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- PDB-1t3f: THREE DIMENSIONAL STRUCTURE OF A HUMANIZED ANTI-IFN-GAMMA FAB (Hu... -

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Basic information

Entry
Database: PDB / ID: 1t3f
TitleTHREE DIMENSIONAL STRUCTURE OF A HUMANIZED ANTI-IFN-GAMMA FAB (HuZAF) IN P21 21 21 SPACE GROUP
Components
  • Huzaf antibody heavy chain
  • Huzaf antibody light chain
KeywordsIMMUNE SYSTEM / Antibody Engineering / Humanized and Chimeric antibody / FAB / Gamma-Interferon
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / :
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 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 26, 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: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue / 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: 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.2Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
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


Theoretical massNumber of molelcules
Total (without water)46,9112
Polymers46,9112
Non-polymers00
Water7,260403
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3690 Å2
ΔGint-30 kcal/mol
Surface area19790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.390, 74.274, 104.643
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 Huzaf antibody light chain


Mass: 23430.879 Da / Num. of mol.: 1
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: 23480.301 Da / Num. of mol.: 1
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


Mass: 18.015 Da / Num. of mol.: 403 / 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: 2.7 Å3/Da / Density % sol: 53.6 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5
Details: PEG6000, SODIUM CITRATE, pH 5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.54 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / 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: 2→30 Å / Num. obs: 30615 / % possible obs: 88.5 % / Observed criterion σ(I): -3 / Redundancy: 3 % / Biso Wilson estimate: 25.13 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 17.9
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 3.15 / Num. unique all: 1518 / % possible all: 93

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B4J

1b4j


Resolution: 2→30 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.796 / SU ML: 0.107 / Isotropic thermal model: Overall anisotropic B-factor / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.186 / ESU R Free: 0.168 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22227 1547 5.1 %RANDOM
Rwork0.17177 ---
all0.17433 ---
obs0.17433 29067 88.41 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.071 Å2
Baniso -1Baniso -2Baniso -3
1-0.05 Å20 Å20 Å2
2---0.68 Å20 Å2
3---0.64 Å2
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3299 0 0 403 3702
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0213384
X-RAY DIFFRACTIONr_bond_other_d0.0020.022909
X-RAY DIFFRACTIONr_angle_refined_deg1.5041.9494610
X-RAY DIFFRACTIONr_angle_other_deg0.84636842
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8135432
X-RAY DIFFRACTIONr_chiral_restr0.0930.2518
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.023767
X-RAY DIFFRACTIONr_gen_planes_other0.0030.02654
X-RAY DIFFRACTIONr_nbd_refined0.2090.2567
X-RAY DIFFRACTIONr_nbd_other0.2590.23381
X-RAY DIFFRACTIONr_nbtor_other0.0850.21977
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2318
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.28
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3260.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1660.219
X-RAY DIFFRACTIONr_mcbond_it0.8711.52161
X-RAY DIFFRACTIONr_mcangle_it1.61623506
X-RAY DIFFRACTIONr_scbond_it2.31731223
X-RAY DIFFRACTIONr_scangle_it3.844.51104
LS refinement shellResolution: 2.001→2.053 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.266 121
Rwork0.2 2213

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