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- PDB-5ig7: Crystal structure of anti-gliadin 1002-1E01 Fab fragment in compl... -

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Basic information

Entry
Database: PDB / ID: 5ig7
TitleCrystal structure of anti-gliadin 1002-1E01 Fab fragment in complex of peptide PLQPQQPFP
Components
  • 1E01 Fab fragment heavy chain
  • 1E01 Fab fragment light chain
  • peptide PRO-LEU-GLN-PRO-GLN-GLN-PRO-PHE-PRO
KeywordsIMMUNE SYSTEM / anti-gliadin antibody / gliadin peptide / celiac disease
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 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
DepositionFeb 27, 2016Deposition site: RCSB / 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

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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: peptide PRO-LEU-GLN-PRO-GLN-GLN-PRO-PHE-PRO
D: 1E01 Fab fragment heavy chain
E: 1E01 Fab fragment light chain
F: peptide PRO-LEU-GLN-PRO-GLN-GLN-PRO-PHE-PRO
G: 1E01 Fab fragment heavy chain
H: 1E01 Fab fragment light chain
I: peptide PRO-LEU-GLN-PRO-GLN-GLN-PRO-PHE-PRO
J: 1E01 Fab fragment heavy chain
K: 1E01 Fab fragment light chain
L: peptide PRO-LEU-GLN-PRO-GLN-GLN-PRO-PHE-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)192,33323
Polymers191,27712
Non-polymers1,05711
Water14,268792
1
A: 1E01 Fab fragment heavy chain
B: 1E01 Fab fragment light chain
C: peptide PRO-LEU-GLN-PRO-GLN-GLN-PRO-PHE-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9154
Polymers47,8193
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
D: 1E01 Fab fragment heavy chain
E: 1E01 Fab fragment light chain
F: peptide PRO-LEU-GLN-PRO-GLN-GLN-PRO-PHE-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1076
Polymers47,8193
Non-polymers2883
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
G: 1E01 Fab fragment heavy chain
H: 1E01 Fab fragment light chain
I: peptide PRO-LEU-GLN-PRO-GLN-GLN-PRO-PHE-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9154
Polymers47,8193
Non-polymers961
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
J: 1E01 Fab fragment heavy chain
K: 1E01 Fab fragment light chain
L: peptide PRO-LEU-GLN-PRO-GLN-GLN-PRO-PHE-PRO
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3969
Polymers47,8193
Non-polymers5766
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)79.900, 112.670, 104.950
Angle α, β, γ (deg.)90.00, 103.47, 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) / Production host: Escherichia coli (E. coli)
#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) / Production host: Escherichia coli (E. coli)
#3: Protein/peptide
peptide PRO-LEU-GLN-PRO-GLN-GLN-PRO-PHE-PRO


Mass: 1051.192 Da / Num. of mol.: 4 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 792 / Source method: isolated from a natural source / Formula: H2O

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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: 2.4 Å3/Da / Density % sol: 48.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.2 M ammonium sulfate, 0.1 M Tris, pH 7.5, 20 % w/v PEG 5000 MME

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I24 / Wavelength: 0.96861 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 6, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96861 Å / Relative weight: 1
ReflectionResolution: 1.97→55.87 Å / Num. obs: 127251 / % possible obs: 99.8 % / Redundancy: 6.7 % / Net I/σ(I): 11.1
Reflection shellResolution: 1.97→2.02 Å

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155)refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5IHZ

5ihz


Resolution: 1.97→55.869 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.97
RfactorNum. reflection% reflection
Rfree0.2359 6374 5.01 %
Rwork0.1896 --
obs0.1919 127204 99.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.97→55.869 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13070 0 55 792 13917
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00713442
X-RAY DIFFRACTIONf_angle_d0.92818308
X-RAY DIFFRACTIONf_dihedral_angle_d13.4997994
X-RAY DIFFRACTIONf_chiral_restr0.0572052
X-RAY DIFFRACTIONf_plane_restr0.0062324
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.97-1.99240.3642190.31383983X-RAY DIFFRACTION100
1.9924-2.01580.3612280.30393989X-RAY DIFFRACTION100
2.0158-2.04040.38862100.28973999X-RAY DIFFRACTION100
2.0404-2.06620.332140.28214019X-RAY DIFFRACTION100
2.0662-2.09340.32432080.26454034X-RAY DIFFRACTION100
2.0934-2.12210.27952080.24743993X-RAY DIFFRACTION100
2.1221-2.15240.27562450.24034026X-RAY DIFFRACTION100
2.1524-2.18460.28482170.23423985X-RAY DIFFRACTION100
2.1846-2.21870.27532080.22984037X-RAY DIFFRACTION100
2.2187-2.25510.28842070.22963981X-RAY DIFFRACTION100
2.2551-2.2940.30092000.23774054X-RAY DIFFRACTION100
2.294-2.33570.28522150.23574038X-RAY DIFFRACTION100
2.3357-2.38060.28722050.23494014X-RAY DIFFRACTION100
2.3806-2.42920.31822100.22264038X-RAY DIFFRACTION100
2.4292-2.4820.28042230.22014001X-RAY DIFFRACTION100
2.482-2.53980.27171990.21724001X-RAY DIFFRACTION100
2.5398-2.60330.26712200.21954046X-RAY DIFFRACTION100
2.6033-2.67370.27352040.20934032X-RAY DIFFRACTION100
2.6737-2.75230.30912110.21964065X-RAY DIFFRACTION100
2.7523-2.84120.26222140.21043995X-RAY DIFFRACTION100
2.8412-2.94270.27192170.21464025X-RAY DIFFRACTION100
2.9427-3.06050.26832280.21714000X-RAY DIFFRACTION100
3.0605-3.19980.27872040.20274035X-RAY DIFFRACTION100
3.1998-3.36850.22881910.18664055X-RAY DIFFRACTION100
3.3685-3.57950.22172140.17954028X-RAY DIFFRACTION100
3.5795-3.85580.19482090.16964086X-RAY DIFFRACTION100
3.8558-4.24370.19332160.13994019X-RAY DIFFRACTION100
4.2437-4.85750.16092030.12534065X-RAY DIFFRACTION100
4.8575-6.11870.17692140.14314086X-RAY DIFFRACTION100
6.1187-55.89180.17732130.174101X-RAY DIFFRACTION99
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.62730.5082-0.21912.1529-0.90870.99180.03680.05420.0435-0.1347-0.03040.10910.004-0.0551-0.00950.1730.02730.01160.2235-0.06020.1585155.093135.3225142.0533
20.5847-0.335-0.04763.6465-1.83361.61530.1154-0.04870.15610.10480.06440.5428-0.1468-0.2059-0.18130.22170.01190.01430.2812-0.09050.3496141.2493138.7455152.4439
30.7549-0.0063-0.15911.59360.82791.05050.060.03920.1372-0.0535-0.0374-0.0981-0.02620.0451-0.01460.20190.0145-0.04070.29150.03710.2647180.9154116.8696140.9829
40.7752-0.6919-0.3232.16811.47751.54130.1077-0.05510.19970.11070.0872-0.38420.04570.1352-0.19980.2171-0.0203-0.02920.25910.04010.3573194.7782111.3125150.7149
50.5897-0.5727-0.12511.53470.89751.23070.05440.0205-0.0147-0.0037-0.0317-0.0174-0.06570.0329-0.02280.1856-0.03060.03310.28250.040.1916181.0471136.7261117.349
60.8349-0.043-0.05583.27992.09552.12970.09550.21750.1233-0.46660.2164-0.3955-0.32960.3858-0.29030.324-0.03260.07420.45220.04960.2937194.947142.0792107.548
70.276-0.25850.00821.7483-0.91350.80920.02730.10690.03040.0165-0.04140.02420.003-0.0111-0.01070.2270.0034-0.03810.3707-0.05220.2312154.7976118.3758115.9305
80.63711.1396-0.36413.6641-1.68171.0775-0.05910.27150.1189-0.2490.26090.33460.106-0.1393-0.21110.23020.0366-0.03380.4113-0.03840.2531141.0833114.757105.7097
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resseq 1:220)
2X-RAY DIFFRACTION2(chain B and resseq 1:213)
3X-RAY DIFFRACTION3(chain D and resseq 1:221)
4X-RAY DIFFRACTION4(chain E and resseq 1:213)
5X-RAY DIFFRACTION5(chain G and resseq 1:220)
6X-RAY DIFFRACTION6(chain H and resseq 1:213)
7X-RAY DIFFRACTION7(chain J and resseq 1:221)
8X-RAY DIFFRACTION8(chain K and resseq 1:213)

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