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- PDB-1pg7: Murine 6A6 Fab in complex with humanized anti-Tissue Factor D3H44 Fab -

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Basic information

Entry
Database: PDB / ID: 1pg7
TitleMurine 6A6 Fab in complex with humanized anti-Tissue Factor D3H44 Fab
Components
  • (humanized antibody D3H44) x 2
  • (murine antibody 6A6 Fab fragment) x 2
KeywordsIMMUNE SYSTEM
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation ...Fc-gamma receptor I complex binding / complement-dependent cytotoxicity / IgG immunoglobulin complex / antibody-dependent cellular cytotoxicity / immunoglobulin receptor binding / immunoglobulin complex, circulating / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin complex / FCGR activation / complement activation, classical pathway / Role of phospholipids in phagocytosis / antigen binding / FCGR3A-mediated IL10 synthesis / Regulation of Complement cascade / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / blood microparticle / adaptive immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin ...: / : / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / 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
: / : / Anti-human Langerin 2G3 lambda chain / Immunoglobulin heavy constant gamma 1 / Ig gamma-2A chain C region, A allele / Ig-like domain-containing protein
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsEigenbrot, C. / Meng, Y.G. / Krishnamurthy, R. / Lipari, M.T. / Presta, L. / Devaux, B. / Wong, T. / Moran, P. / Bullens, S. / Kirchhofer, D.
CitationJournal: J.Mol.Biol. / Year: 2003
Title: Structural insight into how an anti-idiotypic antibody against D3H44 (anti-tissue factor antibody) restores normal coagulation.
Authors: Eigenbrot, C. / Meng, Y.G. / Krishnamurthy, R. / Lipari, M.T. / Presta, L. / Devaux, B. / Wong, T. / Moran, P. / Bullens, S. / Kirchhofer, D.
History
DepositionMay 27, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 26, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 5, 2014Group: Source and taxonomy
Revision 1.4Aug 16, 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 1.5Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 600HETEROGEN SOLVENT ATOMS NUMBERED 1 - 125 ARE ASSOCIATED WITH CHAINS L, H, W, AND/OR X. SOLVENT ...HETEROGEN SOLVENT ATOMS NUMBERED 1 - 125 ARE ASSOCIATED WITH CHAINS L, H, W, AND/OR X. SOLVENT ATOMS NUMBERED 601 - 749 ARE WITH CHAINS M, I, Y AND/OR Z.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: humanized antibody D3H44
I: humanized antibody D3H44
L: humanized antibody D3H44
M: humanized antibody D3H44
W: murine antibody 6A6 Fab fragment
X: murine antibody 6A6 Fab fragment
Y: murine antibody 6A6 Fab fragment
Z: murine antibody 6A6 Fab fragment


Theoretical massNumber of molelcules
Total (without water)185,7158
Polymers185,7158
Non-polymers00
Water4,936274
1
H: humanized antibody D3H44
L: humanized antibody D3H44
W: murine antibody 6A6 Fab fragment
X: murine antibody 6A6 Fab fragment


Theoretical massNumber of molelcules
Total (without water)92,8574
Polymers92,8574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9220 Å2
ΔGint-57 kcal/mol
Surface area37280 Å2
MethodPISA
2
I: humanized antibody D3H44
M: humanized antibody D3H44
Y: murine antibody 6A6 Fab fragment
Z: murine antibody 6A6 Fab fragment


Theoretical massNumber of molelcules
Total (without water)92,8574
Polymers92,8574
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9200 Å2
ΔGint-58 kcal/mol
Surface area37470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)78.890, 85.780, 92.370
Angle α, β, γ (deg.)77.48, 75.92, 63.33
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody humanized antibody D3H44


Mass: 23139.779 Da / Num. of mol.: 2 / Fragment: antigen-binding fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli) / References: GenBank: 15216020, UniProt: P01857*PLUS
#2: Antibody humanized antibody D3H44


Mass: 23419.965 Da / Num. of mol.: 2 / Fragment: antigen-binding fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Escherichia coli (E. coli) / References: GenBank: 15216022, UniProt: Q7Z3Y4*PLUS
#3: Antibody murine antibody 6A6 Fab fragment


Mass: 22481.793 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: G0YP42*PLUS
#4: Antibody murine antibody 6A6 Fab fragment


Mass: 23815.732 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: P01863*PLUS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / 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: 2.89 Å3/Da / Density % sol: 57.49 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
118 mg/mlprotein1drop
225 mMTris-HCl1droppH8.0
320 %PEG33501reservoir
4100 mMTris1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.917 Å
DetectorType: CUSTOM-MADE / Detector: CCD / Date: Dec 21, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.917 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. all: 72248 / Num. obs: 72248 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 52.4 Å2 / Rmerge(I) obs: 0.129 / Net I/σ(I): 12
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 4 % / Rmerge(I) obs: 0.477 / Num. unique all: 7157 / % possible all: 98
Reflection
*PLUS
Num. measured all: 310288
Reflection shell
*PLUS
% possible obs: 98 % / Num. unique obs: 7157 / Num. measured obs: 26775 / Mean I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
X-PLOR98.1refinement
HKL-2000data reduction
CCP4(TRUNCATE)data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1JPS, 1GIG

1jps

1gig


Resolution: 2.5→50 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0.2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.265 2174 3 %RANDOM
Rwork0.217 ---
all0.22 72089 --
obs0.217 71280 98.9 %-
Displacement parametersBiso mean: 34.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.49 Å2-3.07 Å20.05 Å2
2--1.27 Å2-0.64 Å2
3----1.76 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.38 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.42 Å0.29 Å
Refinement stepCycle: LAST / Resolution: 2.5→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13008 0 0 274 13282
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.6
X-RAY DIFFRACTIONx_dihedral_angle_d28.1
X-RAY DIFFRACTIONx_improper_angle_d1.41
X-RAY DIFFRACTIONx_mcbond_it3.82
X-RAY DIFFRACTIONx_mcangle_it52
X-RAY DIFFRACTIONx_scbond_it52
X-RAY DIFFRACTIONx_scangle_it5.92
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.028 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.402 206 2.9 %
Rwork0.332 6829 -
obs-7035 98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1MSI_XPLOR_PARHCSDX.PROMSI_XPLOR_TOPHCSDX.PRO
X-RAY DIFFRACTION2PARWAT.PROTOPWAT.PRO
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Num. reflection Rfree: 2193 / % reflection Rfree: 3 % / Rfactor Rfree: 0.267 / Rfactor Rwork: 0.219
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg28.1
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.41
LS refinement shell
*PLUS
Rfactor Rfree: 0.411 / Rfactor Rwork: 0.341

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