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- PDB-4buh: Human IgE against the major allergen Bet v 1 - Crystal structure ... -

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Basic information

Entry
Database: PDB / ID: 4buh
TitleHuman IgE against the major allergen Bet v 1 - Crystal structure of clone M0418 scFv
ComponentsCLONE M0418 SCFV
KeywordsIMMUNE SYSTEM / ANTIBODY / ALLERGEN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / DI(HYDROXYETHYL)ETHER
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 Å
AuthorsDavies, A.M. / Levin, M. / Lilljekvist, M. / Carlsson, F. / Gould, H.J. / Sutton, B.J. / Ohlin, M.
CitationJournal: Clin.Exp.Allergy / Year: 2014
Title: Human Ige Against the Major Allergen Bet V 1 - Defining an Epitope with Limited Cross-Reactivity between Different Pr-10 Family Proteins
Authors: Levin, M. / Davies, A.M. / Lilljekvist, M. / Carlsson, F. / Gould, H.J. / Sutton, B.J. / Ohlin, M.
History
DepositionJun 20, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 20, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Jan 14, 2015Group: Other
Revision 2.0Mar 11, 2020Group: Derived calculations / Other / Polymer sequence / Category: entity_poly / pdbx_database_status / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CLONE M0418 SCFV
B: CLONE M0418 SCFV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,7857
Polymers57,4312
Non-polymers3545
Water7,368409
1
A: CLONE M0418 SCFV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9464
Polymers28,7151
Non-polymers2303
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: CLONE M0418 SCFV
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,8403
Polymers28,7151
Non-polymers1242
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)99.495, 76.420, 70.181
Angle α, β, γ (deg.)90.00, 118.07, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.51519, -0.08823, 0.85252), (-0.08966, -0.99478, -0.04878), (0.85237, -0.05131, -0.52041)
Vector: -39.0106, 16.01486, 70.77573)

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Components

#1: Antibody CLONE M0418 SCFV


Mass: 28715.406 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)
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 409 / 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: 2.05 Å3/Da / Density % sol: 39.99 % / Description: NONE
Crystal growpH: 7.5 / Details: 0.1M MES PH6.5, 25% PEG 4000, pH 7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I02 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 18, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→27.3 Å / Num. obs: 109350 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 9.1 % / Biso Wilson estimate: 12.58 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 12.6
Reflection shellResolution: 1.3→1.37 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.87 / Mean I/σ(I) obs: 3.5 / % possible all: 93.7

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSIN XIA2 PACKAGEdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2YC1

2yc1


Resolution: 1.3→27.283 Å / SU ML: 0.11 / σ(F): 0 / Phase error: 15.91 / Stereochemistry target values: ML
Details: SCFV CONSTRUCT IS NUMBERED SEQUENTIALLY.NUMBERS IN THE PUBLICATION ASSOCIATED WITH THIS ENTRY USE THE IMGT STANDARD NUMBERING SYSTEM. IN BOTH MOLECULES, TRP47 ADOPTS AN ALTERNATIVE ...Details: SCFV CONSTRUCT IS NUMBERED SEQUENTIALLY.NUMBERS IN THE PUBLICATION ASSOCIATED WITH THIS ENTRY USE THE IMGT STANDARD NUMBERING SYSTEM. IN BOTH MOLECULES, TRP47 ADOPTS AN ALTERNATIVE CONFORMATION. ONE CONFORMER AT 0.5 OCCUPANCY FORMS A HYDROGEN BOND WITH A WATER MOLECULE AT 0.5 OCCUPANCY,WHICH OCCUPIES PART OF THE SAME SPACE AS THE SECOND TRP47 CONFORMER.
RfactorNum. reflection% reflection
Rfree0.1728 5452 5 %
Rwork0.1453 --
obs0.1467 109029 95.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→27.283 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3537 0 23 409 3969
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063864
X-RAY DIFFRACTIONf_angle_d1.1695283
X-RAY DIFFRACTIONf_dihedral_angle_d11.9281429
X-RAY DIFFRACTIONf_chiral_restr0.083558
X-RAY DIFFRACTIONf_plane_restr0.006678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3-1.31480.24611770.19163363X-RAY DIFFRACTION93
1.3148-1.33020.23651780.1853370X-RAY DIFFRACTION94
1.3302-1.34650.20921750.1733316X-RAY DIFFRACTION93
1.3465-1.36350.20421790.16213399X-RAY DIFFRACTION94
1.3635-1.38140.1971760.15693340X-RAY DIFFRACTION94
1.3814-1.40040.18921780.15443405X-RAY DIFFRACTION94
1.4004-1.42040.19261770.14393366X-RAY DIFFRACTION94
1.4204-1.44160.17421790.14253377X-RAY DIFFRACTION94
1.4416-1.46410.18591790.14023414X-RAY DIFFRACTION95
1.4641-1.48810.18731780.133373X-RAY DIFFRACTION95
1.4881-1.51380.16751770.12313387X-RAY DIFFRACTION95
1.5138-1.54130.14791810.11543437X-RAY DIFFRACTION95
1.5413-1.57090.15751810.1143423X-RAY DIFFRACTION95
1.5709-1.6030.1541810.1163432X-RAY DIFFRACTION95
1.603-1.63780.16441790.11643418X-RAY DIFFRACTION96
1.6378-1.67590.18931820.11883457X-RAY DIFFRACTION96
1.6759-1.71780.15981810.1183450X-RAY DIFFRACTION96
1.7178-1.76430.15781830.123456X-RAY DIFFRACTION96
1.7643-1.81620.15111830.12043482X-RAY DIFFRACTION97
1.8162-1.87480.15341820.12233469X-RAY DIFFRACTION97
1.8748-1.94180.16431840.12593484X-RAY DIFFRACTION97
1.9418-2.01950.15561870.12343553X-RAY DIFFRACTION97
2.0195-2.11140.14381830.1263484X-RAY DIFFRACTION97
2.1114-2.22260.16561850.13543503X-RAY DIFFRACTION98
2.2226-2.36180.20991840.14563506X-RAY DIFFRACTION97
2.3618-2.54410.1631870.15453556X-RAY DIFFRACTION98
2.5441-2.79990.18571880.17523570X-RAY DIFFRACTION98
2.7999-3.20450.17531890.173570X-RAY DIFFRACTION99
3.2045-4.03520.18461880.15353587X-RAY DIFFRACTION99
4.0352-27.28920.16361910.15683630X-RAY DIFFRACTION98

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