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- PDB-6jb5: Crystal structure of nanobody D3-L11 mutant Y102A in complex with... -

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Basic information

Entry
Database: PDB / ID: 6jb5
TitleCrystal structure of nanobody D3-L11 mutant Y102A in complex with hen egg-white lysozyme (form II)
Components
  • Lysozyme C
  • Nanobody D3-L11
KeywordsIMMUNE SYSTEM/HYDROLASE / nanobody / hot-spot mutagenesis / thermodynamics / biomolecular recognition / IMMUNE SYSTEM / 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
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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Biological speciesCamelus dromedarius (Arabian camel)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCaaveiro, J.M.M. / Tamura, H. / Akiba, H. / Tsumoto, K.
Funding support Japan, 2items
OrganizationGrant numberCountry
Japan Society for the Promotion of Science15K06962 Japan
Japan Society for the Promotion of Science16H02420 Japan
CitationJournal: Sci Rep / Year: 2019
Title: Structural and thermodynamic basis for the recognition of the substrate-binding cleft on hen egg lysozyme by a single-domain antibody.
Authors: Akiba, H. / Tamura, H. / Kiyoshi, M. / Yanaka, S. / Sugase, K. / Caaveiro, J.M.M. / Tsumoto, K.
History
DepositionJan 25, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 6, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 13, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nanobody D3-L11
B: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4038
Polymers29,0772
Non-polymers3266
Water5,350297
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry, SEC, SPR
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-12 kcal/mol
Surface area11320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.010, 49.440, 57.940
Angle α, β, γ (deg.)90.00, 93.79, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Nanobody D3-L11


Mass: 14746.210 Da / Num. of mol.: 1 / Mutation: Y102A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#2: Protein Lysozyme C


Mass: 14331.160 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 297 / 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: 2.16 Å3/Da / Density % sol: 43.14 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 20mM Tris-HCl pH 8.0, 100mM NaCl, 100mM LiCl, 18 % PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: AR-NW12A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 18, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→49.44 Å / Num. obs: 36086 / % possible obs: 99.7 % / Redundancy: 5.1 % / CC1/2: 0.996 / Rmerge(I) obs: 0.094 / Net I/σ(I): 10.8
Reflection shellResolution: 1.55→1.63 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.594 / Mean I/σ(I) obs: 2.4 / Num. unique obs: 5168 / CC1/2: 0.717 / % possible all: 98

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
MOSFLM7.1.0data reduction
SCALA3.3.21data scaling
PHASER2.5.6phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6JB2

6jb2


Resolution: 1.55→49.44 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.963 / SU B: 3.248 / SU ML: 0.05 / Cross valid method: THROUGHOUT / ESU R: 0.085 / ESU R Free: 0.068 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16856 1083 3 %RANDOM
Rwork0.13182 ---
obs0.13297 34988 99.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 16.792 Å2
Baniso -1Baniso -2Baniso -3
1-0.63 Å20 Å20.49 Å2
2---0.57 Å20 Å2
3----0.13 Å2
Refinement stepCycle: 1 / Resolution: 1.55→49.44 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1955 0 16 297 2268
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.022086
X-RAY DIFFRACTIONr_bond_other_d0.0020.021853
X-RAY DIFFRACTIONr_angle_refined_deg1.5771.9242843
X-RAY DIFFRACTIONr_angle_other_deg1.03234303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2715280
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.92923.29997
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.47915342
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.3161519
X-RAY DIFFRACTIONr_chiral_restr0.1050.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022402
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02465
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_it1.5891.461049
X-RAY DIFFRACTIONr_mcbond_other1.5751.4581048
X-RAY DIFFRACTIONr_mcangle_it1.7712.191315
X-RAY DIFFRACTIONr_mcangle_other1.7742.1911316
X-RAY DIFFRACTIONr_scbond_it1.9531.7011037
X-RAY DIFFRACTIONr_scbond_other1.9511.7011037
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.2192.4531516
X-RAY DIFFRACTIONr_long_range_B_refined3.08118.7152479
X-RAY DIFFRACTIONr_long_range_B_other2.65217.8712398
X-RAY DIFFRACTIONr_rigid_bond_restr2.45233939
X-RAY DIFFRACTIONr_sphericity_free21.4385211
X-RAY DIFFRACTIONr_sphericity_bonded6.04953988
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.361 55 -
Rwork0.248 2492 -
obs--95.79 %

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