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- PDB-2h1p: THE THREE-DIMENSIONAL STRUCTURES OF A POLYSACCHARIDE BINDING ANTI... -

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Basic information

Entry
Database: PDB / ID: 2h1p
TitleTHE THREE-DIMENSIONAL STRUCTURES OF A POLYSACCHARIDE BINDING ANTIBODY TO CRYPTOCOCCUS NEOFORMANS AND ITS COMPLEX WITH A PEPTIDE FROM A PHAGE DISPLAY LIBRARY: IMPLICATIONS FOR THE IDENTIFICATION OF PEPTIDE MIMOTOPES
Components
  • (2H1) x 2
  • PA1
KeywordsCOMPLEX (ANTIBODY/PEPTIDE) / ANTIBODY STRUCTURE / CRYPTOCOCCUS / PHAGE LIBRARY / POLYSACCHARIDE / COMPLEX (ANTIBODY-PEPTIDE) / COMPLEX (ANTIBODY-PEPTIDE) complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / : / :
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsYoung, A.C.M. / Valadon, P. / Casadevall, A. / Scharff, M.D. / Sacchettini, J.C.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: The three-dimensional structures of a polysaccharide binding antibody to Cryptococcus neoformans and its complex with a peptide from a phage display library: implications for the ...Title: The three-dimensional structures of a polysaccharide binding antibody to Cryptococcus neoformans and its complex with a peptide from a phage display library: implications for the identification of peptide mimotopes.
Authors: Young, A.C. / Valadon, P. / Casadevall, A. / Scharff, M.D. / Sacchettini, J.C.
#1: Journal: J.Mol.Biol. / Year: 1996
Title: Peptide Libraries Define the Fine Specificity of Anti-Polysaccharide Antibodies to Cryptococcus Neoformans
Authors: Valadon, P. / Nussbaum, G. / Boyd, L.F. / Margulies, D.H. / Scharff, M.D.
History
DepositionNov 12, 1997Processing site: BNL
Revision 1.0Jan 28, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Refinement description
Category: database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 16, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: 2H1
H: 2H1
P: PA1


Theoretical massNumber of molelcules
Total (without water)49,1653
Polymers49,1653
Non-polymers00
Water1,11762
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-35 kcal/mol
Surface area19640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.790, 51.250, 60.180
Angle α, β, γ (deg.)91.82, 98.57, 107.84
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody 2H1


Mass: 24125.727 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source
Details: FAB PART ISOLATED AFTER PAPAIN DIGESTION OF THE PARENT IGG1/K MOLECULE
Source: (natural) Mus musculus (house mouse) / Cell line: 2H1 BALB/C-NSO HYBRIDOMA / Strain: BALB/C / References: PIR: S16112
#2: Antibody 2H1


Mass: 23687.664 Da / Num. of mol.: 1 / Fragment: FAB / Source method: isolated from a natural source
Details: FAB PART ISOLATED AFTER PAPAIN DIGESTION OF THE PARENT IGG1/K MOLECULE
Source: (natural) Mus musculus (house mouse) / Cell line: 2H1 BALB/C-NSO HYBRIDOMA / Strain: BALB/C / References: PIR: S38864
#3: Protein/peptide PA1


Mass: 1351.570 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.28 Å3/Da / Density % sol: 62.2 %
Crystal growpH: 8.5 / Details: 18% PEG 8K, PH 8.5, 1% GLYCEROL
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
118 %PEG80001reservoir
20.1 MTris1reservoir
31 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 290 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: SIEMENS / Detector: AREA DETECTOR / Date: Sep 1, 1995 / Details: COLLIMATOR
RadiationMonochromator: CU K ALPHA / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. obs: 19345 / % possible obs: 90 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 15.3
Reflection shellResolution: 2.4→2.5 Å / % possible all: 79
Reflection shell
*PLUS
% possible obs: 79 %

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Processing

Software
NameClassification
SAINTdata scaling
SAINTdata reduction
X-PLORmodel building
TNTrefinement
X-PLORrefinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FLR (FAB 4-4-20)

1flr


Resolution: 2.4→20 Å / Isotropic thermal model: TNT / σ(F): 2 / Stereochemistry target values: TNT
RfactorNum. reflection% reflection
Rwork0.186 --
all-19345 -
obs-11416 90 %
Solvent computationSolvent model: TNT
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3447 0 0 62 3509
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.017
X-RAY DIFFRACTIONt_angle_deg1.85
X-RAY DIFFRACTIONt_dihedral_angle_d
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes
X-RAY DIFFRACTIONt_it
X-RAY DIFFRACTIONt_nbd
Software
*PLUS
Name: TNT / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.186
Solvent computation
*PLUS
Displacement parameters
*PLUS

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