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- PDB-2gjj: Crystal structure of a single chain antibody scA21 against Her2/ErbB2 -

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Basic information

Entry
Database: PDB / ID: 2gjj
TitleCrystal structure of a single chain antibody scA21 against Her2/ErbB2
ComponentsA21 single-chain antibody fragment against erbB2
KeywordsIMMUNE SYSTEM / Ig family / scFv
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsZhu, Z.
CitationJournal: Proteins / Year: 2007
Title: Epitope mapping and structural analysis of an anti-ErbB2 antibody A21: Molecular basis for tumor inhibitory mechanism
Authors: Hu, S. / Zhu, Z. / Li, L. / Chang, L. / Li, W. / Cheng, L. / Teng, M. / Liu, J.
History
DepositionMar 31, 2006Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 1, 2006Provider: repository / Type: Initial release
Revision 1.1Jan 7, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Aug 9, 2017Group: Advisory / Refinement description / Source and taxonomy
Category: entity_src_gen / pdbx_unobs_or_zero_occ_atoms / software
Revision 1.4Aug 16, 2017Group: Refinement description / Category: refine / refine_ls_shell
Item: _refine.ls_percent_reflns_obs / _refine_ls_shell.percent_reflns_obs
Revision 1.5Oct 18, 2017Group: Refinement description / Category: software
Revision 1.6Oct 25, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: A21 single-chain antibody fragment against erbB2
B: A21 single-chain antibody fragment against erbB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,2858
Polymers56,7322
Non-polymers5536
Water7,134396
1
A: A21 single-chain antibody fragment against erbB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,7345
Polymers28,3661
Non-polymers3684
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: A21 single-chain antibody fragment against erbB2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5503
Polymers28,3661
Non-polymers1842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)73.943, 86.630, 178.592
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11B-884-

HOH

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Components

#1: Antibody A21 single-chain antibody fragment against erbB2 / anti-p185/HER2 immunoglobulin kappa light chain variable region / anit-p185/HER2 immunoglobulin ...anti-p185/HER2 immunoglobulin kappa light chain variable region / anit-p185/HER2 immunoglobulin gamma heavy chain variable region


Mass: 28366.123 Da / Num. of mol.: 2 / Fragment: A21 fragment, residues 1-114 and 135-254
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: scA21 / Plasmid: pPIC9K / Production host: Pichia pastoris (fungus) / References: GenBank: 19698754, GenBank: 19698750
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 396 / 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: 2.52 Å3/Da / Density % sol: 51.19 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 10000, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BSRF / Beamline: 3W1A / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 16, 2005 / Details: mirrors
RadiationMonochromator: double crystal monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.1→30 Å / Num. all: 33911 / Num. obs: 33345 / % possible obs: 98.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 28 Å2 / Rmerge(I) obs: 0.069
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.401 / Mean I/σ(I) obs: 2.4 / Num. unique all: 3347 / % possible all: 99

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Processing

Software
NameVersionClassification
MAR345data collection
HKL-2000data reduction
MOLREPphasing
REFMAC5.1.24refinement
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H8N

1h8n


Resolution: 2.1→30 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: maximum likelihood refinement
RfactorNum. reflection% reflectionSelection details
Rfree0.2259 1667 -RANDOM
Rwork0.1891 ---
all0.191 33911 --
obs0.1909 33345 98.3 %-
Displacement parametersBiso mean: 28.361 Å2
Baniso -1Baniso -2Baniso -3
1-1.34 Å20 Å20 Å2
2---0.68 Å20 Å2
3----0.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.24 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.23 Å
Refinement stepCycle: LAST / Resolution: 2.1→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3621 0 36 396 4053
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_angle_refined_deg1.176
X-RAY DIFFRACTIONr_bond_refined_d0.008
X-RAY DIFFRACTIONr_chiral_restr0.073
LS refinement shellResolution: 2.1→2.154 Å / Rfactor Rfree error: 0.01
RfactorNum. reflection% reflection
Rfree0.319 131 -
Rwork0.299 --
obs-2311 96.7 %

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