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- PDB-2i26: Crystal structure analysis of the nurse shark new antigen recepto... -

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Basic information

Entry
Database: PDB / ID: 2i26
TitleCrystal structure analysis of the nurse shark new antigen receptor ancestral variable domain in complex with lysozyme
Components
  • Lysozyme C
  • New Antigen Receptor Ancestral
KeywordsIMMUNE SYSTEM / immunoglobulin fold / protein-protein 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 / Immunoglobulin V-Type / Immunoglobulin V-set domain ...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 / 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
Lysozyme C / Antigen receptor
Similarity search - Component
Biological speciesGinglymostoma cirratum (nurse shark)
Gallus gallus (chicken)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsStanfield, R.L. / Wilson, I.A.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: Maturation of Shark Single-domain (IgNAR) Antibodies: Evidence for Induced-fit Binding.
Authors: Stanfield, R.L. / Dooley, H. / Verdino, P. / Flajnik, M.F. / Wilson, I.A.
History
DepositionAug 15, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Remark 999SEQUENCE AT THE TIME OF PROCESSING, A UNP REFERENCE SEQUENCE WAS NOT AVAILABLE FOR THE NEW ANTIGEN ...SEQUENCE AT THE TIME OF PROCESSING, A UNP REFERENCE SEQUENCE WAS NOT AVAILABLE FOR THE NEW ANTIGEN RECEPTOR ANCESTRAL.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
N: New Antigen Receptor Ancestral
L: Lysozyme C
O: New Antigen Receptor Ancestral
M: Lysozyme C
P: New Antigen Receptor Ancestral
Q: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,45312
Polymers82,8776
Non-polymers5766
Water2,018112
1
N: New Antigen Receptor Ancestral
L: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7223
Polymers27,6262
Non-polymers961
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
O: New Antigen Receptor Ancestral
M: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,8184
Polymers27,6262
Non-polymers1922
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
P: New Antigen Receptor Ancestral
Q: Lysozyme C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9145
Polymers27,6262
Non-polymers2883
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.300, 64.694, 159.876
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein New Antigen Receptor Ancestral


Mass: 13294.453 Da / Num. of mol.: 3 / Fragment: variable domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ginglymostoma cirratum (nurse shark) / Plasmid: pims100 / Production host: Escherichia coli (E. coli) / Strain (production host): xl1-blue / References: UniProt: Q8JGG7
#2: Protein Lysozyme C / 1 / 4-beta-N-acetylmuramidase C / Allergen Gal d 4 / Gal d IV


Mass: 14331.160 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Gallus gallus (chicken) / References: UniProt: P00698, lysozyme
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / 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: 2.01 Å3/Da / Density % sol: 38.68 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 11% PEG 4000, 1.8M ammonium sulfate, 0.1M BES, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 21, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.5→45.64 Å / Num. all: 23397 / Num. obs: 23397 / % possible obs: 98.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 2.8 % / Biso Wilson estimate: 36.1 Å2 / Rsym value: 0.087 / Net I/σ(I): 8.7
Reflection shellResolution: 2.5→2.54 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 3186 / Rsym value: 0.546 / % possible all: 97.3

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→45.64 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.865 / SU B: 24.136 / SU ML: 0.258 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2915 1129 4.8 %RANDOM
Rwork0.1994 ---
obs0.20381 22228 100 %-
all-22228 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.499 Å2
Baniso -1Baniso -2Baniso -3
1--3.37 Å20 Å20 Å2
2--3.07 Å20 Å2
3---0.31 Å2
Refinement stepCycle: LAST / Resolution: 2.5→45.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5668 0 30 112 5810
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0215810
X-RAY DIFFRACTIONr_bond_other_d0.0020.023939
X-RAY DIFFRACTIONr_angle_refined_deg1.8461.9237872
X-RAY DIFFRACTIONr_angle_other_deg1.0383.0089449
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4985730
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.13223.466277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.22615949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3371554
X-RAY DIFFRACTIONr_chiral_restr0.1040.2841
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.026586
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021239
X-RAY DIFFRACTIONr_nbd_refined0.2290.21184
X-RAY DIFFRACTIONr_nbd_other0.2110.24049
X-RAY DIFFRACTIONr_nbtor_refined0.190.22735
X-RAY DIFFRACTIONr_nbtor_other0.0910.23144
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.2204
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.160.244
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2340.287
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2320.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.9121.54595
X-RAY DIFFRACTIONr_mcbond_other0.1831.51529
X-RAY DIFFRACTIONr_mcangle_it1.20425780
X-RAY DIFFRACTIONr_scbond_it2.06632612
X-RAY DIFFRACTIONr_scangle_it3.0824.52092
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.44 70 -
Rwork0.263 1598 -
obs-1598 100 %
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)
18.3555-2.869-1.56851.39150.11641.81020.01890.19890.1520.15440.0251-0.0304-0.0442-0.0186-0.0440.0519-0.0167-0.0298-0.08550.02720.018351.30728.962680.9084
24.35550.94990.74391.6540.27841.70580.03190.1425-0.02960.0461-0.0064-0.0418-0.06120.0167-0.0255-0.05190.03320.0253-0.10670.0479-0.090419.856841.461180.0656
38.9109-1.9183-1.88031.42880.55381.6650.0224-0.05890.0888-0.0026-0.0404-0.06090.09120.06170.0179-0.0143-0.01210.0243-0.06790.0369-0.114646.43214.695864.7375
42.21150.87750.56712.2215-0.16011.4184-0.0527-0.0332-0.05680.03410.0679-0.0347-0.0161-0.04-0.0153-0.10560.03190.0089-0.13640.0064-0.13678.354812.475652.1692
59.6704-3.36641.59211.6811-0.01441.0425-0.0488-0.56810.12050.0334-0.00860.0694-0.034-0.18050.05740.0267-0.01810.0046-0.0381-0.0118-0.093948.957440.055854.1404
63.14731.4589-0.80662.7774-0.68191.54380.0978-0.00640.08170-0.04180.01040.00230.12-0.056-0.08880.02330.0077-0.1512-0.0325-0.160518.101941.725941.7829
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1NA2 - 1172 - 117
2X-RAY DIFFRACTION2LB1 - 1291 - 129
3X-RAY DIFFRACTION3OC2 - 1182 - 118
4X-RAY DIFFRACTION4MD1 - 1291 - 129
5X-RAY DIFFRACTION5PE2 - 1142 - 114
6X-RAY DIFFRACTION6QF1 - 1291 - 129

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