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- PDB-1it9: CRYSTAL STRUCTURE OF AN ANTIGEN-BINDING FRAGMENT FROM A HUMANIZED... -

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Entry
Database: PDB / ID: 1it9
TitleCRYSTAL STRUCTURE OF AN ANTIGEN-BINDING FRAGMENT FROM A HUMANIZED VERSION OF THE ANTI-HUMAN FAS ANTIBODY HFE7A
Components
  • HUMANIZED ANTIBODY HFE7A, HEAVY CHAIN
  • HUMANIZED ANTIBODY HFE7A, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / FAB / ANTI_FAS / AGONISTIC_ANTIBODY / APOPTOSIS / ANTIBODY_HUMANIZATION
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsIto, S. / Takayama, T. / Hanzawa, H. / Takahashi, T. / Miyadai, K. / Serizawa, N. / Hata, T. / Haruyama, H.
Citation
Journal: BIOL.PHARM.BULL. / Year: 2002
Title: Humanization of the Mouse Anti-Fas Antibody HFE7A and Crystal Structure of the Humanized HFE7A Fab Fragment
Authors: Haruyama, H. / Ito, S. / Miyadai, K. / Takahashi, T. / Kawaida, R. / Takayama, T. / Hanzawa, H. / Hata, T. / Yamaguchi, J. / Yoshida-Kato, H. / Ichikawa, K. / Ohsumi, J. / Yonehara, S. / Serizawa, N.
#1: Journal: To be Published
Title: CRYSTALLIZATION AND PRELIMINARY X-RAY STUDIES OF THE FAB FRAGMENT FROM A HUMANIZED VERSION OF THE MOUSE ANTI-HUMAN FAS ANTIBODY HFE7A
Authors: Ito, S. / Takayama, T. / Hanzawa, H. / Takahashi, T. / Miyadai, K. / Serizawa, N. / Haruyama, H. / Hata, T.
#2: Journal: J.BIOCHEM.(TOKYO) / Year: 2002
Title: Crystal Structure of the Antigen-Binding Fragment of Apoptosis-Inducing Mouse Anti-Human Fas Monoclonal Antibody HFE7A
Authors: Ito, S. / Takayama, T. / Hanzawa, H. / Ichikawa, K. / Ohsumi, J. / Serizawa, N. / Hata, T. / Haruyama, H.
History
DepositionJan 11, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 25, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 25, 2019Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_description ..._entity_src_gen.gene_src_common_name / _entity_src_gen.pdbx_description / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Apr 10, 2024Group: Source and taxonomy / Category: entity_src_gen / Item: _entity_src_gen.gene_src_genus
Revision 1.6Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: HUMANIZED ANTIBODY HFE7A, LIGHT CHAIN
H: HUMANIZED ANTIBODY HFE7A, HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)47,0952
Polymers47,0952
Non-polymers00
Water1086
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-18 kcal/mol
Surface area20000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.365, 82.746, 104.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody HUMANIZED ANTIBODY HFE7A, LIGHT CHAIN


Mass: 23501.871 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species: , / Strain: , / Description: humanized mouse / Plasmid: pEE / Cell line (production host): cos-1 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q6GMV9
#2: Antibody HUMANIZED ANTIBODY HFE7A, HEAVY CHAIN


Mass: 23593.266 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Species: , / Strain: , / Description: humanized mouse / Plasmid: pEE / Cell line (production host): cos-1 / Production host: Chlorocebus aethiops (grivet) / References: UniProt: Q6PJA4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 6 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: PEG4000, SODIUM ACETATE, METHANOL, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 296K
Crystal grow
*PLUS
Temperature: 22 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 %PEG40001reservoir
20.1 Msodium acetate1reservoirpH4.6
330 %methanol1reservoir

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Data collection

DiffractionMean temperature: 296 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6B / Wavelength: 1 Å
DetectorType: WEISSENBERG / Detector: DIFFRACTOMETER / Date: Jun 29, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 12285 / % possible obs: 90.7 % / Observed criterion σ(I): 1 / Redundancy: 6.3 % / Biso Wilson estimate: 42 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 17.1
Reflection shellResolution: 2.8→2.9 Å / Rmerge(I) obs: 0.314 / Mean I/σ(I) obs: 5.4 / % possible all: 77.1
Reflection
*PLUS
Num. obs: 11136 / % possible obs: 91 % / Num. measured all: 61689 / Rmerge(I) obs: 0.078
Reflection shell
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 2.9 Å / % possible obs: 71.3 % / Num. unique obs: 927 / Num. measured obs: 3790 / Rmerge(I) obs: 0.18

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→30 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.28 1144 10.3 %RANDOM
Rwork0.202 ---
obs0.202 11089 91 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.8→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3313 0 0 6 3319
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.1
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.55
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it2.841.5
X-RAY DIFFRACTIONx_mcangle_it4.592
X-RAY DIFFRACTIONx_scbond_it4.32
X-RAY DIFFRACTIONx_scangle_it6.062.5
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.024 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.325 178 12.7 %
Rwork0.242 1399 -
obs--79.2 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: TOPHCSDX.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 30 Å / % reflection Rfree: 9 % / Rfactor Rfree: 0.28
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.55

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