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- PDB-5ihz: Crystal structure of anti-gliadin 1002-1E01 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 5ihz
TitleCrystal structure of anti-gliadin 1002-1E01 Fab fragment
Components
  • 1E01 Fab fragment heavy chain
  • 1E01 Fab fragment light chain
KeywordsIMMUNE SYSTEM / anti-gliadin antibody / celiac disease
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.64 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 1, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 15, 2017Provider: repository / Type: Initial release
Revision 1.1Oct 4, 2017Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
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 / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 6, 2017Group: Database references / Structure summary / Category: audit_author / citation_author
Revision 1.3Nov 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 1.4Nov 6, 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
A: 1E01 Fab fragment heavy chain
B: 1E01 Fab fragment light chain
C: 1E01 Fab fragment heavy chain
D: 1E01 Fab fragment light chain
E: 1E01 Fab fragment heavy chain
F: 1E01 Fab fragment light chain
H: 1E01 Fab fragment heavy chain
L: 1E01 Fab fragment light chain


Theoretical massNumber of molelcules
Total (without water)187,0728
Polymers187,0728
Non-polymers00
Water21,5101194
1
A: 1E01 Fab fragment heavy chain
B: 1E01 Fab fragment light chain


Theoretical massNumber of molelcules
Total (without water)46,7682
Polymers46,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3010 Å2
ΔGint-22 kcal/mol
Surface area18740 Å2
MethodPISA
2
C: 1E01 Fab fragment heavy chain
D: 1E01 Fab fragment light chain


Theoretical massNumber of molelcules
Total (without water)46,7682
Polymers46,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3080 Å2
ΔGint-21 kcal/mol
Surface area18950 Å2
MethodPISA
3
E: 1E01 Fab fragment heavy chain
F: 1E01 Fab fragment light chain


Theoretical massNumber of molelcules
Total (without water)46,7682
Polymers46,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-22 kcal/mol
Surface area18820 Å2
MethodPISA
4
H: 1E01 Fab fragment heavy chain
L: 1E01 Fab fragment light chain


Theoretical massNumber of molelcules
Total (without water)46,7682
Polymers46,7682
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-24 kcal/mol
Surface area19240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.270, 147.810, 95.230
Angle α, β, γ (deg.)90.00, 103.50, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
1E01 Fab fragment heavy chain


Mass: 23765.488 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#2: Antibody
1E01 Fab fragment light chain


Mass: 23002.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293F / Production host: Homo sapiens (human)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1194 / 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: 2.72 Å3/Da / Density % sol: 54.75 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 20 %w/v Polyethylene Glycol 3350, 0.200 M Potassium Sulphate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.64→92.6 Å / Num. obs: 240238 / % possible obs: 98.8 % / Redundancy: 13.9 % / Net I/σ(I): 18.3
Reflection shellResolution: 1.64→1.68 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
xia2data reduction
xia2data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4Q9Q

4q9q


Resolution: 1.64→78.472 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 24.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2285 11892 4.95 %
Rwork0.2004 --
obs0.2018 240171 98.69 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.64→78.472 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12589 0 0 1194 13783
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112893
X-RAY DIFFRACTIONf_angle_d1.27217547
X-RAY DIFFRACTIONf_dihedral_angle_d12.4267663
X-RAY DIFFRACTIONf_chiral_restr0.0791985
X-RAY DIFFRACTIONf_plane_restr0.0082225
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.64-1.65860.33553880.30677532X-RAY DIFFRACTION97
1.6586-1.67820.34373940.29957456X-RAY DIFFRACTION98
1.6782-1.69860.33314100.28767520X-RAY DIFFRACTION98
1.6986-1.72010.27953670.27037561X-RAY DIFFRACTION98
1.7201-1.74280.31473760.26157464X-RAY DIFFRACTION98
1.7428-1.76660.28044030.25267595X-RAY DIFFRACTION98
1.7666-1.79190.28883870.26867459X-RAY DIFFRACTION98
1.7919-1.81860.3173820.2577578X-RAY DIFFRACTION98
1.8186-1.8470.26194150.23867541X-RAY DIFFRACTION98
1.847-1.87730.2764010.23227530X-RAY DIFFRACTION98
1.8773-1.90970.26114180.2247572X-RAY DIFFRACTION98
1.9097-1.94440.26764160.21527512X-RAY DIFFRACTION98
1.9444-1.98180.26233860.21597592X-RAY DIFFRACTION98
1.9818-2.02230.24733860.21297607X-RAY DIFFRACTION99
2.0223-2.06630.254110.2137590X-RAY DIFFRACTION99
2.0663-2.11430.24933770.2087638X-RAY DIFFRACTION99
2.1143-2.16720.22744010.1977588X-RAY DIFFRACTION99
2.1672-2.22580.23963900.20147595X-RAY DIFFRACTION99
2.2258-2.29130.24864140.20777613X-RAY DIFFRACTION99
2.2913-2.36530.25393720.21157680X-RAY DIFFRACTION99
2.3653-2.44980.2514000.21187608X-RAY DIFFRACTION99
2.4498-2.54790.23363870.20837711X-RAY DIFFRACTION99
2.5479-2.66390.25144080.21777664X-RAY DIFFRACTION99
2.6639-2.80430.25364040.21177682X-RAY DIFFRACTION100
2.8043-2.980.22693810.20887722X-RAY DIFFRACTION100
2.98-3.21010.22044270.20287642X-RAY DIFFRACTION100
3.2101-3.53320.20893910.19397765X-RAY DIFFRACTION100
3.5332-4.04440.20934160.18367661X-RAY DIFFRACTION100
4.0444-5.09540.17324050.15577766X-RAY DIFFRACTION100
5.0954-78.56160.20773790.18227835X-RAY DIFFRACTION100

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