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- PDB-3twi: Variable Lymphocyte Receptor Recognition of the Immunodominant Gl... -

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Basic information

Entry
Database: PDB / ID: 3twi
TitleVariable Lymphocyte Receptor Recognition of the Immunodominant Glycoprotein of Bacillus anthracis Spores
Components
  • BclA protein
  • Variable lymphocyte receptor B
KeywordsIMMUNE SYSTEM / Leucine-Rich Repeat / Antigen-binding / Secreted
Function / homology
Function and homology information


extracellular matrix structural constituent conferring tensile strength / regulation of phagocytosis / extracellular matrix organization / extracellular space
Similarity search - Function
BclA, C-terminal domain / BclA C-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Leucine rich repeat ...BclA, C-terminal domain / BclA C-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Jelly Rolls - #40 / Tumour necrosis factor-like domain superfamily / Collagen triple helix repeat / Collagen triple helix repeat (20 copies) / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Variable lymphocyte receptor B / BclA protein
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
Petromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.55 Å
AuthorsKirchdoerfer, R.N. / Herrin, B.R. / Han, B.W. / Turnbough Jr., C.L. / Cooper, M.D. / Wilson, I.A.
CitationJournal: Structure / Year: 2012
Title: Variable Lymphocyte Receptor Recognition of the Immunodominant Glycoprotein of Bacillus anthracis Spores.
Authors: Kirchdoerfer, R.N. / Herrin, B.R. / Han, B.W. / Turnbough, C.L. / Cooper, M.D. / Wilson, I.A.
History
DepositionSep 21, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2012Provider: repository / Type: Initial release
Revision 1.1Mar 28, 2012Group: Database references
Revision 1.2Sep 13, 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_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_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: BclA protein
B: BclA protein
C: BclA protein
D: Variable lymphocyte receptor B
E: Variable lymphocyte receptor B
F: Variable lymphocyte receptor B
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,9589
Polymers107,6816
Non-polymers2763
Water6,900383
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.809, 146.528, 209.501
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 6 / Auth seq-ID: 85 - 210 / Label seq-ID: 26 - 151

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC

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Components

#1: Protein BclA protein / Spore surface glycoprotein BclA


Mass: 16422.553 Da / Num. of mol.: 3 / Fragment: C-TERMINAL DOMAIN / Mutation: T185N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Gene: bclA, BA_1222, GBAA_1222 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q81JD7
#2: Protein Variable lymphocyte receptor B


Mass: 19471.273 Da / Num. of mol.: 3 / Fragment: ANTIGEN-BINDING DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Gene: VLR-B / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: A9Z0I5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 383 / 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: 2.67 Å3/Da / Density % sol: 53.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 5.26
Details: 15% PEG 6000, 1.2 M LiCl, 0.1 M sodium citrate, pH 5.26, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.033 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 10, 2010
RadiationMonochromator: Si(111), Double crystal cryo-cooled / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.033 Å / Relative weight: 1
ReflectionResolution: 2.55→50 Å / Num. all: 37042 / Num. obs: 37042 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rsym value: 0.122 / Net I/σ(I): 9.5
Reflection shellResolution: 2.55→2.64 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 2 / Rsym value: 0.581 / % possible all: 99.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERfor MRphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 2R6Q, 2R9U

2r6q

2r9u


Resolution: 2.55→41.88 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.911 / SU B: 19.502 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.446 / ESU R Free: 0.267 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23293 1869 5.1 %RANDOM
Rwork0.18932 ---
obs0.19149 35031 96.69 %-
all-35031 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.948 Å2
Baniso -1Baniso -2Baniso -3
1-0.28 Å20 Å20 Å2
2---1.47 Å20 Å2
3---1.19 Å2
Refinement stepCycle: LAST / Resolution: 2.55→41.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6289 0 18 383 6690
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0226411
X-RAY DIFFRACTIONr_bond_other_d00.023994
X-RAY DIFFRACTIONr_angle_refined_deg1.2111.9738761
X-RAY DIFFRACTIONr_angle_other_deg4.41939962
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4065835
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.13526.268209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.42915990
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.503156
X-RAY DIFFRACTIONr_chiral_restr0.0620.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0216954
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021078
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_it01.54241
X-RAY DIFFRACTIONr_mcbond_other01.51739
X-RAY DIFFRACTIONr_mcangle_it026888
X-RAY DIFFRACTIONr_scbond_it032170
X-RAY DIFFRACTIONr_scangle_it04.51873
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 1424 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1Aloose positional0.335
2Bloose positional0.435
3Cloose positional0.365
1Aloose thermal010
2Bloose thermal010
3Cloose thermal010
LS refinement shellResolution: 2.55→2.613 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.335 131 -
Rwork0.291 2559 -
obs--95.32 %
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)
12.73640.5368-0.11182.3060.77942.32820.01970.17780.0055-0.15730.00470.0574-0.0411-0.1546-0.02440.07920.01350.0080.02660.02040.0735-3.0203-23.4728-45.7234
21.3139-0.09170.64822.44760.70491.9960.0267-0.0974-0.16570.1773-0.00720.18450.0613-0.183-0.01960.0861-0.01420.03970.09020.04650.0703-17.7877-32.4931-32.5302
31.85530.34860.12562.21360.72332.97040.0783-0.0577-0.2770.1308-0.086-0.24340.21210.09260.00770.05010.014-0.03780.0260.040.16121.7125-42.1915-35.5686
43.3963-1.6359-1.41694.71752.08722.95120.12890.28970.1707-0.3504-0.0357-0.3365-0.3314-0.0005-0.09320.0625-0.00460.00040.03670.03060.112717.1176-4.3912-48.5188
53.2638-0.3567-0.96182.5014-0.77768.72770.1591-0.14480.02240.05530.07940.3515-0.212-0.689-0.23840.17630.050.09820.22660.05040.1442-34.7048-17.6952-17.6256
610.6072.2740.01889.2415-1.07894.54880.1058-0.8688-1.37620.9862-0.1744-1.36560.65090.42830.06860.64520.1043-0.24040.57570.29060.762812.73-53.8107-15.4961
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A80 - 215
2X-RAY DIFFRACTION2B80 - 215
3X-RAY DIFFRACTION3C80 - 215
4X-RAY DIFFRACTION4D21 - 188
5X-RAY DIFFRACTION5E21 - 187
6X-RAY DIFFRACTION6F24 - 187

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