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- PDB-1t04: Three dimensional structure of a humanized anti-IFN-Gamma Fab in ... -

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Basic information

Entry
Database: PDB / ID: 1t04
TitleThree dimensional structure of a humanized anti-IFN-Gamma Fab in C2 space group
Components
  • Huzaf Antibody Heavy Chain
  • Huzaf Antibody Light Chain
KeywordsIMMUNE SYSTEM / Antibody Engineering / Humanized and Chimeric Antibody / FAB / three-dimensional structure / Gamma-interferon
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsBourne, P.C. / Terzyan, S.S. / Cloud, G. / Landolfi, N.F. / Vasquez, M. / Edmundson, A.B.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2004
Title: Three-dimensional structures of a humanized anti-IFN-gamma Fab (HuZAF) in two crystal forms.
Authors: Bourne, P.C. / Terzyan, S.S. / Cloud, G. / Landolfi, N.F. / Vasquez, M. / Edmundson, A.B.
History
DepositionApr 7, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 5, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Advisory / Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_unobs_or_zero_occ_atoms / struct_conn
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id / _struct_conn.pdbx_leaving_atom_flag
Revision 2.1Aug 23, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE THERE IS NO SEQUENCE DATABASE REFERENCE FOR THIS ENTRY. THE SEQUENCE WAS DETERMINED IN THE ...SEQUENCE THERE IS NO SEQUENCE DATABASE REFERENCE FOR THIS ENTRY. THE SEQUENCE WAS DETERMINED IN THE PROTEIN DESIGN LABORATORY.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Huzaf Antibody Light Chain
B: Huzaf Antibody Heavy Chain
C: Huzaf Antibody Light Chain
D: Huzaf Antibody Heavy Chain


Theoretical massNumber of molelcules
Total (without water)93,6164
Polymers93,6164
Non-polymers00
Water84747
1
A: Huzaf Antibody Light Chain
B: Huzaf Antibody Heavy Chain


Theoretical massNumber of molelcules
Total (without water)46,8082
Polymers46,8082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3540 Å2
ΔGint-26 kcal/mol
Surface area19720 Å2
MethodPISA
2
C: Huzaf Antibody Light Chain
D: Huzaf Antibody Heavy Chain


Theoretical massNumber of molelcules
Total (without water)46,8082
Polymers46,8082
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3440 Å2
ΔGint-25 kcal/mol
Surface area19880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.274, 169.805, 72.825
Angle α, β, γ (deg.)90.00, 97.68, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody Huzaf Antibody Light Chain / FAB


Mass: 23430.879 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The source is engineered human constant and framework regions with CDRs from mouse.
Source: (gene. exp.) Homo sapiens (human) / References: UniProt: Q6GMW1
#2: Antibody Huzaf Antibody Heavy Chain


Mass: 23377.156 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The source is engineered human constant and framework regions with CDRs from mouse.
Source: (gene. exp.) Homo sapiens (human)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / Source method: isolated from a natural source / Formula: H2O

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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: 2.7 Å3/Da / Density % sol: 46 %
Crystal growTemperature: 288 K / pH: 5.6
Details: PEG8000, (NH4)2SO4, MgCl2, MES, pH 5.60, VAPOR DIFFUSION, SITTING DROP, temperature 288K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 20, 2003 / Details: OSMIC BLUE OPTICS
RadiationMonochromator: OSMIC BLUE OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3→25 Å / Num. obs: 19324 / % possible obs: 97.1 % / Observed criterion σ(I): -3 / Redundancy: 2.49 % / Biso Wilson estimate: 51.72 Å2 / Rmerge(I) obs: 0.146 / Net I/σ(I): 6.14
Reflection shellResolution: 3→3.11 Å / Rmerge(I) obs: 0.387 / Mean I/σ(I) obs: 2.27 / % possible all: 96.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1T3F

1t3f


Resolution: 3→25 Å / Isotropic thermal model: OVERALL ANISOTROPIC / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.293 868 5 %RANDOM
Rwork0.217 ---
obs0.217 17707 89.3 %-
all-19324 --
Solvent computationSolvent model: CNS / Bsol: 31.82 Å2 / ksol: 0.36 e/Å3
Displacement parametersBiso mean: 28.27 Å2
Baniso -1Baniso -2Baniso -3
1--26.184 Å20 Å2-2.438 Å2
2--17.416 Å20 Å2
3---8.767 Å2
Refinement stepCycle: LAST / Resolution: 3→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6590 0 0 47 6637
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_deg1.39
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
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
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 DIFFRACTION4PCA.PARAMPCA.TOP

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