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- PDB-1mj8: High Resolution Crystal Structure Of The Fab Fragment of The Este... -

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Basic information

Entry
Database: PDB / ID: 1mj8
TitleHigh Resolution Crystal Structure Of The Fab Fragment of The Esterolytic Antibody MS6-126
Components(IMMUNOGLOBULIN MS6-126) x 2
KeywordsIMMUNE SYSTEM / CATALYTIC ANTIBODY / ESTER HYDROLYSIS / ESTEROLYTIC / FAB / IMMUNOGLOBULIN
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRuzheinikov, S.N. / Muranova, T.A. / Sedelnikova, S.E. / Partridge, L.J. / Blackburn, G.M. / Murray, I.A. / Kakinuma, H. / Takashi, N. / Shimazaki, K. / Sun, J. ...Ruzheinikov, S.N. / Muranova, T.A. / Sedelnikova, S.E. / Partridge, L.J. / Blackburn, G.M. / Murray, I.A. / Kakinuma, H. / Takashi, N. / Shimazaki, K. / Sun, J. / Nishi, Y. / Rice, D.W.
Citation
Journal: J.Mol.Biol. / Year: 2003
Title: High-resolution crystal structure of the Fab-fragments of a family of mouse catalytic antibodies with esterase activity
Authors: Ruzheinikov, S.N. / Muranova, T.A. / Sedelnikova, S.E. / Partridge, L.J. / Blackburn, G.M. / Murray, I.A. / Kakinuma, H. / Takashi, N. / Shimazaki, K. / Sun, J. / Nishi, Y. / Rice, D.W.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: The preparation and crystallization of Fab fragments of a family of mouse esterolytic catalytic antibodies and their complexes with a transition-state analogue
Authors: Muranova, T.A. / Ruzheinikov, S.N. / Sedelnikova, S.E. / Moir, A. / Partridge, L.J. / Kakinuma, H. / Takashi, N. / Shimazaki, K. / Sun, J. / Nishi, Y. / Rice, D.W.
History
DepositionAug 27, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 23, 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 1.3Oct 30, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_remark / pdbx_entry_details / pdbx_initial_refinement_model / pdbx_modification_feature / pdbx_validate_close_contact / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_remark.text / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence an appropriate sequence database reference was not available at the time of processing.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: IMMUNOGLOBULIN MS6-126
H: IMMUNOGLOBULIN MS6-126
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,5519
Polymers48,8922
Non-polymers6597
Water11,764653
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5570 Å2
ΔGint-62 kcal/mol
Surface area19600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.020, 138.284, 45.186
Angle α, β, γ (deg.)90.00, 106.11, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody IMMUNOGLOBULIN MS6-126


Mass: 24205.926 Da / Num. of mol.: 1 / Fragment: Fab Fragment, LIGHT CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: fusing of mouse splenocytes with myeloma cell / Cell line: hybridoma / Production host: Mus musculus (house mouse)
#2: Antibody IMMUNOGLOBULIN MS6-126


Mass: 24685.738 Da / Num. of mol.: 1 / Fragment: Fab Fragment, HEAVY CHAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Description: fusing of mouse splenocytes with myeloma cell / Cell line: hybridoma / Production host: Mus musculus (house mouse)
#3: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: PO4
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 653 / 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: 2.27 Å3/Da / Density % sol: 45.85 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: Ammonium phosphate, Tris-HCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
130 %(w/v)PEG40001reservoir
20.2 M1reservoirMgCl2
30.1 MTris-HCl1reservoirpH8.5
420 %PEG33501reservoir
50.2 Mpotassium thiocyanate1reservoirpH7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX9.6 / Wavelength: 0.87 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 6, 2000 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.87 Å / Relative weight: 1
ReflectionResolution: 1.75→10 Å / Num. all: 39166 / Num. obs: 39166 / % possible obs: 89.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.037 / Net I/σ(I): 31
Reflection shellResolution: 1.75→1.78 Å / Rmerge(I) obs: 0.183 / Mean I/σ(I) obs: 4.7 / % possible all: 58.4
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 58.4 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1mh5

1mh5


Resolution: 1.75→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.221 1960 RANDOM
Rwork0.155 --
all-39166 -
obs-39166 -
Displacement parametersBiso mean: 24.8 Å2
Refinement stepCycle: LAST / Resolution: 1.75→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 37 653 3995
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.78063
X-RAY DIFFRACTIONc_angle_d0.012513
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4gol.par
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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