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- PDB-4tsb: Structure of a lysozyme antibody complex -

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Basic information

Entry
Database: PDB / ID: 4tsb
TitleStructure of a lysozyme antibody complex
Components
  • FAb Heavy ChainFragment antigen-binding
  • FAb Light ChainFragment antigen-binding
  • Lysozyme C
KeywordsImmune system/hydrolase / antibody / affinity maturation / immune system-hydrolase complex
Function / homology
Function and homology information


Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / killing of cells of another organism / defense response to Gram-negative bacterium / defense response to Gram-positive bacterium / defense response to bacterium / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
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 speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsWensley, B.
CitationJournal: To Be Published
Title: Structure of a lysozyme antibody complex
Authors: Wensley, B.
History
DepositionJun 18, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jul 8, 2015Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysozyme C
H: FAb Heavy Chain
L: FAb Light Chain


Theoretical massNumber of molelcules
Total (without water)60,6513
Polymers60,6513
Non-polymers00
Water6,702372
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4760 Å2
ΔGint-18 kcal/mol
Surface area24510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)80.600, 99.910, 75.090
Angle α, β, γ (deg.)90.00, 110.12, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11L-341-

HOH

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Components

#1: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#2: Antibody FAb Heavy Chain / Fragment antigen-binding


Mass: 23493.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Antibody FAb Light Chain / Fragment antigen-binding


Mass: 22826.322 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 372 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.34 Å3/Da / Density % sol: 47.44 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100mM PCPT pH 5.5, 200mM MgCl2, 22 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.979 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 11, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→34.89 Å / Num. obs: 34734 / % possible obs: 85.4 % / Redundancy: 4.1 % / Biso Wilson estimate: 25.51 Å2 / Net I/σ(I): 12.2
Reflection shellResolution: 1.95→2 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.391 / Mean I/σ(I) obs: 2.2 / % possible all: 39.1

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Processing

SoftwareName: BUSTER / Version: 2.11.5 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→34.89 Å / Cor.coef. Fo:Fc: 0.9344 / Cor.coef. Fo:Fc free: 0.915 / SU R Cruickshank DPI: 0.209 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.215 / SU Rfree Blow DPI: 0.169 / SU Rfree Cruickshank DPI: 0.168
RfactorNum. reflection% reflectionSelection details
Rfree0.2267 1747 5.03 %RANDOM
Rwork0.1937 ---
obs0.1954 34733 85.38 %-
Displacement parametersBiso mean: 23.59 Å2
Baniso -1Baniso -2Baniso -3
1--0.0598 Å20 Å2-0.0339 Å2
2--0.0444 Å20 Å2
3---0.0154 Å2
Refine analyzeLuzzati coordinate error obs: 0.254 Å
Refinement stepCycle: 1 / Resolution: 1.95→34.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4182 0 0 372 4554
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094284HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.15831HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1409SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes86HARMONIC2
X-RAY DIFFRACTIONt_gen_planes635HARMONIC5
X-RAY DIFFRACTIONt_it4284HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.39
X-RAY DIFFRACTIONt_other_torsion16.69
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion556SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4978SEMIHARMONIC4
LS refinement shellResolution: 1.95→2.01 Å / Total num. of bins used: 17
RfactorNum. reflection% reflection
Rfree0.3529 66 4.71 %
Rwork0.2979 1334 -
all0.3003 1400 -
obs--85.38 %

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