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- PDB-4tsa: Structure of a lysozyme FAb complex -

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Basic information

Entry
Database: PDB / ID: 4tsa
TitleStructure of a lysozyme FAb 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


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 ...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
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-like domain superfamily / Immunoglobulins / Immunoglobulin-like ...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-like domain superfamily / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.27 Å
AuthorsWensley, B.
CitationJournal: To Be Published
Title: Structure of a lysozyme FAb 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

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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)60,5313
Polymers60,5313
Non-polymers00
Water99155
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-20 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.740, 97.570, 57.850
Angle α, β, γ (deg.)90.00, 93.61, 90.00
Int Tables number4
Space group name H-MP1211

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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) / Organ: egg / Plasmid details: egg white / References: UniProt: P00698, lysozyme
#2: Antibody FAb Heavy Chain / Fragment antigen-binding


Mass: 23415.156 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: 22784.215 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.: 55 / 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: 2.08 Å3/Da / Density % sol: 40.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: PCTP 100mM pH 6.5, 25% Peg10k / PH range: 5-6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04-1 / Wavelength: 0.92 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Apr 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.92 Å / Relative weight: 1
ReflectionResolution: 2.27→48.79 Å / Num. obs: 22427 / % possible obs: 97.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 41.19 Å2 / Net I/σ(I): 8.6
Reflection shellResolution: 2.27→2.33 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.587 / Mean I/σ(I) obs: 2 / % possible all: 91.8

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
RefinementResolution: 2.27→48.78 Å / Cor.coef. Fo:Fc: 0.8558 / Cor.coef. Fo:Fc free: 0.827 / SU R Cruickshank DPI: 0.448 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.422 / SU Rfree Blow DPI: 0.278 / SU Rfree Cruickshank DPI: 0.288
RfactorNum. reflection% reflectionSelection details
Rfree0.3098 1109 4.95 %RANDOM
Rwork0.281 ---
obs0.2824 22407 97.58 %-
Displacement parametersBiso mean: 32.76 Å2
Baniso -1Baniso -2Baniso -3
1-2.6067 Å20 Å2-2.9382 Å2
2---7.7715 Å20 Å2
3---5.1648 Å2
Refine analyzeLuzzati coordinate error obs: 0.492 Å
Refinement stepCycle: 1 / Resolution: 2.27→48.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3636 0 0 55 3691
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083719HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.085057HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1204SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes71HARMONIC2
X-RAY DIFFRACTIONt_gen_planes543HARMONIC5
X-RAY DIFFRACTIONt_it3719HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.59
X-RAY DIFFRACTIONt_other_torsion18.96
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion488SEMIHARMONIC5
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_contact3852SEMIHARMONIC4
LS refinement shellResolution: 2.27→2.38 Å / Total num. of bins used: 11
RfactorNum. reflection% reflection
Rfree0.3759 166 5.61 %
Rwork0.3368 2794 -
all0.339 2960 -
obs--97.58 %

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