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- PDB-1wt5: The Crystal Structure Of A Humanized Antibody Fv 528 -

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Basic information

Entry
Database: PDB / ID: 1wt5
TitleThe Crystal Structure Of A Humanized Antibody Fv 528
Components(ANTI EGFR ANTIBODY FV REGION) x 2
KeywordsIMMUNE SYSTEM / HUMANIZED ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsMakabe, K. / 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
DepositionNov 16, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 16, 2005Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: ANTI EGFR ANTIBODY FV REGION
B: ANTI EGFR ANTIBODY FV REGION
C: ANTI EGFR ANTIBODY FV REGION
D: ANTI EGFR ANTIBODY FV REGION


Theoretical massNumber of molelcules
Total (without water)55,2544
Polymers55,2544
Non-polymers00
Water2,342130
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: ANTI EGFR ANTIBODY FV REGION
C: ANTI EGFR ANTIBODY FV REGION


Theoretical massNumber of molelcules
Total (without water)27,6272
Polymers27,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1470 Å2
ΔGint-12.6 kcal/mol
Surface area10200 Å2
MethodPISA
3
B: ANTI EGFR ANTIBODY FV REGION
D: ANTI EGFR ANTIBODY FV REGION


Theoretical massNumber of molelcules
Total (without water)27,6272
Polymers27,6272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
ΔGint-12.5 kcal/mol
Surface area10270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.282, 63.282, 225.339
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Antibody ANTI EGFR ANTIBODY FV REGION


Mass: 14162.790 Da / Num. of mol.: 2 / Fragment: VH fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#2: Antibody ANTI EGFR ANTIBODY FV REGION


Mass: 13464.060 Da / Num. of mol.: 2 / Fragment: VL fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 130 / 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

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Sample preparation

CrystalDensity Matthews: 2.6 Å3/Da / Density % sol: 52.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: NaCl, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 0.978 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 14, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.0695→49.3865 Å / Num. all: 30360 / Num. obs: 30360 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.2 % / Biso Wilson estimate: 29.8 Å2 / Rmerge(I) obs: 0.063 / Rsym value: 0.061 / Net I/σ(I): 8.1
Reflection shellResolution: 2.07→2.18 Å / Redundancy: 11.3 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 3.8 / Num. unique all: 4392 / Rsym value: 0.186 / % possible all: 100

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→19.97 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 1839882.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.301 1451 5 %RANDOM
Rwork0.273 ---
obs0.273 29028 98 %-
all-29634 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 50.5896 Å2 / ksol: 0.371454 e/Å3
Displacement parametersBiso mean: 47.9 Å2
Baniso -1Baniso -2Baniso -3
1-4.29 Å21.22 Å20 Å2
2--4.29 Å20 Å2
3----8.58 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.44 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.4 Å0.36 Å
Refinement stepCycle: LAST / Resolution: 2.1→19.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3514 0 0 130 3644
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_d26.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.78
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2.1→2.23 Å / Rfactor Rfree error: 0.025 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.4 248 5.1 %
Rwork0.351 4581 -
obs--97.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: PROTEIN.TOP

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