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- PDB-1iqw: CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF THE MOUSE ANTI-HUMAN FAS... -

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Basic information

Entry
Database: PDB / ID: 1iqw
TitleCRYSTAL STRUCTURE OF THE FAB FRAGMENT OF THE MOUSE ANTI-HUMAN FAS ANTIBODY HFE7A
Components
  • ANTIBODY M-HFE7A, HEAVY CHAIN
  • ANTIBODY M-HFE7A, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN / FAB / ANTI_FAS / AGONISTIC ANTIBODY / APOPTOSIS
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsIto, S. / Takayama, T. / Hanzawa, H. / Ichikawa, K. / Ohsumi, J. / Serizawa, N. / Hata, T. / Haruyama, H.
Citation
Journal: J.Biochem. / 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.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: Crystallization and preliminary X-ray crystallographic studies on a Fab fragment of the mouse anti-human Fas monoclonal antibody HFE7A
Authors: Ito, S. / Takayama, T. / Hanzawa, H. / Ichikawa, K. / Ohsumi, J. / Serizawa, N. / Haruyama, H. / Hata, T.
#2: Journal: BIOSCI.BIOTECHNOL.BIOCHEM. / Year: 2000
Title: Cloning and expression of a novel murine anti-human Fas antibody
Authors: Yoshida-Kato, H. / Ichikawa, K. / Yamaguchi, J. / Watanabe, K. / Ohsumi, J. / Yonehara, S. / Serizawa, N.
#3: Journal: INT.IMMUNOL. / Year: 2000
Title: A novel murine anti-human Fas mAb which mitigates lymphadenopathy without hepatotoxicity
Authors: Ichikawa, K. / Yoshida-Kato, H. / Ohtsuki, M. / Ohsumi, J. / Yamaguchi, J. / Takahashi, S. / Tani, Y. / Watanabe, M. / Shiraishi, A. / Nishioka, K. / Yonehara, S. / Serizawa, N.
History
DepositionAug 10, 2001Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jun 20, 2018Group: Data collection / Database references / Structure summary
Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.4Oct 9, 2019Group: Data collection / Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.pdbx_database_id_DOI
Revision 1.5Dec 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 1.6Oct 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: ANTIBODY M-HFE7A, LIGHT CHAIN
H: ANTIBODY M-HFE7A, HEAVY CHAIN


Theoretical massNumber of molelcules
Total (without water)48,8062
Polymers48,8062
Non-polymers00
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-21 kcal/mol
Surface area19470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.435, 73.965, 133.773
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 ANTIBODY M-HFE7A, LIGHT CHAIN


Mass: 23919.178 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / Strain: FAS-DEFICIENT (FAS-/-)
#2: Antibody ANTIBODY M-HFE7A, HEAVY CHAIN


Mass: 24886.852 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: HYBRIDOMA / Strain: FAS-DEFICIENT (FAS-/-)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / 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: 2.2 Å3/Da / Density % sol: 44.1 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: SODIUM CITRATE, SODIUM BORATE, pH 8.50, VAPOR DIFFUSION, HANGING DROP, temperature 296.0K
Crystal grow
*PLUS
Temperature: 296 K / pH: 7.4 / Details: used seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
210 mMTris-HCl1droppH7.4
31.2 Msodium citrate1reservoir
43 %MPD1reservoir
510 mMsodium borate1reservoirpH8.5

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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: Dec 5, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→100 Å / Num. obs: 15256 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 4.6 % / Biso Wilson estimate: 23.7 Å2 / Rmerge(I) obs: 0.045 / Net I/σ(I): 32.3
Reflection shellResolution: 2.5→2.59 Å / Rmerge(I) obs: 0.092 / Mean I/σ(I) obs: 10.5 / % possible all: 97.8
Reflection
*PLUS
Num. measured all: 69732
Reflection shell
*PLUS
% possible obs: 97.8 %

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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: 2.5→40 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 10000000 / Data cutoff low absF: 0.001 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.241 1178 7.9 %RANDOM
Rwork0.168 ---
obs-14984 96.2 %-
Displacement parametersBiso mean: 24.5 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.34 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.22 Å
Refinement stepCycle: LAST / Resolution: 2.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 0 57 3399
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_deg1.3
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d30.4
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d0.62
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it3.371.5
X-RAY DIFFRACTIONx_mcangle_it4.992
X-RAY DIFFRACTIONx_scbond_it5.522
X-RAY DIFFRACTIONx_scangle_it7.512.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.022 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.306 195 8 %
Rwork0.211 2245 -
obs-2245 95.6 %
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
σ(F): 2 / Rfactor obs: 0.168
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 24.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_angle_deg1.3
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30.4
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg0.62
X-RAY DIFFRACTIONx_mcbond_it3.371.5
X-RAY DIFFRACTIONx_scbond_it5.522
X-RAY DIFFRACTIONx_mcangle_it4.992
X-RAY DIFFRACTIONx_scangle_it7.512.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.306 / % reflection Rfree: 8 % / Rfactor Rwork: 0.211 / Rfactor obs: 0.211

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