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- PDB-5ufd: Crystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 (Apo) -

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Basic information

Entry
Database: PDB / ID: 5ufd
TitleCrystal Structure of Variable Lymphocyte Receptor (VLR) RBC36 (Apo)
ComponentsRBC36
KeywordsIMMUNE SYSTEM / variable lymphocyte receptors / VLR / leucine-rich repeat / LRR / adaptive immunity / sea lamprey / jawless fish / receptor / glycan binding / glycan receptor
Biological speciesPetromyzon marinus (sea lamprey)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.696 Å
AuthorsCollins, B.C. / Gunn, R.J. / McKitrick, T.R. / Herrin, B.R. / Cummings, R.D. / Cooper, M.D. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) United States
CitationJournal: Structure / Year: 2017
Title: Structural Insights into VLR Fine Specificity for Blood Group Carbohydrates.
Authors: Collins, B.C. / Gunn, R.J. / McKitrick, T.R. / Cummings, R.D. / Cooper, M.D. / Herrin, B.R. / Wilson, I.A.
History
DepositionJan 4, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 18, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2017Group: Database references / Category: citation
Item: _citation.journal_id_ISSN / _citation.page_first / _citation.page_last
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 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 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry
Revision 1.4Oct 9, 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: RBC36
B: RBC36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,3364
Polymers50,2872
Non-polymers492
Water6,720373
1
A: RBC36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1682
Polymers25,1441
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: RBC36
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,1682
Polymers25,1441
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.339, 78.895, 158.804
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein RBC36


Mass: 25143.574 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Production host: Spodoptera frugiperda (fall armyworm)
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 373 / 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: 2.7 Å3/Da / Density % sol: 54.43 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop
Details: 17.3 mg/mL RBC36, 100 mM Tris, pH 8.5, 200 mM magnesium chloride, 20% PEG8000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.03316 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 22, 2015
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03316 Å / Relative weight: 1
ReflectionResolution: 1.696→43.957 Å / Num. obs: 60711 / % possible obs: 99 % / Redundancy: 11.3 % / Rpim(I) all: 0.02 / Net I/σ(I): 23.6
Reflection shellResolution: 1.696→1.76 Å / Num. measured obs: 29524 / Num. unique all: 5444 / Rpim(I) all: 0.16

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3E6J

3e6j


Resolution: 1.696→43.957 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 23.48
RfactorNum. reflection% reflection
Rfree0.2177 3002 4.95 %
Rwork0.1846 --
obs0.1862 60687 98.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 69.72 Å2 / Biso mean: 22.5177 Å2 / Biso min: 12.24 Å2
Refinement stepCycle: final / Resolution: 1.696→43.957 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3495 0 2 373 3870
Biso mean--24.69 27.49 -
Num. residues----457
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063623
X-RAY DIFFRACTIONf_angle_d1.0624937
X-RAY DIFFRACTIONf_chiral_restr0.04570
X-RAY DIFFRACTIONf_plane_restr0.005641
X-RAY DIFFRACTIONf_dihedral_angle_d12.9771309
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 21

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6961-1.72390.30041030.25492326242984
1.7239-1.75360.26381250.22572605273095
1.7536-1.78550.26491560.20352672282899
1.7855-1.81990.23341570.19162706286399
1.8199-1.8570.20791150.187127492864100
1.857-1.89740.2371560.194927622918100
1.8974-1.94150.24031440.195527212865100
1.9415-1.99010.2251350.179627642899100
1.9901-2.04390.21461340.177527522886100
2.0439-2.1040.22211500.185127372887100
2.104-2.1720.21441330.187427952928100
2.172-2.24960.20581370.185327502887100
2.2496-2.33960.2231510.190327502901100
2.3396-2.44610.24391610.196227542915100
2.4461-2.57510.25411650.207927582923100
2.5751-2.73640.22281550.209927752930100
2.7364-2.94760.21241400.205427862926100
2.9476-3.24420.22761490.208328072956100
3.2442-3.71340.22051490.182228222971100
3.7134-4.67760.19791380.147628813019100
4.6776-43.97190.16691490.150830133162100

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