.52583203
Refine LS restraints NCS
Ens-IDDom-IDAsym-IDAuth asym-IDRefine-IDTypeRms dev position (Å)
ens_1d_2AAX-RAY DIFFRACTIONTorsion NCS0.638328490135
ens_1d_3AAX-RAY DIFFRACTIONTorsion NCS0.555507577012
ens_1d_4AAX-RAY DIFFRACTIONTorsion NCS0.633732575953
ens_2d_2EEX-RAY DIFFRACTIONTorsion NCS1.42038517011
ens_2d_3EEX-RAY DIFFRACTIONTorsion NCS1.30678757286
ens_2d_4EEX-RAY DIFFRACTIONTorsion NCS1.35321193236
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.99-2.010.56161360.51942637X-RAY DIFFRACTION67.87
2.01-2.040.47841970.44873720X-RAY DIFFRACTION96.08
2.04-2.060.40991990.43283772X-RAY DIFFRACTION96.76
2.06-2.090.48852040.41043888X-RAY DIFFRACTION96.99
2.09-2.110.41291970.37053726X-RAY DIFFRACTION96.89
2.11-2.140.4041940.34883693X-RAY DIFFRACTION97.39
2.14-2.170.34891990.33313785X-RAY DIFFRACTION97.36
2.17-2.210.4082030.32583843X-RAY DIFFRACTION97.4
2.21-2.240.34092010.30663821X-RAY DIFFRACTION97.5
2.24-2.280.31751960.28723717X-RAY DIFFRACTION97.51
2.28-2.320.32191980.28983768X-RAY DIFFRACTION97.47
2.32-2.360.32582020.28123836X-RAY DIFFRACTION97.89
2.36-2.40.28812010.27613808X-RAY DIFFRACTION97.66
2.4-2.450.29921970.26233751X-RAY DIFFRACTION97.6
2.45-2.510.31962010.2653817X-RAY DIFFRACTION98.02
2.51-2.560.31962030.26383869X-RAY DIFFRACTION97.74
2.56-2.630.32091960.25163725X-RAY DIFFRACTION98.07
2.63-2.70.31671990.24493786X-RAY DIFFRACTION97.94
2.7-2.780.26622080.22693952X-RAY DIFFRACTION98.39
2.78-2.870.26931950.22463706X-RAY DIFFRACTION98.16
2.87-2.970.26992010.21273835X-RAY DIFFRACTION98.27
2.97-3.090.26542020.21963832X-RAY DIFFRACTION98.49
3.09-3.230.27712010.22663807X-RAY DIFFRACTION98.21
3.23-3.40.28052010.2133830X-RAY DIFFRACTION98.27
3.4-3.610.242000.18933797X-RAY DIFFRACTION98.3
3.61-3.890.23482000.18063803X-RAY DIFFRACTION98.35
3.89-4.280.19012050.16733887X-RAY DIFFRACTION99.08
4.28-4.90.17092030.14473858X-RAY DIFFRACTION99.15
4.9-6.170.20282010.1693825X-RAY DIFFRACTION99.19
6.17-420.20612040.1823864X-RAY DIFFRACTION99.03

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