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- PDB-2z4q: Crystal structure of a murine antibody FAB 528 -

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Basic information

Entry
Database: PDB / ID: 2z4q
TitleCrystal structure of a murine antibody FAB 528
Components
  • anti egfr antibody fab, heavy chain
  • anti egfr antibody fab, light chain
KeywordsIMMUNE SYSTEM
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsNakanishi, T. / Tsumoto, K. / Asano, R. / Kondo, H. / Kumagai, I.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Thermodynamic consequences of mutations in vernier zone residues of a humanized anti-human epidermal growth factor receptor murine antibody, 528
Authors: Makabe, K. / Nakanishi, T. / Tsumoto, K. / Tanaka, Y. / Kondo, H. / Umetsu, M. / Sone, Y. / Asano, R. / Kumagai, I.
History
DepositionJun 22, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 30, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 13, 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
A: anti egfr antibody fab, light chain
B: anti egfr antibody fab, heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,1375
Polymers47,8762
Non-polymers2603
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4000 Å2
ΔGint-45.8 kcal/mol
Surface area19730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)126.600, 126.600, 68.278
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number171
Space group name H-MP62

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Components

#1: Antibody anti egfr antibody fab, light chain


Mass: 24268.941 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: This protein was generated by papain digestion of IgG from hybridoma.
Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#2: Antibody anti egfr antibody fab, heavy chain


Mass: 23607.381 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: This protein was generated by papain digestion of IgG from hybridoma.
Source: (natural) Mus musculus (house mouse) / Strain: BALB/C
#3: Chemical ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cd
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 240 / 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: 3.3 Å3/Da / Density % sol: 62.7 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.1
Details: 1.4M ammonium sulfate, 0.01M cadmium chloride, 0.1M Tris-HCl, pH 7.1, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-6A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 19, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 27846 / % possible obs: 99.8 % / Redundancy: 10.7 % / Biso Wilson estimate: 26.4 Å2 / Rmerge(I) obs: 0.062
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 8 % / Rmerge(I) obs: 0.273

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data collection
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1WT5, 1E4X

1wt5

1e4x


Resolution: 2.3→19.95 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1889779.34 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.228 1389 5 %RANDOM
Rwork0.191 ---
obs0.191 27828 99.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 33.9897 Å2 / ksol: 0.367326 e/Å3
Displacement parametersBiso mean: 29.9 Å2
Baniso -1Baniso -2Baniso -3
1--4.27 Å21.19 Å20 Å2
2---4.27 Å20 Å2
3---8.53 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.19 Å
Refinement stepCycle: LAST / Resolution: 2.3→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3367 0 3 240 3610
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d27.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.82
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.351.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it2.242
X-RAY DIFFRACTIONc_scangle_it3.192.5
LS refinement shellResolution: 2.3→2.44 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.264 219 4.7 %
Rwork0.216 4395 -
obs--99.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2dna-rna_rep.paramdna-rna.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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