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- PDB-4h0g: Crystal structure of mimicry-recognizing native 2D10 scFv -

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Basic information

Entry
Database: PDB / ID: 4h0g
TitleCrystal structure of mimicry-recognizing native 2D10 scFv
Components2D10 scFv
KeywordsIMMUNE SYSTEM / molecular mimicry / antigen binding / sugar
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.1Jul 10, 2013Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 2D10 scFv
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,0172
Polymers26,8951
Non-polymers1221
Water3,171176
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)79.980, 79.980, 72.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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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: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.48 Å3/Da / Density % sol: 50.44 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 50 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: Apr 9, 2009 / 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: 2.2→35 Å / Num. all: 12529 / Num. obs: 12216 / % possible obs: 100 % / Redundancy: 14.1 % / Rmerge(I) obs: 0.077 / Net I/σ(I): 26.3
Reflection shellResolution: 2.2→2.32 Å / Redundancy: 14 % / Rmerge(I) obs: 0.597 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
MOLREPphasing
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4H0H

4h0h


Resolution: 2.3→35 Å / Occupancy max: 1 / Occupancy min: 1 / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2746 1248 10.2 %RANDOM
Rwork0.2624 10968 --
obs-12216 99.9 %-
Solvent computationBsol: 71.3332 Å2
Displacement parametersBiso max: 136.55 Å2 / Biso mean: 44.5573 Å2 / Biso min: 14.09 Å2
Baniso -1Baniso -2Baniso -3
1--0.324 Å20 Å20 Å2
2---0.324 Å20 Å2
3---0.647 Å2
Refinement stepCycle: LAST / Resolution: 2.3→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1852 0 8 176 2036
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.010436
X-RAY DIFFRACTIONc_angle_deg2.08727
LS refinement shellResolution: 2.2→2.25 Å
RfactorNum. reflection% reflection
Rfree0.419 104 -
Rwork0.406 --
obs-897 100 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:dna-rna_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION4CNS_TOPPAR:ion.param
X-RAY DIFFRACTION5CNS_TOPPAR:carbohydrate.param
X-RAY DIFFRACTION6tris.param
X-RAY DIFFRACTION7urea.param

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