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- PDB-1ymh: anti-HCV Fab 19D9D6 complexed with protein L (PpL) mutant A66W -

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Basic information

Entry
Database: PDB / ID: 1ymh
Titleanti-HCV Fab 19D9D6 complexed with protein L (PpL) mutant A66W
Components
  • Fab 16D9D6, heavy chain
  • Fab 16D9D6, light chain
  • Protein L
KeywordsIMMUNE SYSTEM / Engineering of Crystal contacts / PpL-Fab complex
Function / homology
Function and homology information


IgG binding / immunoglobulin binding
Similarity search - Function
Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding / Protein L b1 domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Ubiquitin-like (UB roll) - #10 / GA-like domain ...Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding / Protein L b1 domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Ubiquitin-like (UB roll) - #10 / GA-like domain / GA-like domain / Immunoglobulin/albumin-binding domain superfamily / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Ubiquitin-like (UB roll) / Immunoglobulins / Roll / Immunoglobulin-like / Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesFinegoldia magna (bacteria)
Mus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsGranata, V. / Housden, N.G. / Harrison, S. / Jolivet-Reynaud, C. / Gore, M.G. / Stura, E.A.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2005
Title: Comparison of the crystallization and crystal packing of two Fab single-site mutant protein L complexes.
Authors: Granata, V. / Housden, N.G. / Harrison, S. / Jolivet-Reynaud, C. / Gore, M.G. / Stura, E.A.
History
DepositionJan 21, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0May 31, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Fab 16D9D6, light chain
B: Fab 16D9D6, heavy chain
E: Protein L
C: Fab 16D9D6, light chain
D: Fab 16D9D6, heavy chain
F: Protein L


Theoretical massNumber of molelcules
Total (without water)110,4156
Polymers110,4156
Non-polymers00
Water2,090116
1
A: Fab 16D9D6, light chain
B: Fab 16D9D6, heavy chain
E: Protein L


Theoretical massNumber of molelcules
Total (without water)55,2083
Polymers55,2083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
C: Fab 16D9D6, light chain
D: Fab 16D9D6, heavy chain
F: Protein L


Theoretical massNumber of molelcules
Total (without water)55,2083
Polymers55,2083
Non-polymers00
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)77.143, 111.469, 148.698
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 16D9D6, light chain


Mass: 24334.051 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma
#2: Antibody Fab 16D9D6, heavy chain


Mass: 23563.430 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / Cell line: Hybridoma
#3: Protein Protein L / / PpL


Mass: 7310.145 Da / Num. of mol.: 2 / Mutation: A866W
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna (bacteria) / Strain: ATCC 29328 / Plasmid: PKK223-3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q51918
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 2.5 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.1
Details: 9% PEG5K, 100mM Na cacodylate, pH 5.1, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.720169 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 5, 2004
RadiationMonochromator: Si / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.720169 Å / Relative weight: 1
ReflectionResolution: 2.6→88 Å / Num. all: 39989 / Num. obs: 39109 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 79.237 Å2 / Rmerge(I) obs: 0.058 / Net I/σ(I): 15
Reflection shellResolution: 2.6→2.66 Å / Redundancy: 11 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 4 / Num. unique all: 2806 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1MHH

1mhh


Resolution: 2.6→87.71 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.893 / SU B: 13.137 / SU ML: 0.283 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.71 / ESU R Free: 0.372 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.30228 1957 5 %RANDOM
Rwork0.22431 ---
all0.2284 39989 --
obs0.2284 37096 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 64.086 Å2
Baniso -1Baniso -2Baniso -3
1-0.6 Å20 Å20 Å2
2---1.19 Å20 Å2
3---0.58 Å2
Refinement stepCycle: LAST / Resolution: 2.6→87.71 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7768 0 0 116 7884
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0650.0217951
X-RAY DIFFRACTIONr_bond_other_d0.0020.026867
X-RAY DIFFRACTIONr_angle_refined_deg4.3441.9410818
X-RAY DIFFRACTIONr_angle_other_deg2.155316116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg11.6455999
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.4460.21211
X-RAY DIFFRACTIONr_gen_planes_refined0.0220.028846
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021567
X-RAY DIFFRACTIONr_nbd_refined0.3110.31972
X-RAY DIFFRACTIONr_nbd_other0.3210.38554
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.150.54887
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2540.5458
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2710.312
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3680.334
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2660.54
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.57425011
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.48238118
X-RAY DIFFRACTIONr_scbond_it4.51422940
X-RAY DIFFRACTIONr_scangle_it6.62932700
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.603→2.671 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.453 133
Rwork0.342 2754

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