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- PDB-1nc4: Crystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed wit... -

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Basic information

Entry
Database: PDB / ID: 1nc4
TitleCrystal Structure of Monoclonal Antibody 2D12.5 Fab Complexed with Gd-DOTA
Components
  • (MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY ...) x 2
  • MONOCLONAL ANTIBODY 2D12.5, LAMBDA LIGHT CHAIN
KeywordsIMMUNE SYSTEM / ANTIBODY-DOTA COMPLEX / RARE EARTH / DOTA / METAL CHELATE / GADOLINIUM / GAMMA TURN / N-LINKED GLYCOSYLATION
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-DOF / GADOLINIUM ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.25 Å
AuthorsCorneillie, T.M. / Fisher, A.J. / Meares, C.F.
CitationJournal: J.Am.Chem.Soc. / Year: 2003
Title: Crystal structures of two complexes of the rare-earth-DOTA-binding antibody 2D12.5: ligand generality from a chiral system.
Authors: Corneillie, T.M. / Fisher, A.J. / Meares, C.F.
History
DepositionDec 4, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / 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 2.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.2Aug 16, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 2.3Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 999SEQUENCE AUTHORS INFORMED THAT THE SEQUENCE OF THIS PROTEIN IS NOT YET AVAILBLE IN ANY REFERENCE ...SEQUENCE AUTHORS INFORMED THAT THE SEQUENCE OF THIS PROTEIN IS NOT YET AVAILBLE IN ANY REFERENCE SEQUENCE DATABASE. Actual amino acid sequence positions are used for the atomic coordinates. Kabat numbering is used in the cited journal article. An alignment of Kabat position vs. actual amino acid sequence position is available in the supporting information that accompanies the article.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: MONOCLONAL ANTIBODY 2D12.5, LAMBDA LIGHT CHAIN
B: MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY CHAIN
C: MONOCLONAL ANTIBODY 2D12.5, LAMBDA LIGHT CHAIN
D: MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,52911
Polymers93,8434
Non-polymers1,6867
Water5,981332
1
A: MONOCLONAL ANTIBODY 2D12.5, LAMBDA LIGHT CHAIN
B: MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6455
Polymers46,9132
Non-polymers7323
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4980 Å2
ΔGint-44 kcal/mol
Surface area19590 Å2
MethodPISA
2
C: MONOCLONAL ANTIBODY 2D12.5, LAMBDA LIGHT CHAIN
D: MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8846
Polymers46,9302
Non-polymers9534
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-38 kcal/mol
Surface area19420 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.569, 82.239, 160.934
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 3 types, 4 molecules ACBD

#1: Antibody MONOCLONAL ANTIBODY 2D12.5, LAMBDA LIGHT CHAIN


Mass: 23150.602 Da / Num. of mol.: 2 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
Cell line: MYELOMA LINE PX63 AG8 FUSED WITH ANTIBODY EXPRESSING SPLEEN CELLS
Strain: BALB/c
#2: Antibody MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY CHAIN


Mass: 23762.586 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
Cell line: MYELOMA LINE PX63 AG8 FUSED WITH ANTIBODY EXPRESSING SPLEEN CELLS
Strain: BALB/c
#3: Antibody MONOCLONAL ANTIBODY 2D12.5, IGG1 GAMMA HEAVY CHAIN


Mass: 23779.615 Da / Num. of mol.: 1 / Fragment: Fab / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
Cell line: MYELOMA LINE PX63 AG8 FUSED WITH ANTIBODY EXPRESSING SPLEEN CELLS
Strain: BALB/c

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Sugars , 1 types, 1 molecules

#7: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 4 types, 338 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-DOF / (S)-2-(4-NITROBENZYL)-1,4,7,10-TETRAAZACYCLODODECANE-N,N',N'',N'''-TETRAACETATE


Mass: 539.536 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H33N5O10
#6: Chemical ChemComp-GD3 / GADOLINIUM ION


Mass: 157.250 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Gd
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.3 Å3/Da / Density % sol: 46.1 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, HEPES, sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295.0K
Crystal grow
*PLUS
Temperature: 290 K / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
1100 mMHEPES1reservoirpH7.5
218-20 %PEG80001reservoir
39.7 mg/mlFab1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: May 1, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.25→50 Å / Num. all: 39939 / Num. obs: 39939 / % possible obs: 91 % / Observed criterion σ(F): -1.7 / Observed criterion σ(I): -3 / Redundancy: 3.16 % / Biso Wilson estimate: 25 Å2 / Rmerge(I) obs: 0.089 / Net I/σ(I): 14.3
Reflection shellResolution: 2.25→2.33 Å / Redundancy: 2.95 % / Rmerge(I) obs: 0.257 / Mean I/σ(I) obs: 5.07 / Num. unique all: 3602 / % possible all: 83.4
Reflection
*PLUS
Lowest resolution: 50 Å / Num. measured all: 126214
Reflection shell
*PLUS
% possible obs: 83.4 % / Num. unique obs: 3602 / Num. measured obs: 10640

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Processing

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

1gig


Resolution: 2.25→29.39 Å / Rfactor Rfree error: 0.006 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2014 5.1 %RANDOM
Rwork0.208 ---
all0.258 39698 --
obs0.208 39698 91.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 11.7156 Å2 / ksol: 0.319542 e/Å3
Displacement parametersBiso mean: 30.6 Å2
Baniso -1Baniso -2Baniso -3
1-3.27 Å20 Å20 Å2
2--1.93 Å20 Å2
3----5.21 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.25 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.25→29.39 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6518 0 94 332 6944
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.013
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_deg1.8
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28.2
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.67
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
LS refinement shellResolution: 2.25→2.39 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.271 311 4.9 %
Rwork0.23 5997 -
obs-6308 88.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2XDOTA8_1_ONEARM.PARXDOTA8_1_ONEARM.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER_REP.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg28.2
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.67

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