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- PDB-7kpj: Crystal structure of Ruminococcus gnavus immunoglobulin binding p... -

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Basic information

Entry
Database: PDB / ID: 7kpj
TitleCrystal structure of Ruminococcus gnavus immunoglobulin binding protein in complex with 338E6 Fab
Components
  • 338E6 Fab heavy chain
  • 338E6 Fab light chain kappa
  • GRAM_POS_ANCHORING domain-containing protein
KeywordsIMMUNE SYSTEM / superantigen / immunoglobulin binding protein / immunoglobulin complex
Function / homologycell wall / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / membrane => GO:0016020 / extracellular region / GRAM_POS_ANCHORING domain-containing protein
Function and homology information
Biological speciesMus musculus (house mouse)
Ruminococcus gnavus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBorowska, M.T. / Adams, E.J.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI147954 United States
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)AI115471 United States
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2021
Title: The molecular characterization of antibody binding to a superantigen-like protein from a commensal microbe.
Authors: Borowska, M.T. / Drees, C. / Yarawsky, A.E. / Viswanathan, M. / Ryan, S.M. / Bunker, J.J. / Herr, A.B. / Bendelac, A. / Adams, E.J.
History
DepositionNov 11, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2022Provider: repository / Type: Initial release
Revision 1.1Oct 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
B: 338E6 Fab light chain kappa
E: GRAM_POS_ANCHORING domain-containing protein
F: GRAM_POS_ANCHORING domain-containing protein
A: 338E6 Fab heavy chain
C: 338E6 Fab heavy chain
D: 338E6 Fab light chain kappa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)156,1438
Polymers156,0626
Non-polymers802
Water4,918273
1
B: 338E6 Fab light chain kappa
E: GRAM_POS_ANCHORING domain-containing protein
A: 338E6 Fab heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0714
Polymers78,0313
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
F: GRAM_POS_ANCHORING domain-containing protein
C: 338E6 Fab heavy chain
D: 338E6 Fab light chain kappa
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,0714
Polymers78,0313
Non-polymers401
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.240, 102.191, 118.280
Angle α, β, γ (deg.)90.000, 102.050, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody 338E6 Fab light chain kappa


Mass: 23472.873 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#2: Protein GRAM_POS_ANCHORING domain-containing protein / Immunoglobulin binding protein A


Mass: 30495.400 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus gnavus (bacteria) / Gene: CDL27_16280 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A2N5NGA8
#3: Antibody 338E6 Fab heavy chain


Mass: 24062.938 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Trichoplusia ni (cabbage looper)
#4: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 273 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.23 Å3/Da / Density % sol: 61.9 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 0.2 M calcium chloride, 18% PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.9791 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 9, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.1→83.36 Å / Num. obs: 115284 / % possible obs: 99.1 % / Redundancy: 33.4 % / CC1/2: 0.971 / CC star: 0.993 / Net I/σ(I): 21.03
Reflection shellResolution: 2.1→2.177 Å / Redundancy: 32.5 % / Num. unique obs: 11391 / CC1/2: 0.307 / CC star: 0.686 / % possible all: 98.16

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHENIX1.18.2_3874refinement
PDB_EXTRACT3.27data extraction
iMOSFLMdata reduction
PHASERphasing
BUCCANEERmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1dee

1dee


Resolution: 2.1→83.36 Å / SU ML: 0.35 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.11 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.266 1997 1.75 %
Rwork0.2293 112346 -
obs0.2299 114343 99.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 116.59 Å2 / Biso mean: 48.7058 Å2 / Biso min: 19.89 Å2
Refinement stepCycle: final / Resolution: 2.1→83.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9724 0 2 273 9999
Biso mean--41.6 39.36 -
Num. residues----1265
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0089927
X-RAY DIFFRACTIONf_angle_d0.99213495
X-RAY DIFFRACTIONf_dihedral_angle_d22.5333557
X-RAY DIFFRACTIONf_chiral_restr0.061532
X-RAY DIFFRACTIONf_plane_restr0.0071739
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1-2.150.38671400.3577885802598
2.15-2.210.4091430.33688007815099
2.21-2.280.35681400.33857917805799
2.28-2.350.34211420.30057971811399
2.35-2.440.30641420.29278039818199
2.44-2.530.31331420.27787969811199
2.53-2.650.29581440.270680708214100
2.65-2.790.31911420.2588012815499
2.79-2.960.3151420.25618024816699
2.96-3.190.29761440.242180518195100
3.19-3.510.24891430.22438056819999
3.51-4.020.23771430.19888038818199
4.02-5.070.20871440.165181038247100
5.07-83.360.20651460.19128204835099
Refinement TLS params.Method: refined / Origin x: -2.8509 Å / Origin y: -20.9307 Å / Origin z: -34.2326 Å
111213212223313233
T0.4119 Å20.0004 Å20.0376 Å2-0.3638 Å20.0155 Å2--0.366 Å2
L-0.012 °2-0.0418 °20.1002 °2-0.0077 °20.0312 °2--0.0618 °2
S0.0235 Å °0.1081 Å °-0.0146 Å °-0.1709 Å °-0.0228 Å °-0.1332 Å °-0.0446 Å °0.0796 Å °0.0037 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1allB1 - 213
2X-RAY DIFFRACTION1allE7 - 224
3X-RAY DIFFRACTION1allF9 - 223
4X-RAY DIFFRACTION1allA1 - 217
5X-RAY DIFFRACTION1allC1 - 216
6X-RAY DIFFRACTION1allD1 - 210
7X-RAY DIFFRACTION1allS2 - 539
8X-RAY DIFFRACTION1allG1 - 2

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