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- PDB-1e4x: crossreactive binding of a circularized peptide to an anti-TGFalp... -

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Basic information

Entry
Database: PDB / ID: 1e4x
Titlecrossreactive binding of a circularized peptide to an anti-TGFalpha antibody Fab-fragment
Components
  • (TAB2) x 3
  • CYCLIC PEPTIDE
KeywordsIMMUNE SYSTEM / COMPLEX (ANTIBODY-ANTIGEN) / CROSS-REACTIVITY / PROTEIN-PEPTIDE RECOGNITION
Function / homology
Function and homology information


B cell differentiation / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant
Similarity search - Component
Biological speciesMUS MUSCULUS (house mouse)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsHahn, M. / Winkler, D. / Misselwitz, R. / Wessner, H. / Welfle, K. / Zahn, G. / Schneider-Mergener, J. / Hoehne, W.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: Cross-Reactive Binding of Cyclic Peptides to an Anti-Tgf Alpha Antibody Fab Fragment: An X-Ray Structural and Thermodynamic Analysis
Authors: Hahn, M. / Winkler, D. / Welfle, K. / Misselwitz, R. / Welfle, H. / Wessner, H. / Zahn, G. / Scholz, C. / Seifert, M. / Harkins, R. / Schneider-Mergener, J. / Hoehne, W.
History
DepositionJul 12, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 12, 2001Provider: repository / Type: Initial release
Revision 1.1Feb 8, 2017Group: Derived calculations / Non-polymer description ...Derived calculations / Non-polymer description / Other / Source and taxonomy / Version format compliance
Revision 1.2May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: TAB2
I: TAB2
L: TAB2
M: TAB2
P: CYCLIC PEPTIDE
Q: CYCLIC PEPTIDE


Theoretical massNumber of molelcules
Total (without water)95,5206
Polymers95,5206
Non-polymers00
Water7,332407
1
H: TAB2
L: TAB2
P: CYCLIC PEPTIDE


Theoretical massNumber of molelcules
Total (without water)47,7473
Polymers47,7473
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-41.6 kcal/mol
Surface area23440 Å2
MethodPQS
2
I: TAB2
M: TAB2
Q: CYCLIC PEPTIDE


Theoretical massNumber of molelcules
Total (without water)47,7733
Polymers47,7733
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5060 Å2
ΔGint-40.5 kcal/mol
Surface area24030 Å2
MethodPQS
Unit cell
Length a, b, c (Å)173.820, 45.090, 120.410
Angle α, β, γ (deg.)90.00, 99.13, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.23405, -0.18859, -0.95376), (-0.47839, -0.87637, 0.0559), (-0.84639, 0.44318, -0.29533)
Vector: 70.50833, 13.18252, 32.89835)

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Components

#1: Antibody TAB2


Mass: 23351.205 Da / Num. of mol.: 1 / Fragment: IG KAPPA HEAVY CHAIN / Source method: isolated from a natural source / Details: MURINE FAB-FRAGMENT / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MOUSE HYBRIDOMA / Organ: SPLEEN
#2: Antibody TAB2


Mass: 23377.242 Da / Num. of mol.: 1 / Fragment: IG KAPPA HEAVY CHAIN / Source method: isolated from a natural source / Details: MURINE FAB-FRAGMENT / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MOUSE HYBRIDOMA / Organ: SPLEEN
#3: Antibody TAB2


Mass: 23577.947 Da / Num. of mol.: 2 / Fragment: IG KAPPA LIGHT CHAIN / Source method: isolated from a natural source / Details: MURINE FAB-FRAGMENT / Source: (natural) MUS MUSCULUS (house mouse) / Cell line: MOUSE HYBRIDOMA / Organ: SPLEEN / Strain: BALB/C / References: UniProt: P01837*PLUS
#4: Protein/peptide CYCLIC PEPTIDE


Mass: 817.866 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 407 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCHAIN P IS A EPITOPE PEPTIDE WITH THE SEQUENCE VAL-VAL-SER-HIS-PHE-ASN-ASP, DERIVED FROM THE N- ...CHAIN P IS A EPITOPE PEPTIDE WITH THE SEQUENCE VAL-VAL-SER-HIS-PHE-ASN-ASP, DERIVED FROM THE N-TERMINUS OF TGFALPHA. CHAIN L, M: THE C-TERMINAL REGION IS THE CONSTANT REGION OF THE IG KAPPA LIGHT CHAIN. THE N-TERMINAL REGION IS THE VARIABLE REGION OF THE IG KAPPA LIGHT CHAIN. THE VARIABLE REGION IS AUTOANTIBODY REACTIVE WITH SPECTRIN, (4-HYRDOXY-3-NITROPHENYL) ACETYL, AND FLUORESCEIN, WHICH PROMOTES CENTRAL NERVOUS SYSTEM REMYELINATION
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: 2.5 Å3/Da / Density % sol: 40.7 %
Crystal growpH: 8.5
Details: PROTEIN IN TRIS-HCL, 8.5, 6-10 MG/ML PRECIPITANT: 12% PEG 8000, 20 MM NA-ACETATE, pH 8.50
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
16-10 mg/mlprotein1drop
212 %PEG80001reservoir
320 mMsodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.3
DetectorType: XRAY RESEARCH / Detector: CCD / Date: Jun 17, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.3 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 68086 / % possible obs: 92.9 % / Redundancy: 5.2 % / Biso Wilson estimate: 22.7 Å2 / Rmerge(I) obs: 0.038 / Net I/σ(I): 29.7
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.7 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 2.4 / % possible all: 82.8
Reflection
*PLUS
Lowest resolution: 20 Å
Reflection shell
*PLUS
% possible obs: 82.8 % / Mean I/σ(I) obs: 2.2

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: TAB2

Resolution: 1.9→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.311 3427 5 %RANDOM
Rwork0.245 ---
obs-68086 94.6 %-
Displacement parametersBiso mean: 36 Å2
Refinement stepCycle: LAST / Resolution: 1.9→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6708 0 0 407 7115
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0130.02
X-RAY DIFFRACTIONp_angle_d0.0360.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.060.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.6252
X-RAY DIFFRACTIONp_mcangle_it2.4253
X-RAY DIFFRACTIONp_scbond_it1.852
X-RAY DIFFRACTIONp_scangle_it2.7053
X-RAY DIFFRACTIONp_plane_restr0.0119
X-RAY DIFFRACTIONp_chiral_restr0.1670.15
X-RAY DIFFRACTIONp_singtor_nbd0.190.3
X-RAY DIFFRACTIONp_multtor_nbd0.2450.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor7.67
X-RAY DIFFRACTIONp_staggered_tor19.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor22.820
X-RAY DIFFRACTIONp_special_tor015
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor obs: 0.245
Solvent computation
*PLUS
Displacement parameters
*PLUS

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