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- PDB-4n1c: Structural evidence for antigen receptor evolution -

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Basic information

Entry
Database: PDB / ID: 4n1c
TitleStructural evidence for antigen receptor evolution
Components
  • Lysozyme C
  • immunoglobulin variable light chain domain
KeywordsImmune system/Hydrolase / immunoglobulin variable domain homodimer / protein-protein complex / Ig domain / 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 / defense response to Gram-negative bacterium / killing of cells of another organism / defense response to Gram-positive bacterium ...Lactose synthesis / Antimicrobial peptides / Neutrophil degranulation / beta-N-acetylglucosaminidase activity / cell wall macromolecule catabolic process / lysozyme / lysozyme activity / defense response to Gram-negative bacterium / killing of cells of another organism / 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 / molecular replacement / Resolution: 1.7 Å
AuthorsLangley, D.B. / Rouet, R. / Roome, B. / Stock, D. / Christ, D.
CitationJournal: Proc. Natl. Acad. Sci. U.S.A. / Year: 2017
Title: Structural reconstruction of protein ancestry.
Authors: Rouet, R. / Langley, D.B. / Schofield, P. / Christie, M. / Roome, B. / Porebski, B.T. / Buckle, A.M. / Clifton, B.E. / Jackson, C.J. / Stock, D. / Christ, D.
History
DepositionOct 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 29, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 29, 2017Group: Database references
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.3Sep 20, 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: immunoglobulin variable light chain domain
B: immunoglobulin variable light chain domain
C: Lysozyme C


Theoretical massNumber of molelcules
Total (without water)38,2803
Polymers38,2803
Non-polymers00
Water2,774154
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)126.789, 126.789, 40.660
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number173
Space group name H-MP63

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Components

#1: Antibody immunoglobulin variable light chain domain


Mass: 11974.279 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: pET12a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 gold DE3
#2: 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 / Details: Purified from hen eggs whites / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 154 / 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: 2.46 Å3/Da / Density % sol: 50.09 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 0.2 M ammonium acetate, 0.1 M BisTris (pH 5.5), 25% PEG3350, vapor diffusion, sitting drop, temperature 293K, VAPOR DIFFUSION, SITTING DROP

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.95369 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 1, 2012
RadiationMonochromator: Silicon Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.95369 Å / Relative weight: 1
ReflectionResolution: 1.7→109.8 Å / Num. all: 41399 / Num. obs: 41399 / % possible obs: 99.8 % / Redundancy: 7.9 % / Rsym value: 0.092 / Net I/σ(I): 12.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.796.50.5751.33867559610.57599.5
1.79-1.96.80.3482.23820556590.34899.7
1.9-2.037.10.2193.33780153590.219100
2.03-2.197.50.164.33733349840.16100
2.19-2.480.1255.53664046010.125100
2.4-2.698.50.1026.43529641670.102100
2.69-3.19.60.0936.63529536950.093100
3.1-3.810.10.0916.53150531340.091100
3.8-5.389.80.0659.12404324520.06599.9
5.38-41.502100.05110.71380513870.05199

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å41.5 Å
Translation2.5 Å41.5 Å

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Processing

Software
NameVersionClassificationNB
MOSFLM3.3.16data reduction
SCALA3.3.16data scaling
PHASER2.3.0phasing
REFMACrefinement
PDB_EXTRACT3.11data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 3UPA and 1ZVY

3upa

1zvy


Resolution: 1.7→41.5 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / WRfactor Rfree: 0.2424 / WRfactor Rwork: 0.2073 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8794 / SU B: 3.836 / SU ML: 0.064 / SU R Cruickshank DPI: 0.102 / SU Rfree: 0.1034 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.102 / ESU R Free: 0.103 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2325 2080 5 %RANDOM
Rwork0.1968 ---
obs0.1986 41386 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 54.01 Å2 / Biso mean: 23.537 Å2 / Biso min: 7.01 Å2
Baniso -1Baniso -2Baniso -3
1--0.65 Å2-0.32 Å20 Å2
2---0.65 Å20 Å2
3---0.97 Å2
Refinement stepCycle: LAST / Resolution: 1.7→41.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2417 0 0 154 2571
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0212504
X-RAY DIFFRACTIONr_bond_other_d0.0010.021591
X-RAY DIFFRACTIONr_angle_refined_deg1.3851.9363422
X-RAY DIFFRACTIONr_angle_other_deg0.87633878
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7145334
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92724.2100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.81215347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9961511
X-RAY DIFFRACTIONr_chiral_restr0.090.2377
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0212889
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02530
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 146 -
Rwork0.255 2752 -
all-2898 -
obs--99.28 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.73730.50570.00751.7457-0.30740.576-0.02760.01240.0169-0.05150.05670.1854-0.05740.0374-0.02910.0597-0.0104-0.0080.04580.0210.02787.54471.8603-2.4185
21.0733-0.56580.08551.0911-0.32031.01530.04230.0502-0.0603-0.0158-0.02130.14470.14740.0954-0.0210.08750.0229-0.00630.03930.00620.022992.1171-19.0933.2611
31.6078-0.09260.55990.14330.36721.465-0.0206-0.0208-0.1657-0.0066-0.0230.0922-0.0193-0.09740.04350.0193-0.0026-0.00340.01120.01780.237261.8117-19.0889-1.3754
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 107
2X-RAY DIFFRACTION2B1 - 106
3X-RAY DIFFRACTION3C1 - 127

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