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- PDB-1fh5: CRYSTAL STRUCTURE OF THE FAB FRAGMENT OF THE MONOCLONAL ANTIBODY MAK33 -

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Basic information

Entry
Database: PDB / ID: 1fh5
TitleCRYSTAL STRUCTURE OF THE FAB FRAGMENT OF THE MONOCLONAL ANTIBODY MAK33
Components(MONOCLONAL ANTIBODY MAK33) x 2
KeywordsIMMUNE SYSTEM / Fab / BiP
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.9 Å
AuthorsAugustine, J.G. / de la Calle, A. / Knarr, G. / Buchner, J. / Frederick, C.A.
CitationJournal: J.Biol.Chem. / Year: 2001
Title: The crystal structure of the fab fragment of the monoclonal antibody MAK33. Implications for folding and interaction with the chaperone bip.
Authors: Augustine, J.G. / de La Calle, A. / Knarr, G. / Buchner, J. / Frederick, C.A.
History
DepositionJul 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 13, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 26, 2014Group: Other
Revision 1.4Jan 3, 2024Group: Data collection / Database references / Source and taxonomy
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_src_nat
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_src_nat.common_name / _entity_src_nat.genus / _entity_src_nat.pdbx_ncbi_taxonomy_id / _entity_src_nat.pdbx_organism_scientific
Revision 1.5Oct 30, 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: MONOCLONAL ANTIBODY MAK33
H: MONOCLONAL ANTIBODY MAK33


Theoretical massNumber of molelcules
Total (without water)44,9352
Polymers44,9352
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-20 kcal/mol
Surface area19360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.910, 65.660, 73.460
Angle α, β, γ (deg.)109.14, 106.94, 95.91
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2generate(0.14197, -0.98933, 0.03277), (-0.98874, -0.14331, -0.04307), (0.04731, -0.02629, -0.99853)31.70477, 41.30268, 1.61292

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Components

#1: Antibody MONOCLONAL ANTIBODY MAK33


Mass: 23474.762 Da / Num. of mol.: 1 / Fragment: FAB LIGHT CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody MONOCLONAL ANTIBODY MAK33


Mass: 21460.160 Da / Num. of mol.: 1 / Fragment: FAB HEAVY CHAIN / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
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: 5.58 Å3/Da / Density % sol: 77.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: na citrate, 16% PEG 8k, 16% glycerol 1.0 M NaCl, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal
*PLUS
Density % sol: 53 %
Crystal grow
*PLUS
Temperature: 4 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
116 %(w/v)PEG80001reservoir
21.0 M1reservoirNaCl
350 mMcitrate1reservoir
416 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 277 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 8, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.9→25 Å / Num. all: 21497 / Num. obs: 20143 / % possible obs: 93.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.9 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 10
Reflection shellHighest resolution: 2.9 Å / Rmerge(I) obs: 0.279
Reflection shell
*PLUS
% possible obs: 87.1 % / Mean I/σ(I) obs: 2.5

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.9→8 Å / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber /
RfactorSelection details
Rfree0.243 Random
Rwork0.198 -
Refinement stepCycle: LAST / Resolution: 2.9→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3159 0 0 0 3159
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.9
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Num. reflection all: 18312 / % reflection Rfree: 8 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_bond_d / Dev ideal: 0.014
LS refinement shell
*PLUS
Highest resolution: 2.9 Å / Lowest resolution: 2.97 Å / Rfactor Rfree: 0.329 / Rfactor Rwork: 0.281

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