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- PDB-1mh5: The Structure Of The Complex Of The Fab Fragment Of The Esterolyt... -

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Basic information

Entry
Database: PDB / ID: 1mh5
TitleThe Structure Of The Complex Of The Fab Fragment Of The Esterolytic Antibody MS6-164 and A Transition-State Analog
Components(IMMUNOGLOBULIN MS6-164) x 2
KeywordsIMMUNE SYSTEM / CATALYTIC ANTIBODY / ESTER HYDROLYSIS / ESTEROLYTIC / FAB / IMMUNOGLOBULIN
Function / homology
Function and homology information


Fc-gamma receptor I complex binding / immunoglobulin complex, circulating / IgG immunoglobulin complex / immunoglobulin receptor binding / complement activation, classical pathway / antigen binding / B cell differentiation / antibacterial humoral response / extracellular space / extracellular region / plasma membrane
Similarity search - Function
Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold ...Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-HAL / Immunoglobulin kappa constant / Ig gamma-2A chain C region, A allele
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 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 19, 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: Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
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
A: IMMUNOGLOBULIN MS6-164
B: IMMUNOGLOBULIN MS6-164
L: IMMUNOGLOBULIN MS6-164
H: IMMUNOGLOBULIN MS6-164
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,2178
Polymers98,0724
Non-polymers1,1454
Water9,314517
1
A: IMMUNOGLOBULIN MS6-164
B: IMMUNOGLOBULIN MS6-164
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6084
Polymers49,0362
Non-polymers5732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-30 kcal/mol
Surface area17540 Å2
MethodPISA
2
L: IMMUNOGLOBULIN MS6-164
H: IMMUNOGLOBULIN MS6-164
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,6084
Polymers49,0362
Non-polymers5732
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-29 kcal/mol
Surface area18050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.346, 117.104, 114.645
Angle α, β, γ (deg.)90.00, 90.14, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-285-

HOH

21A-292-

HOH

31L-215-

HOH

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Components

#1: Antibody IMMUNOGLOBULIN MS6-164


Mass: 24181.863 Da / Num. of mol.: 2 / 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) / References: UniProt: P01837*PLUS
#2: Antibody IMMUNOGLOBULIN MS6-164


Mass: 24853.977 Da / Num. of mol.: 2 / 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) / References: UniProt: P01863*PLUS
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-HAL / N-{[2-({[1-(4-CARBOXYBUTANOYL)AMINO]-2-PHENYLETHYL}-HYDROXYPHOSPHINYL)OXY]ACETYL}-2-PHENYLETHYLAMINE


Mass: 476.459 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H29N2O7P
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 517 / Source method: isolated from a natural source / Formula: H2O

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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: 2.61 Å3/Da / Density % sol: 52.9 %
Crystal growTemperature: 290 K / Method: vapor diffusion, hanging drop / pH: 3.3
Details: PEG 8000, LITIUM SULPHATE, ACETIC ACID, pH 3.3, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal grow
*PLUS
pH: 8.5 / 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: PX14.1 / Wavelength: 1.244 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 5, 2000 / Details: mirrors
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.244 Å / Relative weight: 1
ReflectionResolution: 2.1→10 Å / Num. all: 51508 / Num. obs: 51508 / % possible obs: 88.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.052 / Net I/σ(I): 18
Reflection shellResolution: 2.1→2.15 Å / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 2 / % possible all: 47.5
Reflection
*PLUS
Reflection shell
*PLUS
% possible obs: 47.5 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A3L

1a3l


Resolution: 2.1→10 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.288 2585 RANDOM
Rwork0.218 --
all-51508 -
obs-51508 -
Displacement parametersBiso mean: 54 Å2
Refinement stepCycle: LAST / Resolution: 2.1→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5966 0 76 517 6559
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009939
X-RAY DIFFRACTIONc_angle_d1.5482
X-RAY DIFFRACTIONc_mcbond_it4.8583.5
X-RAY DIFFRACTIONc_scbond_it6.6424
X-RAY DIFFRACTIONc_mcangle_it7.3014
X-RAY DIFFRACTIONc_scangle_it9.1984.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2ion.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4hap.param
Refinement
*PLUS
% reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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