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- PDB-1bql: STRUCTURE OF AN ANTI-HEL FAB FRAGMENT COMPLEXED WITH BOBWHITE QUA... -

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Basic information

Entry
Database: PDB / ID: 1bql
TitleSTRUCTURE OF AN ANTI-HEL FAB FRAGMENT COMPLEXED WITH BOBWHITE QUAIL LYSOZYME
Components
  • BOBWHITE QUAIL LYSOZYME
  • HYHEL-5 FAB (HEAVY CHAIN)
  • HYHEL-5 FAB (LIGHT CHAIN)
KeywordsANTIBODY/ANTIGEN / ANTIBODY-ANTIGEN complex / HYHEL-5 / ANTI-LYSOZYME / BOBWHITE QUAIL
Function / homology
Function and homology information


metabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium / extracellular region
Similarity search - Function
Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily ...Lysozyme - #10 / Glycoside hydrolase, family 22, lysozyme / Glycoside hydrolase family 22 domain / Glycosyl hydrolases family 22 (GH22) domain signature. / Glycoside hydrolase, family 22 / C-type lysozyme/alpha-lactalbumin family / Glycosyl hydrolases family 22 (GH22) domain profile. / Alpha-lactalbumin / lysozyme C / Lysozyme / Lysozyme-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Biological speciesMus musculus (house mouse)
Colinus virginianus (northern bobwhite)
MethodX-RAY DIFFRACTION / Resolution: 2.6 Å
AuthorsChacko, S. / Davies, D.R.
Citation
Journal: Proteins / Year: 1996
Title: Refined structures of bobwhite quail lysozyme uncomplexed and complexed with the HyHEL-5 Fab fragment.
Authors: Chacko, S. / Silverton, E.W. / Smith-Gill, S.J. / Davies, D.R. / Shick, K.A. / Xavier, K.A. / Willson, R.C. / Jeffrey, P.D. / Chang, C.Y. / Sieker, L.C. / Sheriff, S.
#1: Journal: J. Mol. Biol. / Year: 1995
Title: Structure of an antibody-lysozyme complex unexpected effect of conservative mutation.
Authors: Chacko, S. / Silverton, E. / Kam-Morgan, L. / Smith-Gill, S. / Cohen, G. / Davies, D.
#2: Journal: Proc. Natl. Acad. Sci. U.S.A. / Year: 1987
Title: Three-dimensional structure of an antibody-antigen complex.
Authors: Sheriff, S. / Silverton, E.W. / Padlan, E.A. / Cohen, G.H. / Smith-Gill, S.J. / Finzel, B.C. / Davies, D.R.
History
DepositionFeb 3, 1995Processing site: BNL
Revision 1.0Apr 20, 1995Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2017Group: Database references / Other / Category: citation / citation_author / pdbx_database_status
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name / _pdbx_database_status.process_site

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: HYHEL-5 FAB (LIGHT CHAIN)
H: HYHEL-5 FAB (HEAVY CHAIN)
Y: BOBWHITE QUAIL LYSOZYME


Theoretical massNumber of molelcules
Total (without water)60,5643
Polymers60,5643
Non-polymers00
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.800, 74.800, 79.000
Angle α, β, γ (deg.)90.00, 101.80, 90.00
Int Tables number4
Space group name H-MP1211
Atom site foot note1: CIS PROLINE - PRO L 8 / 2: CIS PROLINE - PRO L 139 / 3: CIS PROLINE - PRO H 150 / 4: CIS PROLINE - PRO H 152 / 5: CIS PROLINE - PRO H 192

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Components

#1: Antibody HYHEL-5 FAB (LIGHT CHAIN)


Mass: 23326.729 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / References: GenBank: 1042224
#2: Antibody HYHEL-5 FAB (HEAVY CHAIN)


Mass: 22948.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#3: Protein BOBWHITE QUAIL LYSOZYME


Mass: 14289.119 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Colinus virginianus (northern bobwhite)
References: UniProt: P00700
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 86 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCOMPND FAB FRAGMENT OF AN ANTI-LYSOZYME IGG1 ANTIBODY HYHEL-5 - BOBWHITE QUAIL LYSOZYME COMPLEX.
Sequence detailsTHE LIGHT CHAIN OF THE FAB HAS THE CHAIN INDICATOR L. THE HEAVY CHAIN OF THE FAB HAS THE CHAIN ...THE LIGHT CHAIN OF THE FAB HAS THE CHAIN INDICATOR L. THE HEAVY CHAIN OF THE FAB HAS THE CHAIN INDICATOR H. THE LYSOZYME HAS THE CHAIN INDICATOR Y. THE NUMBERING SYSTEM USED IS SEQUENTIAL, FROM 1 - 212 FOR THE LIGHT CHAIN AND FROM 1 - 215 FOR THE HEAVY CHAIN. THE CONVERSION TO KABAT NUMBERING (E.A. KABAT, T.T. WU, M. REID-MILLER, H.M. PERRY, K.S. GOTTESMAN (1991) SEQUENCES OF PROTEINS OF IMMUNOLOGICAL INTEREST, 5TH ED, NATIONAL INSTITUTES OF HEALTH, BETHESDA, MD) FOR THE VARIABLE REGIONS OF THE LIGHT AND HEAVY CHAINS IS GIVEN BELOW. THE NUMBERING SYSTEM USED IS THE SAME AS IN THE PDB COORDINATE FILE FOR THE WILD-TYPE HYHEL-5-LYSOZYME COMPLEX. SEQUENTIAL NUMBERING KABAT NUMBERING L1 - L27 1 - 27 L28 - L94 29 - 95 L95 - L106 97 - 108 H2 - H52 2 - 52 H53 52A H54 - H83 53 - 82 H84 - H86 82A - 82C H87 - H102 83 - 98 H103 - H116 100 - 113

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.62 Å3/Da / Density % sol: 52.98 %
Crystal grow
*PLUS
Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
19.1 mg/mlFab1drop
23.8 mg/mlBWQL1drop
314 %PEG40001reservoir
40.1 Mimidazole1reservoirpH7.0
50.007 %spermine1reservoir

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Data collection

ReflectionNum. obs: 18884 / % possible obs: 94.5 % / Observed criterion σ(I): 0
Reflection
*PLUS
Highest resolution: 2.6 Å / Num. obs: 15950 / % possible obs: 80.8 % / Num. measured all: 30801 / Rmerge(I) obs: 0.074

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Processing

Software
NameClassification
X-PLORmodel building
X-PLORrefinement
X-PLORphasing
RefinementResolution: 2.6→8 Å / σ(F): 2
RfactorNum. reflection% reflection
Rfree0.291 --
Rwork0.191 --
obs0.191 15713 55 %
Displacement parametersBiso mean: 22.35 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.6→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4240 0 0 86 4326
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.015
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.5
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Refinement
*PLUS
Lowest resolution: 8 Å / Num. reflection obs: 14290 / σ(F): 2
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_angle_deg1.9
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.7

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