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- PDB-4h0h: Crystal structure of mimicry-recognizing 2D10 scFv with peptide -

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Basic information

Entry
Database: PDB / ID: 4h0h
TitleCrystal structure of mimicry-recognizing 2D10 scFv with peptide
Components
  • 2D10 scFv
  • peptide
KeywordsIMMUNE SYSTEM / molecular mimicry / sugar
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsTapryal, S. / Gaur, V. / Kaur, K.J. / Salunke, D.M.
CitationJournal: J.Immunol. / Year: 2013
Title: Structural evaluation of a mimicry-recognizing paratope: plasticity in antigen-antibody interactions manifests in molecular mimicry.
Authors: Tapryal, S. / Gaur, V. / Kaur, K.J. / Salunke, D.M.
History
DepositionSep 8, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 19, 2013Provider: repository / Type: Initial release
Revision 1.1Jun 26, 2013Group: Refinement description
Revision 1.2Jul 10, 2013Group: Database references
Revision 1.3Jul 17, 2019Group: Data collection / Refinement description / Category: software
Item: _software.classification / _software.name / _software.version
Revision 1.4Sep 13, 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
B: 2D10 scFv
D: peptide


Theoretical massNumber of molelcules
Total (without water)28,2602
Polymers28,2602
Non-polymers00
Water3,675204
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1090 Å2
ΔGint-8 kcal/mol
Surface area11550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.330, 80.330, 74.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121
Components on special symmetry positions
IDModelComponents
11D-101-

HOH

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Components

#1: Antibody 2D10 scFv


Mass: 26894.973 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Strain: BALB/C / Cell: B-cell / Organ: spleen / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
#2: Protein/peptide peptide


Mass: 1365.444 Da / Num. of mol.: 1 / Source method: obtained synthetically
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.47 Å3/Da / Density % sol: 50.23 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 100 mM MES, pH 6.5, 1.6 M magnesium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 16, 2008 / Details: mirrors
RadiationMonochromator: Ni filter CMF 12 38CU-6 (Osmic Inc.) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→69.568 Å / Num. all: 19310 / Num. obs: 19310 / % possible obs: 100 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 24.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.427 / Mean I/σ(I) obs: 5.5 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0102refinement
MOLREPphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
MAR345dtbdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H0I

4h0i


Resolution: 2→25.5 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.942 / SU B: 3.385 / SU ML: 0.096 / Cross valid method: THROUGHOUT / ESU R: 0.197 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THE COORDINATES FOR RESIDUES 4-9 OF CHAIN D HAVE BEEN MODELED WHILE VISUALIZING THE 2FO-FC AND FO-FC MAPS AT SIGMA CUT-OFFS OF 0.7 AND 1.6, RESPECTIVELY, WITH AN OCCUPANCY OF 0.8 AND AN ...Details: THE COORDINATES FOR RESIDUES 4-9 OF CHAIN D HAVE BEEN MODELED WHILE VISUALIZING THE 2FO-FC AND FO-FC MAPS AT SIGMA CUT-OFFS OF 0.7 AND 1.6, RESPECTIVELY, WITH AN OCCUPANCY OF 0.8 AND AN AVERAGE B-FACTOR OF 92.1. THEREFORE, HIGHER REAL SPACE R-FACTORS AND LOWER DENSITY CORRELATION ARE EXPECTED FOR THESE RESIDUES.
RfactorNum. reflection% reflectionSelection details
Rfree0.21525 1899 9.9 %RANDOM
Rwork0.19524 ---
obs0.19725 17376 99.96 %-
all-19310 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.33 Å20.17 Å20 Å2
2--0.33 Å20 Å2
3----0.5 Å2
Refinement stepCycle: LAST / Resolution: 2→25.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1914 0 0 204 2118
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0280.0221964
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8651.9552661
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.9985245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.48324.02677
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.45915319
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.046155
X-RAY DIFFRACTIONr_chiral_restr0.1680.2286
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211476
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.5751.51224
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.53821968
X-RAY DIFFRACTIONr_scbond_it3.1593740
X-RAY DIFFRACTIONr_scangle_it4.5464.5693
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.257 135 -
Rwork0.22 1262 -
obs--100 %

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