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- PDB-2jb5: Fab fragment in complex with small molecule hapten, crystal form-1 -

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Basic information

Entry
Database: PDB / ID: 2jb5
TitleFab fragment in complex with small molecule hapten, crystal form-1
Components
  • FAB FRAGMENT MOR03268 HEAVY CHAIN
  • FAB FRAGMENT MOR03268 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / CDR / TSC / FAB / HUCAL / FLUORESCENT DYE / IMMUNOGLOBULIN DOMAIN / ANTIBODY FRAGMENT / DIAGNOSTIC IMAGING
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin mediated immune response ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / IgG immunoglobulin complex / immunoglobulin mediated immune response / FCGR activation / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / Potential therapeutics for SARS / adaptive immune response / extracellular space / extracellular exosome / 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 / Immunoglobulins / 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 / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-T5C / Immunoglobulin lambda constant 3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsHillig, R.C. / Baesler, S. / Malawski, G. / Badock, V. / Bahr, I. / Schirner, M. / Licha, K.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Fab Mor03268 Triggers Absorption Shift of a Diagnostic Dye Via Packaging in a Solvent-Shielded Fab Dimer Interface
Authors: Hillig, R.C. / Urlinger, S. / Fanghanel, J. / Brocks, B. / Haenel, C. / Stark, Y. / Sulzle, D. / Svergun, D.I. / Baesler, S. / Malawski, G. / Moosmayer, D. / Menrad, A. / Schirner, M. / Licha, K.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: Crystallization and Molecular-Replacement Solution of a Diagnostic Fluorescent Dye in Complex with a Specific Fab Fragment.
Authors: Hillig, R.C. / Baesler, S. / Urlinger, S. / Stark, Y. / Bauer, S. / Badock, V. / Huber, M. / Bahr, I. / Schirner, M. / Licha, K.
History
DepositionDec 3, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 8, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: 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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: FAB FRAGMENT MOR03268 HEAVY CHAIN
L: FAB FRAGMENT MOR03268 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,8553
Polymers49,0832
Non-polymers7721
Water84747
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4040 Å2
ΔGint-30.7 kcal/mol
Surface area23370 Å2
MethodPQS
Unit cell
Length a, b, c (Å)71.949, 98.480, 153.782
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Antibody FAB FRAGMENT MOR03268 HEAVY CHAIN


Mass: 26328.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: IN VITRO SELECTED FROM A LIBRARY AND OPTIMIZED IN SEVERAL MATURATION STEPS
Production host: ESCHERICHIA COLI (E. coli)
#2: Antibody FAB FRAGMENT MOR03268 LIGHT CHAIN


Mass: 22754.982 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human)
Description: IN VITRO SELECTED FROM A LIBRARY AND OPTIMIZED IN SEVERAL MATURATION STEPS
Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P0DOY3*PLUS
#3: Chemical ChemComp-T5C / 2-{(1E,3Z,5E,7E)-7-[3,3-DIMETHYL-5-SULFO-1-(2-SULFOETHYL)-1,3-DIHYDRO-2H-INDOL-2-YLIDENE]-4-METHYLHEPTA-1,3,5-TRIEN-1-YL}-3,3-DIMETHYL-5-SULFO-1-(2-SULFOETHYL)-3H-INDOLIUM / TETRASULFOCYANINE


Mass: 771.918 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H39N2O12S4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsHEAVY CHAIN HAS A C-TERMINAL MYC-HIS6 TAG FAB FRAGMENT SELECTED IN VITRO FROM A LIBRARY, AND ...HEAVY CHAIN HAS A C-TERMINAL MYC-HIS6 TAG FAB FRAGMENT SELECTED IN VITRO FROM A LIBRARY, AND OPTIMIZED FURTHER BY MATURATION STEPS.

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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: 2.8 Å3/Da / Density % sol: 56 % / Description: NONE
Crystal growpH: 4
Details: 2.3M AMMONIUM SULPHATE, 5% PEG400, 0.1M SODIUM CITRATE PH 4.0, FOR CRYO BUFFER ADITIONAL 15% GLYCEROL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 30, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 2.8→41.7 Å / Num. obs: 13432 / % possible obs: 97.6 % / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 61.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.1
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 2.2 / % possible all: 79.8

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Processing

Software
NameVersionClassification
CNX2005refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VGE

1vge


Resolution: 2.8→41.7 Å / Rfactor Rfree error: 0.011 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE LIGAND TSC IS PARTIALLY DISORDERED. THEREFORE ONLY A FRAGMENT WAS MODELLED. H222-244 REPRESENTS A C-TERMINAL MYC- AND HIS-6 TAG
RfactorNum. reflection% reflectionSelection details
Rfree0.2715 656 4.7 %RANDOM
Rwork0.2112 ---
obs-13432 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.9918 Å2 / ksol: 0.34733 e/Å3
Displacement parametersBiso mean: 51 Å2
Baniso -1Baniso -2Baniso -3
1--0.012 Å20 Å20 Å2
2---0.077 Å20 Å2
3---0.089 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.52 Å0.43 Å
Refinement stepCycle: LAST / Resolution: 2.8→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3191 0 30 47 3268
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d26.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.91
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.092
X-RAY DIFFRACTIONc_mcangle_it3.533
X-RAY DIFFRACTIONc_scbond_it5.534.5
X-RAY DIFFRACTIONc_scangle_it7.356
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.056 / Total num. of bins used: 10 /
Rfactor% reflection
Rfree0.396 4.7 %
Rwork0.352 -
obs-79 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: LIG_FULL_LINKER.TOP

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