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- PDB-1mhh: Structure of P. magnus protein L mutant bound to a mouse Fab -

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Basic information

Entry
Database: PDB / ID: 1mhh
TitleStructure of P. magnus protein L mutant bound to a mouse Fab
Components
  • Fab, heavy chainFragment antigen-binding
  • Fab, light chainFragment antigen-binding
  • protein L domain C
KeywordsIMMUNE SYSTEM / Antibody-antigen complex / B cell superantigen / Immunoglobulin binding protein
Function / homologyUbiquitin-like (UB roll) - #10 / Ubiquitin-like (UB roll) / Immunoglobulins / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Function and homology information
Biological speciesFinegoldia magna (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsGraille, M. / Stura, E.A.
Citation
Journal: J.Biol.Chem. / Year: 2002
Title: Evidence for plasticity and structural mimicry at the immunoglobulin light chain-protein L interface
Authors: Graille, M. / Harrison, S. / Crump, M.P. / Findlow, S.C. / Housden, N.G. / Muller, B.H. / Battail-Poirot, N. / Sibai, G. / Sutton, B.J. / Taussig, M.J. / Jolivet-Reynaud, C. / Gore, M.G. / Stura, E.A.
#1: Journal: Structure / Year: 2001
Title: Complex between Peptostreptococcus Magnus Protein L and a Human Antibody Reveals Structural Convergence in the Interaction Modes of Fab Binding Modes
Authors: Graille, M. / Stura, E.A. / Housden, N.G. / Beckingham, J.A. / Bottomley, S.P. / Beale, D. / Taussig, M.J. / Sutton, B.J. / Gore, M.G. / Charbonnier, J.-B.
History
DepositionAug 20, 2002Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 14, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jan 3, 2018Group: Database references / Structure summary / Category: citation_author / struct / Item: _citation_author.name / _struct.title

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Fab, light chain
B: Fab, heavy chain
C: Fab, light chain
D: Fab, heavy chain
E: protein L domain C
F: protein L domain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,5508
Polymers109,4266
Non-polymers1242
Water13,313739
1
A: Fab, light chain
B: Fab, heavy chain
E: protein L domain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7754
Polymers54,7133
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Fab, light chain
D: Fab, heavy chain
F: protein L domain C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,7754
Polymers54,7133
Non-polymers621
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)78.486, 100.957, 149.147
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Fab, light chain / Fragment antigen-binding


Mass: 24391.102 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody Fab, heavy chain / Fragment antigen-binding


Mass: 23406.236 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Protein protein L domain C


Mass: 6915.743 Da / Num. of mol.: 2 / Mutation: D855A/Y864W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna (bacteria) / Strain: ATCC 29328 / Plasmid: pKK233-3 / Production host: Escherichia coli (E. coli) / Strain (production host): JM103
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 739 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.42 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 10%(wt/wt) MPEG 5K, 100mM sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
16 mg/mlFab1drop
216 mg/mlPpL1drop
310 %(w/w)MPEG50001reservoir
4100 mMsodium acetate1reservoirpH4.5

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONESRF ID14-210.934
SYNCHROTRONESRF ID14-420.91842
Detector
TypeIDDetectorDate
ADSC QUANTUM 41CCDFeb 18, 2001
ADSC QUANTUM 42CCDJun 4, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9341
20.918421
ReflectionResolution: 2.1→20 Å / Num. all: 69885 / Num. obs: 69723 / % possible obs: 97.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 6.77 % / Biso Wilson estimate: 38 Å2 / Rsym value: 0.067 / Net I/σ(I): 26.6
Reflection shellResolution: 2.1→2.16 Å / Redundancy: 5.86 % / Mean I/σ(I) obs: 3.5 / Num. unique all: 4986 / Rsym value: 0.417 / % possible all: 85
Reflection
*PLUS
Lowest resolution: 20 Å / Rmerge(I) obs: 0.067
Reflection shell
*PLUS
% possible obs: 85 % / Rmerge(I) obs: 0.417

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 3138 -RANDOM
Rwork0.197 ---
all-69751 --
obs-62052 89 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--9.08 Å20 Å20 Å2
2--3.596 Å20 Å2
3---5.484 Å2
Refine analyzeLuzzati coordinate error obs: 0.24 Å
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7649 0 8 739 8396
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.296
LS refinement shellResolution: 2.1→2.11 Å
RfactorNum. reflection
Rfree0.2349 54
Rwork0.2244 -
obs-971
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 2 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.3
LS refinement shell
*PLUS
Highest resolution: 2.1 Å / Rfactor Rfree: 0.236 / Rfactor Rwork: 0.223

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