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- PDB-2v7h: Crystal structure of an immunogen specific anti-mannopyranoside m... -

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Basic information

Entry
Database: PDB / ID: 2v7h
TitleCrystal structure of an immunogen specific anti-mannopyranoside monoclonal antibody Fab fragment
Components(MONOCLONAL ANTIBODY) x 2
KeywordsIMMUNE SYSTEM / MONOCLONAL ANTIBODY / MANNOPYRANOSIDE SPECIFICITY / MOLECULAR MIMICRY
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKrishnan, L. / Sahni, G. / Kaur, K.J. / Salunke, D.M.
CitationJournal: Biophys.J. / Year: 2008
Title: Role of Antibody Paratope Conformational Flexibility in the Manifestation of Molecular Mimicry.
Authors: Krishnan, L. / Sahni, G. / Kaur, K.J. / Salunke, D.M.
History
DepositionJul 30, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 19, 2008Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
Revision 1.4Oct 9, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MONOCLONAL ANTIBODY
B: MONOCLONAL ANTIBODY
L: MONOCLONAL ANTIBODY
H: MONOCLONAL ANTIBODY


Theoretical massNumber of molelcules
Total (without water)94,8454
Polymers94,8454
Non-polymers00
Water1,910106
1
A: MONOCLONAL ANTIBODY
B: MONOCLONAL ANTIBODY


Theoretical massNumber of molelcules
Total (without water)47,4222
Polymers47,4222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-32.4 kcal/mol
Surface area23610 Å2
MethodPQS
2
L: MONOCLONAL ANTIBODY
H: MONOCLONAL ANTIBODY


Theoretical massNumber of molelcules
Total (without water)47,4222
Polymers47,4222
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4570 Å2
ΔGint-35 kcal/mol
Surface area23220 Å2
MethodPQS
Unit cell
Length a, b, c (Å)40.021, 79.737, 132.276
Angle α, β, γ (deg.)90.00, 90.75, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody MONOCLONAL ANTIBODY


Mass: 23632.947 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT LIGHT CHAIN / Source method: isolated from a natural source
Details: MONOCLONAL ANTIBODY AGAINST ALPHA-D-MANNOPYRANOSIDE
Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-LYMPHOCYTE / Cell line: 1H7 MURINE HYBRIDOMA / Strain: BALB/C
#2: Antibody MONOCLONAL ANTIBODY


Mass: 23789.480 Da / Num. of mol.: 2 / Fragment: FAB FRAGMENT HEAVY CHAIN / Source method: isolated from a natural source
Details: MONOCLONAL ANTIBODY AGAINST ALPHA-D-MANNOPYRANOSIDE
Source: (natural) MUS MUSCULUS (house mouse) / Cell: B-LYMPHOCYTE / Cell line: 1H7 MURINE HYBRIDOMA / Strain: BALB/C
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 106 / 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: 2.2 Å3/Da / Density % sol: 43.5 % / Description: NONE
Crystal growpH: 7.4 / Details: 50MM TRISCL, PH 7.4 WITH 20% PEG 4000

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 20, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.8→50 Å / Num. obs: 19865 / % possible obs: 95.9 % / Observed criterion σ(I): 0 / Redundancy: 3.25 % / Biso Wilson estimate: 38.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.3
Reflection shellResolution: 2.8→2.9 Å / Redundancy: 3.23 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 1.2 / % possible all: 94.4

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Processing

Software
NameVersionClassification
CNS1refinement
AUTOMARdata reduction
AUTOMARdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 6FAB

6fab


Resolution: 2.8→17.46 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 10000 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: DISORDERED REGIONS IN THE PROTEIN HAVE NOT BEEN MODELED
RfactorNum. reflection% reflectionSelection details
Rfree0.2676 1922 9.9 %RANDOM
Rwork0.2424 ---
obs0.2424 19482 94.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 34.0601 Å2 / ksol: 0.290378 e/Å3
Displacement parametersBiso mean: 45.68 Å2
Baniso -1Baniso -2Baniso -3
1--10.23 Å20 Å20.925 Å2
2---7.157 Å20 Å2
3---17.387 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.6 Å0.39 Å
Luzzati d res low-5 Å
Luzzati sigma a0.58 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.8→17.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6598 0 0 106 6704
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009746
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.75834
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d28
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.18
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.251.5
X-RAY DIFFRACTIONc_mcangle_it3.752
X-RAY DIFFRACTIONc_scbond_it3.352
X-RAY DIFFRACTIONc_scangle_it4.782.5
LS refinement shellResolution: 2.8→2.9 Å / Rfactor Rfree error: 0.027 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.351 173 8.4 %
Rwork0.351 1668 -
obs--89.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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