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- PDB-2r9u: Crystal Structure of Lamprey Variable Lymphocyte Receptor 2913 Ec... -

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Basic information

Entry
Database: PDB / ID: 2r9u
TitleCrystal Structure of Lamprey Variable Lymphocyte Receptor 2913 Ectodomain
ComponentsVariable lymphocyte receptor
KeywordsIMMUNE SYSTEM / Adaptive immunity / VLR / Leucine-rich repeat / LRR / Receptor
Function / homology
Function and homology information


Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / : / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype ...Variable lymphocyte receptor, C-terminal / Domain of unknown function (DUF3439) / : / Leucine-rich repeat N-terminal domain / Leucine rich repeat N-terminal domain / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Alpha-Beta Horseshoe / Leucine rich repeat / Leucine-rich repeat, typical subtype / Leucine-rich repeats, typical (most populated) subfamily / Leucine-rich repeat profile. / Leucine-rich repeat / Leucine-rich repeat domain superfamily / Prokaryotic membrane lipoprotein lipid attachment site profile. / Alpha Beta
Similarity search - Domain/homology
Variable lymphocyte receptor
Similarity search - Component
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsHan, B.W. / Herrin, B.R. / Choe, J. / Cooper, M.D. / Wilson, I.A.
CitationJournal: To be Published
Title: Crystal Structure of Lamprey Variable Lymphocyte Receptor 2913 Ectodomain.
Authors: Han, B.W. / Herrin, B.R. / Morris, G.M. / Choe, J. / Cooper, M.D. / Wilson, I.A.
History
DepositionSep 13, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 10, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Aug 30, 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 / struct_ncs_dom_lim / struct_ref_seq_dif
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.end_auth_comp_id / _struct_ref_seq_dif.details
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Variable lymphocyte receptor
B: Variable lymphocyte receptor
C: Variable lymphocyte receptor
D: Variable lymphocyte receptor


Theoretical massNumber of molelcules
Total (without water)77,9644
Polymers77,9644
Non-polymers00
Water5,783321
1
A: Variable lymphocyte receptor


Theoretical massNumber of molelcules
Total (without water)19,4911
Polymers19,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Variable lymphocyte receptor


Theoretical massNumber of molelcules
Total (without water)19,4911
Polymers19,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Variable lymphocyte receptor


Theoretical massNumber of molelcules
Total (without water)19,4911
Polymers19,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Variable lymphocyte receptor


Theoretical massNumber of molelcules
Total (without water)19,4911
Polymers19,4911
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)72.109, 61.057, 98.081
Angle α, β, γ (deg.)90.000, 107.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11B
21A
12C
22A
13D
23A

NCS domain segments:

Component-ID: 1 / Beg auth comp-ID: HIS / Beg label comp-ID: HIS / End auth comp-ID: CYS / End label comp-ID: CYS / Refine code: 1 / Auth seq-ID: 17 - 190 / Label seq-ID: 1 - 174

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11BB
21AA
12CC
22AA
13DD
23AA

NCS ensembles :
ID
1
2
3
DetailsThe biological assembly is not clear yet.

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Components

#1: Protein
Variable lymphocyte receptor


Mass: 19490.996 Da / Num. of mol.: 4 / Fragment: EXTRACELLULAR DOMAIN
Source method: isolated from a genetically manipulated source
Details: VLR2913 construct in pBAC6 and linearlized DNA ProFold-ER1 (AB Vector) were cotransfected.
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Plasmid: pBAC6 / Production host: Spodoptera frugiperda (fall armyworm) / Strain (production host): HI 5 / References: UniProt: Q6E4B4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 321 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.64 Å3/Da / Density % sol: 53.47 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 2.0-2.4 M NaH2PO4/K2HPO4, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å
DetectorType: MarUSA MarMosaic -325 / Detector: CCD / Date: Jun 3, 2007 / Details: Flat Mirror
RadiationMonochromator: SINGLE CRYSTAL Si(111) BENT / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.1→50 Å / Num. obs: 43844 / % possible obs: 91.3 % / Redundancy: 3.1 % / Rsym value: 0.115 / Net I/σ(I): 9
Reflection shellResolution: 2.1→2.18 Å / Redundancy: 2.8 % / Mean I/σ(I) obs: 3 / Num. unique all: 3847 / Rsym value: 0.293 / % possible all: 81.3

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Processing

Software
NameVersionClassificationNB
REFMACrefinement
PDB_EXTRACT3data extraction
Blu-Icedata collection
MOSFLMdata reduction
HKL-2000data reduction
HKL-2000data scaling
CaspRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2O6R

2o6r


Resolution: 2.1→50 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.921 / SU B: 11.135 / SU ML: 0.149 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.27 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2232 5.1 %RANDOM
Rwork0.217 ---
obs0.22 41594 91.06 %-
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: 20.107 Å2
Baniso -1Baniso -2Baniso -3
1-3.91 Å20 Å2-0.36 Å2
2---1.39 Å20 Å2
3----2.73 Å2
Refinement stepCycle: LAST / Resolution: 2.1→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5456 0 0 321 5777
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0215665
X-RAY DIFFRACTIONr_bond_other_d0.0030.023740
X-RAY DIFFRACTIONr_angle_refined_deg1.6541.9337755
X-RAY DIFFRACTIONr_angle_other_deg1.0683.0079137
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3245706
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.54325.075268
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.42315923
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.631528
X-RAY DIFFRACTIONr_chiral_restr0.0960.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026313
X-RAY DIFFRACTIONr_gen_planes_other0.0030.021063
X-RAY DIFFRACTIONr_nbd_refined0.210.21143
X-RAY DIFFRACTIONr_nbd_other0.210.24153
X-RAY DIFFRACTIONr_nbtor_refined0.1810.22838
X-RAY DIFFRACTIONr_nbtor_other0.090.22982
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1810.2318
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2690.257
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3090.289
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1580.226
X-RAY DIFFRACTIONr_mcbond_it1.5424400
X-RAY DIFFRACTIONr_mcbond_other0.31321383
X-RAY DIFFRACTIONr_mcangle_it2.27245715
X-RAY DIFFRACTIONr_scbond_it4.52662498
X-RAY DIFFRACTIONr_scangle_it5.94582033
Refine LS restraints NCS

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

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1B2296TIGHT POSITIONAL0.050.05
1B2296TIGHT THERMAL0.210.5
2C2296TIGHT POSITIONAL0.040.05
2C2296TIGHT THERMAL0.190.5
3D2290TIGHT POSITIONAL0.050.05
3D2290TIGHT THERMAL0.220.5
LS refinement shellResolution: 2.1→2.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 126 -
Rwork0.235 2618 -
all-2744 -
obs--77.95 %
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)
11.48150.72390.56842.824-0.06721.61120.006-0.0217-0.0915-0.02790.0170.05140.0416-0.0584-0.023-0.07880.0057-0.09280.0992-0.00260.085430.01231.86153.502
20.83670.17790.74862.1540.242.8498-0.04460.01710.0386-0.09510.0448-0.0468-0.12530.1473-0.0002-0.0543-0.0151-0.08770.12270.00020.088943.63538.54682.777
31.3983-0.94540.62582.62340.00841.89320.03940.0347-0.0804-0.0067-0.0277-0.02260.09340.0172-0.0117-0.0427-0.0066-0.09850.1065-0.0070.088770.29960.4887.026
40.7301-0.16210.35342.5513-0.81661.5870.0284-0.020.04030.18380.00280.03890.0411-0.0799-0.0312-0.0380.0127-0.08990.1156-0.00770.080456.57166.97357.626
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA17 - 1901 - 174
2X-RAY DIFFRACTION2BB17 - 1901 - 174
3X-RAY DIFFRACTION3CC17 - 1901 - 174
4X-RAY DIFFRACTION4DD17 - 1901 - 174

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