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- PDB-3mbx: Crystal structure of chimeric antibody X836 -

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Basic information

Entry
Database: PDB / ID: 3mbx
TitleCrystal structure of chimeric antibody X836
Components
  • X836 HEAVY CHAIN
  • X836 LIGHT CHAIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / MONOCLONAL ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsTeplyakov, A. / Obmolova, G. / Gilliland, G.L.
CitationJournal: Mol.Immunol. / Year: 2010
Title: On the domain pairing in chimeric antibodies.
Authors: Teplyakov, A. / Obmolova, G. / Carton, J.M. / Gao, W. / Zhao, Y. / Gilliland, G.L.
History
DepositionMar 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence
Category: entity_poly / pdbx_struct_mod_residue ...entity_poly / pdbx_struct_mod_residue / pdbx_struct_special_symmetry / 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 2.1Sep 6, 2023Group: Data collection / Database references ...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_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: X836 LIGHT CHAIN
H: X836 HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,4004
Polymers49,2822
Non-polymers1182
Water5,963331
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3960 Å2
ΔGint-32 kcal/mol
Surface area20260 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.930, 99.840, 125.330
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
11L-1002-

NA

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Components

#1: Antibody X836 LIGHT CHAIN


Mass: 24518.090 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
Cell (production host): Human embryonic kidney (HEK) 293 cells
Production host: Homo sapiens (human)
#2: Antibody X836 HEAVY CHAIN


Mass: 24763.795 Da / Num. of mol.: 1
Fragment: CHIMERIC MOLECULE OF MOUSE VARIABLE DOMAIN AND HUMAN CONSTANT DOMAIN, FD fragment
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens
Cell (production host): Human embryonic kidney (HEK) 293 cells
Production host: Homo sapiens (human)
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 331 / 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: 2.76 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 0.1 M PHOSPHATE-CITRATE PH 4.2, 0.2 M SODIUM CHLORIDE, 10% PEG 3350; CRYO CONDITIONS: MOTHER LIQUOR + 20% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 118 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Jun 28, 2007 / Details: VARIMAX HF
RadiationMonochromator: NONE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→43.5 Å / Num. all: 69807 / Num. obs: 69807 / % possible obs: 96.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 12.6
Reflection shellResolution: 1.6→1.66 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 3 / Num. unique all: 6545 / % possible all: 91.8

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0005refinement
d*TREK9.6Ldata reduction
d*TREK9.6Ldata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1Q9Q

1q9q
PDB Unreleased entry


Resolution: 1.6→15 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.622 / SU ML: 0.058 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.092 / ESU R Free: 0.089 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.23204 2111 3 %RANDOM
Rwork0.20993 ---
all0.21062 67553 --
obs0.21062 67553 93.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 28.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.35 Å20 Å2
3----0.42 Å2
Refine analyzeLuzzati coordinate error obs: 0.09 Å
Refinement stepCycle: LAST / Resolution: 1.6→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3468 0 6 331 3805
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0223608
X-RAY DIFFRACTIONr_angle_refined_deg1.4111.9454922
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3345455
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.28224.196143
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.82315577
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2041512
X-RAY DIFFRACTIONr_chiral_restr0.1010.2545
X-RAY DIFFRACTIONr_gen_planes_refined00.022721
X-RAY DIFFRACTIONr_nbd_refined0.1940.21489
X-RAY DIFFRACTIONr_nbtor_refined0.3010.22470
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1030.2294
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2150.251
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0990.219
X-RAY DIFFRACTIONr_mcbond_it3.61222263
X-RAY DIFFRACTIONr_mcangle_it5.56243680
X-RAY DIFFRACTIONr_scbond_it29.696881422
X-RAY DIFFRACTIONr_scangle_it32.981881240
LS refinement shellResolution: 1.6→1.641 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 151 -
Rwork0.274 4603 -
obs--91.8 %

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