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- PDB-2znx: 5-Fluorotryptophan Incorporated ScFv10 Complexed to Hen Egg Lysozyme -

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Basic information

Entry
Database: PDB / ID: 2znx
Title5-Fluorotryptophan Incorporated ScFv10 Complexed to Hen Egg Lysozyme
Components
  • Lysozyme C
  • ScFvSingle-chain variable fragment
KeywordsIMMUNE SYSTEM/HYDROLASE / fluorotryptohpan / 5-fluorotryptophan / 19F / Single Chain Fv / Lysozyme / Allergen / Antimicrobial / Bacteriolytic enzyme / Glycosidase / Hydrolase / IMMUNE SYSTEM-HYDROLASE COMPLEX
Function / homology
Function and homology information


Lactose synthesis / 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 ...Lactose synthesis / 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 / MOLECULAR REPLACEMENT / Resolution: 2.3 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
Revision 1.5Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)81,7086
Polymers81,2034
Non-polymers5052
Water5,603311
1
A: ScFv
Y: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8543
Polymers40,6022
Non-polymers2521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: ScFv
Z: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,8543
Polymers40,6022
Non-polymers2521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)149.240, 149.240, 81.143
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
11Y
21Z
12A
22B
13A
23B

NCS domain segments:

Component-ID: 1 / Refine code: 4

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11LYSLYSLEULEUYB1 - 1291 - 129
21LYSLYSLEULEUZD1 - 1291 - 129
12ASPASPTHRTHRAA1 - 1071 - 107
22ASPASPTHRTHRBC1 - 1071 - 107
13ASPASPALAALAAA123 - 236123 - 236
23ASPASPALAALABC123 - 236123 - 236

NCS ensembles :
ID
1
2
3

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Components

#1: Antibody ScFv / Single-chain variable fragment


Mass: 26270.408 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): CT19 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.: 311 / 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% PEG400, 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-ID / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 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: 2.2→50 Å / Num. all: 47378 / Num. obs: 47378 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 9 % / Rsym value: 0.12 / Net I/σ(I): 22.5
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 8.8 % / Mean I/σ(I) obs: 4.2 / Num. unique all: 4648 / Rsym value: 0.786 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.4.0057refinement
MAR345data collection
HKL-3000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2DQJ

2dqj


Resolution: 2.3→50 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.908 / SU B: 5.36 / SU ML: 0.135 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.272 / ESU R Free: 0.209 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23173 2051 5 %RANDOM
Rwork0.19274 ---
obs0.19476 39131 83 %-
all-47378 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 26.604 Å2
Baniso -1Baniso -2Baniso -3
1-0.72 Å20 Å20 Å2
2--0.72 Å20 Å2
3----1.45 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5448 0 34 311 5793
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0215618
X-RAY DIFFRACTIONr_angle_refined_deg1.4231.9797636
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8375694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.28724240
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.39515868
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1841536
X-RAY DIFFRACTIONr_chiral_restr0.0940.2816
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214290
X-RAY DIFFRACTIONr_mcbond_it0.7371.53460
X-RAY DIFFRACTIONr_mcangle_it1.43625564
X-RAY DIFFRACTIONr_scbond_it1.89432158
X-RAY DIFFRACTIONr_scangle_it3.0544.52072
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1Y1001MEDIUM POSITIONAL0.310.5
1Y1001MEDIUM THERMAL0.592
2A817MEDIUM POSITIONAL0.410.5
2A817MEDIUM THERMAL0.562
3A907MEDIUM POSITIONAL0.530.5
3A907MEDIUM THERMAL0.712
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.283 160 -
Rwork0.213 2826 -
obs--99.93 %

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