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- PDB-5ijk: Crystal structure of anti-gliadin 1002-1E03 Fab fragment in compl... -

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Basic information

Entry
Database: PDB / ID: 5ijk
TitleCrystal structure of anti-gliadin 1002-1E03 Fab fragment in complex of peptide PLQPEQPFP
Components
  • 1E03 Fab fragment heavy chain
  • 1E03 Fab fragment light chain
  • peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO
KeywordsIMMUNE SYSTEM / anti-gliadin antibody / celiac disease
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
Triticum aestivum (bread wheat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsSnir, O. / Chen, X. / Gidoni, M. / du Pre, M.F. / Zhao, Y. / Steinsbo, O. / Lundin, K.E. / Yaari, G. / Sollid, L.M.
CitationJournal: JCI Insight / Year: 2017
Title: Stereotyped antibody responses target posttranslationally modified gluten in celiac disease.
Authors: Snir, O. / Chen, X. / Gidoni, M. / du Pre, M.F. / Zhao, Y. / Steinsbo, O. / Lundin, K.E. / Yaari, G. / Sollid, L.M.
History
DepositionMar 2, 2016Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.2Nov 22, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Dec 6, 2017Group: Structure summary / Category: audit_author
Revision 1.4Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
X: peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO
Y: peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO
A: 1E03 Fab fragment heavy chain
B: 1E03 Fab fragment heavy chain
C: 1E03 Fab fragment light chain
D: 1E03 Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,08717
Polymers99,0306
Non-polymers1,05711
Water1,00956
1
X: peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO
A: 1E03 Fab fragment heavy chain
C: 1E03 Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,9968
Polymers49,5153
Non-polymers4805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Y: peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO
B: 1E03 Fab fragment heavy chain
D: 1E03 Fab fragment light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,0929
Polymers49,5153
Non-polymers5766
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)144.639, 144.639, 106.678
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212

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Components

#1: Protein/peptide peptide PRO-LEU-GLN-PRO-GLU-GLN-PRO-PHE-PRO


Mass: 1052.177 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Triticum aestivum (bread wheat)
#2: Antibody 1E03 Fab fragment heavy chain


Mass: 24137.041 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody 1E03 Fab fragment light chain


Mass: 24326.008 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#4: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 56 / 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: 2.88 Å3/Da / Density % sol: 57.35 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: 2.256M (NH4)2SO4, 0.1M Citrate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.972 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 20, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 2.5→47.29 Å / Num. obs: 39676 / % possible obs: 99.9 % / Redundancy: 8.8 % / Net I/σ(I): 21.5
Reflection shellResolution: 2.5→2.6 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IHZ, 5IT2

5ihz

5it2


Resolution: 2.5→47.29 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 30.21
RfactorNum. reflection% reflection
Rfree0.265 1991 5.02 %
Rwork0.209 --
obs0.212 39640 99.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.5→47.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6701 0 55 56 6812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076920
X-RAY DIFFRACTIONf_angle_d1.1749439
X-RAY DIFFRACTIONf_dihedral_angle_d13.7324109
X-RAY DIFFRACTIONf_chiral_restr0.0621061
X-RAY DIFFRACTIONf_plane_restr0.0071196
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.56250.36411410.28852633X-RAY DIFFRACTION100
2.5625-2.63180.34971590.29052638X-RAY DIFFRACTION100
2.6318-2.70920.31141270.26812647X-RAY DIFFRACTION100
2.7092-2.79670.28531280.26532651X-RAY DIFFRACTION100
2.7967-2.89660.31021260.25772702X-RAY DIFFRACTION100
2.8966-3.01260.32651180.25552661X-RAY DIFFRACTION100
3.0126-3.14970.36661610.25132653X-RAY DIFFRACTION100
3.1497-3.31570.30461310.23782664X-RAY DIFFRACTION100
3.3157-3.52340.30551380.21912699X-RAY DIFFRACTION100
3.5234-3.79530.29481490.20782669X-RAY DIFFRACTION100
3.7953-4.1770.23931460.17992683X-RAY DIFFRACTION99
4.177-4.78090.20351580.16112704X-RAY DIFFRACTION100
4.7809-6.02150.21621630.17872746X-RAY DIFFRACTION100
6.0215-47.30220.24881460.20582899X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: -1.4087 Å / Origin y: -32.7301 Å / Origin z: 25.3417 Å
111213212223313233
T0.4396 Å20.0259 Å20.0714 Å2-0.3906 Å20.0603 Å2--0.4568 Å2
L0.6342 °20.0553 °2-0.2271 °2-0.312 °2-0.0072 °2--0.4122 °2
S0.0758 Å °0.1286 Å °0.2379 Å °-0.0849 Å °0.0027 Å °-0.0025 Å °-0.1165 Å °-0.0635 Å °-0.063 Å °
Refinement TLS groupSelection details: ALL

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