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- PDB-1jpt: Crystal Structure of Fab D3H44 -

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Basic information

Entry
Database: PDB / ID: 1jpt
TitleCrystal Structure of Fab D3H44
Components
  • immunoglobulin Fab D3H44, heavy chain
  • immunoglobulin Fab D3h44, light chain
KeywordsIMMUNE SYSTEM / antigen-antibody recognition / humanized antibody / blood coagulation
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsFaelber, K. / Kirchhofer, D. / Presta, L. / Kelley, R.F. / Muller, Y.A.
Citation
Journal: J.Mol.Biol. / Year: 2001
Title: The 1.85 A resolution crystal structures of tissue factor in complex with humanized Fab D3h44 and of free humanized Fab D3h44: revisiting the solvation of antigen combining sites.
Authors: Faelber, K. / Kirchhofer, D. / Presta, L. / Kelley, R.F. / Muller, Y.A.
#1: Journal: THROMB.HAEMOST. / Year: 2001
Title: Generation of a humanized, high affinity anti-tissue factor antibody for use as a novel antithrombotic therapeutic
Authors: Presta, L. / Sims, P. / Meng, Y.G. / Moran, P. / Bullens, S. / Bunting, S. / Schoenfeld, J. / Lowe, D. / Lai, J. / Rancatore, P. / Iverson, M. / Lim, A. / Chisholm, V. / Kelley, R.F. / ...Authors: Presta, L. / Sims, P. / Meng, Y.G. / Moran, P. / Bullens, S. / Bunting, S. / Schoenfeld, J. / Lowe, D. / Lai, J. / Rancatore, P. / Iverson, M. / Lim, A. / Chisholm, V. / Kelley, R.F. / Riederer, M. / Kirchhofer, D.
History
DepositionAug 3, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 1.4Apr 3, 2024Group: 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 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: immunoglobulin Fab D3h44, light chain
H: immunoglobulin Fab D3H44, heavy chain


Theoretical massNumber of molelcules
Total (without water)47,5672
Polymers47,5672
Non-polymers00
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-25 kcal/mol
Surface area18970 Å2
MethodPISA
Unit cell
Length a, b, c (Å)49.12, 78.20, 58.92
Angle α, β, γ (deg.)90.00, 107.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody immunoglobulin Fab D3h44, light chain


Mass: 23523.107 Da / Num. of mol.: 1 / Fragment: Fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEMX1 / Production host: Escherichia coli (E. coli)
#2: Antibody immunoglobulin Fab D3H44, heavy chain


Mass: 24043.805 Da / Num. of mol.: 1 / Fragment: Fab fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pEMX1 / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 372 / 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: 2.27 Å3/Da / Density % sol: 45.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: ammonium sulphate, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
110 mg/mlprotein1drop
220 mMTris-HCl1droppH7.5
350 mM1dropNaCl
42.0 Mammonium sulfate1reservoir
50.1 Msodium acetate1reservoirpH4.6

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.933 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 10, 1999 / Details: mirrors
RadiationMonochromator: diamond + germanium / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 1.85→40 Å / Num. all: 36063 / Num. obs: 36063 / % possible obs: 96.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.4 % / Biso Wilson estimate: 24.7 Å2 / Rsym value: 0.077 / Net I/σ(I): 11.3
Reflection shellResolution: 1.85→1.9 Å / Redundancy: 3.4 % / Mean I/σ(I) obs: 2.8 / Num. unique all: 2779 / Rsym value: 0.416 / % possible all: 91.6
Reflection
*PLUS
Lowest resolution: 40 Å / Num. measured all: 124061 / Rmerge(I) obs: 0.077
Reflection shell
*PLUS
% possible obs: 91.6 % / Rmerge(I) obs: 0.416

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Processing

Software
NameVersionClassification
MAR345data collection
XDSdata reduction
AMoREphasing
CNS1refinement
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: complex D3h44 - TF

Resolution: 1.85→40 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.228 2556 7.095 %random
Rwork0.182 ---
all-36025 --
obs-36025 99.2 %-
Displacement parametersBiso mean: 20.5 Å2
Baniso -1Baniso -2Baniso -3
1--2.901 Å20 Å22.906 Å2
2--1.535 Å20 Å2
3---1.366 Å2
Refinement stepCycle: LAST / Resolution: 1.85→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3241 0 0 372 3613
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
X-RAY DIFFRACTIONc_angle_deg1.83
LS refinement shellResolution: 1.85→1.97 Å / Rfactor Rfree error: 0.013
RfactorNum. reflection% reflection
Rfree0.27 421 -
Rwork0.242 --
obs-5980 98.6 %
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 40 Å / Num. reflection obs: 33469 / σ(F): 0 / Num. reflection Rfree: 2550 / Rfactor obs: 0.183
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 20.5 Å2
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.79
LS refinement shell
*PLUS
Rfactor Rfree: 0.27 / Rfactor Rwork: 0.242

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