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- PDB-2gcy: humanized antibody C25 Fab fragment -

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Basic information

Entry
Database: PDB / ID: 2gcy
Titlehumanized antibody C25 Fab fragment
Components
  • huC25 fab fragment heavy chain
  • huC25 fab fragment light chain
KeywordsIMMUNE SYSTEM / antibody fragment mouse humanized
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsLaPorte, S.L. / Finer-Moore, J. / Marks, J.D. / Forsyth, C.M.
CitationJournal: To be Published
Title: Humanization and structure of antibody clone C25
Authors: LaPorte, S.L. / Finer-Moore, J. / Marks, J.D. / Forsyth, C.M.
History
DepositionMar 14, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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
Remark 999SEQUENCE THERE IS NO SUITABLE SEQUENCE DATABASE REFERENCE AT THE TIME OF PROCESSING.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: huC25 fab fragment light chain
B: huC25 fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,5396
Polymers47,1542
Non-polymers3844
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4100 Å2
ΔGint-65 kcal/mol
Surface area19400 Å2
MethodPISA
2
A: huC25 fab fragment light chain
B: huC25 fab fragment heavy chain
hetero molecules

A: huC25 fab fragment light chain
B: huC25 fab fragment heavy chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,07712
Polymers94,3094
Non-polymers7698
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_565x,x-y+1,-z+5/61
Buried area9830 Å2
ΔGint-147 kcal/mol
Surface area37160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)90.260, 90.260, 217.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Antibody huC25 fab fragment light chain


Mass: 23666.188 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: humanized mouse gene / Production host: Cricetulus griseus (Chinese hamster)
#2: Antibody huC25 fab fragment heavy chain


Mass: 23488.143 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: humanized mouse gene / Production host: Cricetulus griseus (Chinese hamster)
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.71 Å3/Da / Density % sol: 54.58 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: PEG MME 550, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.11587 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 30, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.11587 Å / Relative weight: 1
ReflectionResolution: 2.5→44.6 Å / Num. all: 17714 / Num. obs: 17714 / % possible obs: 93.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 50.1 Å2

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Processing

SoftwareName: CNS / Version: 1.1 / Classification: refinement
RefinementMethod to determine structure: SAD / Resolution: 2.5→44.6 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 183455.84 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1733 9.8 %RANDOM
Rwork0.225 ---
all0.225 17714 --
obs0.225 17714 93.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 47.4683 Å2 / ksol: 0.38839 e/Å3
Displacement parametersBiso mean: 38.9 Å2
Baniso -1Baniso -2Baniso -3
1-2.17 Å24.58 Å20 Å2
2--2.17 Å20 Å2
3----4.35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.5→44.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3318 0 20 112 3450
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_d27.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.331.5
X-RAY DIFFRACTIONc_mcangle_it2.312
X-RAY DIFFRACTIONc_scbond_it22
X-RAY DIFFRACTIONc_scangle_it32.5
LS refinement shellResolution: 2.5→2.59 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.295 163 10.1 %
Rwork0.293 1446 -
obs--87.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top
X-RAY DIFFRACTION4carbonate.paramtopo.formic
X-RAY DIFFRACTION5dtt_odt_gcl.paramdtt_odt_gcl.top

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