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- PDB-1dqm: CRYSTAL STRUCTURE OF ANTI-LYSOZYME ANTIBODY -

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Basic information

Entry
Database: PDB / ID: 1dqm
TitleCRYSTAL STRUCTURE OF ANTI-LYSOZYME ANTIBODY
Components
  • ANTI-LYSOZYME ANTIBODY HYHEL-63 (HEAVY CHAIN)
  • ANTI-LYSOZYME ANTIBODY HYHEL-63 (LIGHT CHAIN)
KeywordsIMMUNE SYSTEM / antibody / hen egg white lysozyme
Function / homology
Function and homology information


immunoglobulin receptor binding / B cell differentiation / extracellular region / plasma membrane
Similarity search - Function
: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold ...: / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
: / Immunoglobulin kappa constant / Ig gamma-2A chain C region, A allele
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / Resolution: 2.1 Å
AuthorsLi, H. / Mariuzza, R.A.
CitationJournal: Biochemistry / Year: 2000
Title: Three-dimensional structures of the free and antigen-bound Fab from monoclonal antilysozyme antibody HyHEL-63(,).
Authors: Li, Y. / Li, H. / Smith-Gill, S.J. / Mariuzza, R.A.
History
DepositionJan 4, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 19, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
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
L: ANTI-LYSOZYME ANTIBODY HYHEL-63 (LIGHT CHAIN)
H: ANTI-LYSOZYME ANTIBODY HYHEL-63 (HEAVY CHAIN)


Theoretical massNumber of molelcules
Total (without water)46,1402
Polymers46,1402
Non-polymers00
Water6,053336
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3510 Å2
ΔGint-27 kcal/mol
Surface area19000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)162.36, 39.74, 70.29
Angle α, β, γ (deg.)90.0, 98.1, 90.0
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11H-222-

HOH

21H-223-

HOH

31H-224-

HOH

DetailsThe biological assembly is a heterodimer composed of heavy and light chains.

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Components

#1: Antibody ANTI-LYSOZYME ANTIBODY HYHEL-63 (LIGHT CHAIN)


Mass: 23583.869 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: GenBank: 2950241, UniProt: P01837*PLUS
#2: Antibody ANTI-LYSOZYME ANTIBODY HYHEL-63 (HEAVY CHAIN)


Mass: 22556.023 Da / Num. of mol.: 1 / Fragment: FAB FRAGMENT
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PET22B / Production host: Escherichia coli (E. coli) / References: UniProt: P01863*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 8000, KH2PO4, Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
216 %(w/v)PEG80001reservoir
30.1 M1reservoirKH2PO4
40.1 MTris-HCl1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MACSCIENCE / Detector: IMAGE PLATE / Date: May 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→100 Å / Num. all: 26702 / Num. obs: 88367 / % possible obs: 94 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3.3 % / Biso Wilson estimate: 18.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 12.8
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2 % / Rmerge(I) obs: 0.328 / % possible all: 67.3
Reflection
*PLUS
Num. obs: 26702 / Num. measured all: 88367
Reflection shell
*PLUS
% possible obs: 67.3 % / Mean I/σ(I) obs: 1.7

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.1→100 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.268 1975 -RANDOM
Rwork0.225 ---
all0.225 24815 --
obs0.225 24815 8 %-
Refinement stepCycle: LAST / Resolution: 2.1→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3263 0 0 336 3599
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.006
Software
*PLUS
Name: 'CNS' / Classification: refinement
Refinement
*PLUS
Rfactor Rfree: 0.269
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.5 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.37
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg27.5
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.83

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