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- PDB-2znw: Crystal Structure of ScFv10 in Complex with Hen Egg Lysozyme -

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Basic information

Entry
Database: PDB / ID: 2znw
TitleCrystal Structure of ScFv10 in Complex with Hen Egg Lysozyme
Components
  • Lysozyme C
  • ScFv10
KeywordsIMMUNE SYSTEM/HYDROLASE / Single Chain Fv / Lysozyme / Allergen / Antimicrobial / Bacteriolytic enzyme / Glycosidase / Hydrolase / IMMUNE SYSTEM-HYDROLASE COMPLEX
Function / homology
Function and homology information


Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / RNA-directed DNA polymerase 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 ...Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / RNA-directed DNA polymerase 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 / immune response / endoplasmic reticulum / extracellular space / identical protein binding / cytoplasm
Similarity search - Function
Lysozyme - #10 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 - #10 / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain / Lysozyme / Immunoglobulin V-set domain / Lysozyme-like domain superfamily / Immunoglobulin subtype / Immunoglobulin / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Immunoglobulin-like fold / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
Chem-1PG / Lysozyme C / Anti-HIV-1 reverse transcriptase single-chain variable
Similarity search - Component
Biological speciesMus musculus (house mouse)
synthetic construct (others)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.71 Å
AuthorsDeSantis, M.E. / Acchione, M. / Li, M. / Walter, R.L. / Wlodawer, A. / Smith-Gill, S.
CitationJournal: Biochemistry / Year: 2012
Title: Specific fluorine labeling of the HyHEL10 antibody affects antigen binding and dynamics
Authors: Acchione, M. / Lee, Y.C. / DeSantis, M.E. / Lipschultz, C.A. / Wlodawer, A. / Li, M. / Shanmuganathan, A. / Walter, R.L. / Smith-Gill, S. / Barchi, J.J.
History
DepositionMay 2, 2008Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 27, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 2, 2013Group: Database references / Source and taxonomy
Revision 1.3Jun 28, 2017Group: Source and taxonomy / Category: entity_src_gen
Revision 1.4Oct 11, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: ScFv10
Y: Lysozyme C
B: ScFv10
Z: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,4926
Polymers80,9874
Non-polymers5052
Water3,477193
1
A: ScFv10
Y: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7463
Polymers40,4942
Non-polymers2521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ScFv10
Z: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7463
Polymers40,4942
Non-polymers2521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.228, 149.228, 80.948
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22B
13Y
23Z

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 1061 - 106
21BC1 - 1061 - 106
12AA123 - 236123 - 236
22BC123 - 236123 - 236
13YB1 - 1291 - 129
23ZD1 - 1291 - 129

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody ScFv10


Mass: 26162.457 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: This molecule contains antibody light chain(residues 1-107), linker(residues 108-122) and antibody heavy chain(residues 123-236)
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) synthetic construct (others)
Plasmid: pET30 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q65ZI1*PLUS
#2: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d 4 / Allergen Gal d IV


Mass: 14331.160 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / Tissue: egg white / References: UniProt: P00698, lysozyme
#3: Chemical ChemComp-1PG / 2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL / Polyethylene glycol


Mass: 252.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C11H24O6
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 193 / Source method: isolated from a natural source / Formula: H2O

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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: 2.78 Å3/Da / Density % sol: 55.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 30% PEG 400, 0.2M Na Citrate, 0.1M Tris, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 18, 2007 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. all: 25548 / Num. obs: 25548 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 10.1 % / Rsym value: 0.154 / Net I/σ(I): 16.4
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 10.1 % / Mean I/σ(I) obs: 3.9 / Num. unique all: 2500 / Rsym value: 0.621 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0057refinement
MAR345data collection
HKL-3000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.71→50 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.877 / SU B: 10.942 / SU ML: 0.226 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.022 / ESU R Free: 0.334 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25043 1297 5.1 %RANDOM
Rwork0.19273 ---
obs0.19568 24187 99.86 %-
all-25548 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.582 Å2
Baniso -1Baniso -2Baniso -3
1-1.08 Å20 Å20 Å2
2--1.08 Å20 Å2
3----2.15 Å2
Refinement stepCycle: LAST / Resolution: 2.71→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5436 0 34 193 5663
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0215606
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3931.937612
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9115694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.85223.81252
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.04515880
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.5941536
X-RAY DIFFRACTIONr_chiral_restr0.10.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214278
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6771.53460
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.33425564
X-RAY DIFFRACTIONr_scbond_it1.70432146
X-RAY DIFFRACTIONr_scangle_it2.9394.52048
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A808MEDIUM POSITIONAL0.360.5
1A808MEDIUM THERMAL0.422
2B903MEDIUM POSITIONAL0.50.5
2B903MEDIUM THERMAL0.682
3Y1001MEDIUM POSITIONAL0.280.5
3Y1001MEDIUM THERMAL0.722
LS refinement shellResolution: 2.705→2.775 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.352 83 -
Rwork0.259 1734 -
obs--98.97 %

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