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- PDB-3mck: Crystal structure of anti-beta-amyloid antibody C705 -

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Basic information

Entry
Database: PDB / ID: 3mck
TitleCrystal structure of anti-beta-amyloid antibody C705
Components
  • C705 MONOCLONAL HEAVY CHAIN
  • C705 MONOCLONAL LIGHT CHAIN
KeywordsIMMUNE SYSTEM / IMMUNOGLOBULIN FOLD / MONOCLONAL ANTIBODY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsTeplyakov, A. / Obmolova, G. / Gilliland, G.L.
CitationJournal: Proteins / Year: 2011
Title: Antibody modeling assessment.
Authors: Almagro, J.C. / Beavers, M.P. / Hernandez-Guzman, F. / Maier, J. / Shaulsky, J. / Butenhof, K. / Labute, P. / Thorsteinson, N. / Kelly, K. / Teplyakov, A. / Luo, J. / Sweet, R. / Gilliland, G.L.
History
DepositionMar 29, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 10, 2011Group: Database references
Revision 1.3Nov 2, 2011Group: Database references
Revision 1.4Sep 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 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
L: C705 MONOCLONAL LIGHT CHAIN
H: C705 MONOCLONAL HEAVY CHAIN
A: C705 MONOCLONAL LIGHT CHAIN
B: C705 MONOCLONAL HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,9826
Polymers96,8644
Non-polymers1182
Water4,504250
1
L: C705 MONOCLONAL LIGHT CHAIN
H: C705 MONOCLONAL HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4913
Polymers48,4322
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3900 Å2
ΔGint-29 kcal/mol
Surface area20310 Å2
MethodPISA
2
A: C705 MONOCLONAL LIGHT CHAIN
B: C705 MONOCLONAL HEAVY CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,4913
Polymers48,4322
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
ΔGint-31 kcal/mol
Surface area20180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)172.250, 78.250, 74.630
Angle α, β, γ (deg.)90.00, 95.45, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody C705 MONOCLONAL LIGHT CHAIN


Mass: 24117.834 Da / Num. of mol.: 2
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 C705 MONOCLONAL HEAVY CHAIN


Mass: 24314.346 Da / Num. of mol.: 2 / Fragment: FD fragment of the heavy chain
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)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / 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: 2.6 Å3/Da / Density % sol: 52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 25% PEG 8K, 0.2 M LITHIUM SULFATE, 0.1 M SODIUM ACETATE PH 4.5; CRYO CONDITIONS: MOTHER LIQUOR + 15% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944 / Detector: CCD / Date: Oct 19, 2006 / 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: 2.3→50 Å / Num. all: 42606 / Num. obs: 42606 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.8 % / Biso Wilson estimate: 52.5 Å2 / Rmerge(I) obs: 0.074 / Rsym value: 0.074 / Net I/σ(I): 12
Reflection shellResolution: 2.3→2.4 Å / Redundancy: 4.5 % / Rmerge(I) obs: 0.429 / Mean I/σ(I) obs: 2.6 / Rsym value: 0.429 / % possible all: 79.6

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Processing

Software
NameVersionClassification
CrystalCleardata collection
MOLREPphasing
REFMAC5.2.0005refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1E4X

1e4x


Resolution: 2.3→15 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.921 / SU B: 6.765 / SU ML: 0.167 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.347 / ESU R Free: 0.226 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 1328 3.1 %RANDOM
Rwork0.203 ---
all0.204 41062 --
obs0.204 41062 93.7 %-
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: 50.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.05 Å2
Refine analyzeLuzzati coordinate error obs: 0.347 Å
Refinement stepCycle: LAST / Resolution: 2.3→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6766 0 8 250 7024
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226940
X-RAY DIFFRACTIONr_angle_refined_deg1.3821.9569458
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9475886
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.02824.141256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.365151120
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9151528
X-RAY DIFFRACTIONr_chiral_restr0.090.21088
X-RAY DIFFRACTIONr_gen_planes_refined00.025168
X-RAY DIFFRACTIONr_nbd_refined0.210.22920
X-RAY DIFFRACTIONr_nbtor_refined0.3030.24585
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2388
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.276
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2340.212
X-RAY DIFFRACTIONr_mcbond_it2.28524558
X-RAY DIFFRACTIONr_mcangle_it4.24747222
X-RAY DIFFRACTIONr_scbond_it15.428202761
X-RAY DIFFRACTIONr_scangle_it20.55882236
LS refinement shellResolution: 2.3→2.358 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.304 72 -
Rwork0.27 2376 -
obs-2376 79.6 %

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