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- PDB-1k6q: Crystal structure of antibody Fab fragment D3 -

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Basic information

Entry
Database: PDB / ID: 1k6q
TitleCrystal structure of antibody Fab fragment D3
Components
  • immunoglobulin Fab D3, heavy chain
  • immunoglobulin Fab D3, light chain
KeywordsIMMUNE SYSTEM / antigen-antibody recognition / blood coagulation / tissue factor
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsFaelber, K. / Kelley, R.F. / Kirchhofer, D. / Muller, Y.A.
Citation
Journal: To be Published
Title: The crystal structure of murine Fab D3 at 2.4 A resolution in comparison with the humanised Fab D3h44 (1.85A) provides structural insight into the humanisation process of the D3 anti-tissue factor antibody
Authors: Faelber, K. / Kelley, R.F. / Kirchhofer, D. / Muller, Y.A.
#1: Journal: THROMB.HAEMOST. / Year: 2000
Title: Epitope location on tissue factor determines the anticoagulant potency of monoclonal anti-tissue factor antibodies
Authors: Kirchhofer, D. / Moran, P. / Chiang, N. / Kim, J. / Riederer, M.A. / Eigenbrot, C. / Kelley, R.F.
History
DepositionOct 17, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Apr 17, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / diffrn_source / pdbx_initial_refinement_model / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: immunoglobulin Fab D3, light chain
H: immunoglobulin Fab D3, heavy chain


Theoretical massNumber of molelcules
Total (without water)46,4462
Polymers46,4462
Non-polymers00
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3520 Å2
ΔGint-27 kcal/mol
Surface area18800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)84.17, 77.48, 75.19
Angle α, β, γ (deg.)90.00, 114.75, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody immunoglobulin Fab D3, light chain


Mass: 23121.465 Da / Num. of mol.: 1 / Fragment: Fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pEMX1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9R1A5
#2: Antibody immunoglobulin Fab D3, heavy chain


Mass: 23325.008 Da / Num. of mol.: 1 / Fragment: Fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: pEMX1 / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 48.66 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 3.6
Details: lithium sulphate, sodium acetate, pH 3.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.835 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Dec 2, 1998 / Details: mirrors
RadiationMonochromator: triangular monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.835 Å / Relative weight: 1
ReflectionResolution: 2.39→40 Å / Num. all: 16837 / Num. obs: 16837 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 40.9 Å2 / Rsym value: 0.077 / Net I/σ(I): 11.7
Reflection shellResolution: 2.39→2.58 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 4.4 / Num. unique all: 3144 / Rsym value: 0.239 / % possible all: 84.5

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
AMoREphasing
CNS1refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: humanised Fab D3h44

Resolution: 2.4→19.6 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.298 1214 7.22 %RANDOM
Rwork0.225 ---
all-16820 --
obs-16820 97.6 %-
Displacement parametersBiso mean: 51.4 Å2
Baniso -1Baniso -2Baniso -3
1-6.54 Å20 Å2-8.02 Å2
2---1.46 Å20 Å2
3----5.51 Å2
Refinement stepCycle: LAST / Resolution: 2.4→19.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3200 0 0 175 3375
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.011
X-RAY DIFFRACTIONc_angle_deg1.68
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.029
RfactorNum. reflection% reflection
Rfree0.413 203 -
Rwork0.318 --
obs-2650 93.6 %

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