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- PDB-5uf4: Crystal Structure of Variable Lymphocyte Receptor (VLR) O13 with ... -

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Basic information

Entry
Database: PDB / ID: 5uf4
TitleCrystal Structure of Variable Lymphocyte Receptor (VLR) O13 with LNnT bound
ComponentsO13
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: 2.04 Å
AuthorsGunn, R.J. / Collins, B.C. / McKitrick, T.R. / Cummings, R.D. / Cooper, M.D. / Herrin, B.R. / 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 3, 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 1.2Feb 20, 2019Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.3Dec 11, 2019Group: Author supporting evidence / Data collection / Category: chem_comp / pdbx_audit_support
Item: _chem_comp.type / _pdbx_audit_support.funding_organization
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_special_symmetry / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_entity_id / _chem_comp.name / _chem_comp.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_special_symmetry.label_asym_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 2.2Oct 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: O13
B: O13
C: O13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,4596
Polymers82,3363
Non-polymers2,1233
Water14,394799
1
A: O13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1532
Polymers27,4451
Non-polymers7081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: O13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1532
Polymers27,4451
Non-polymers7081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: O13
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1532
Polymers27,4451
Non-polymers7081
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)82.423, 82.423, 227.481
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number95
Space group name H-MP4322
Components on special symmetry positions
IDModelComponents
11A-464-

HOH

21C-615-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11(chain A and (resseq 22:23 or resseq 25:62 or (resid...
21(chain B and (resseq 22:23 or resseq 25:118 or resseq 120:142 or resseq 144:161 or resseq 163:262))
31(chain C and (resseq 22:23 or resseq 25:62 or (resid...
12(chain C and (resseq 301:304))
22(chain A and (resseq 301:304))
32(chain B and (resseq 301:304))

NCS domain segments:
Dom-IDComponent-IDEns-IDSelection detailsAuth asym-IDAuth seq-ID
111(chain A and (resseq 22:23 or resseq 25:62 or (resid...A22 - 23
121(chain A and (resseq 22:23 or resseq 25:62 or (resid...A25 - 62
131(chain A and (resseq 22:23 or resseq 25:62 or (resid...A63
141(chain A and (resseq 22:23 or resseq 25:62 or (resid...A22 - 262
151(chain A and (resseq 22:23 or resseq 25:62 or (resid...A22 - 262
161(chain A and (resseq 22:23 or resseq 25:62 or (resid...A22 - 262
171(chain A and (resseq 22:23 or resseq 25:62 or (resid...A22 - 262
181(chain A and (resseq 22:23 or resseq 25:62 or (resid...A22 - 262
191(chain A and (resseq 22:23 or resseq 25:62 or (resid...A22 - 262
1101(chain A and (resseq 22:23 or resseq 25:62 or (resid...A22 - 262
211(chain B and (resseq 22:23 or resseq 25:118 or resseq 120:142 or resseq 144:161 or resseq 163:262))B22 - 23
221(chain B and (resseq 22:23 or resseq 25:118 or resseq 120:142 or resseq 144:161 or resseq 163:262))B25 - 118
231(chain B and (resseq 22:23 or resseq 25:118 or resseq 120:142 or resseq 144:161 or resseq 163:262))B120 - 142
241(chain B and (resseq 22:23 or resseq 25:118 or resseq 120:142 or resseq 144:161 or resseq 163:262))B144 - 161
251(chain B and (resseq 22:23 or resseq 25:118 or resseq 120:142 or resseq 144:161 or resseq 163:262))B163 - 262
311(chain C and (resseq 22:23 or resseq 25:62 or (resid...C22 - 23
321(chain C and (resseq 22:23 or resseq 25:62 or (resid...C25 - 62
331(chain C and (resseq 22:23 or resseq 25:62 or (resid...C63
341(chain C and (resseq 22:23 or resseq 25:62 or (resid...C22 - 262
351(chain C and (resseq 22:23 or resseq 25:62 or (resid...C22 - 262
361(chain C and (resseq 22:23 or resseq 25:62 or (resid...C22 - 262
371(chain C and (resseq 22:23 or resseq 25:62 or (resid...C22 - 262
381(chain C and (resseq 22:23 or resseq 25:62 or (resid...C22 - 262
391(chain C and (resseq 22:23 or resseq 25:62 or (resid...C22 - 262
3101(chain C and (resseq 22:23 or resseq 25:62 or (resid...C22 - 262
112(chain C and (resseq 301:304))C301 - 304
212(chain A and (resseq 301:304))A301 - 304
312(chain B and (resseq 301:304))B301 - 304

NCS ensembles :
ID
1
2

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Components

#1: Protein O13


Mass: 27445.322 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Petromyzon marinus (sea lamprey) / Production host: Homo sapiens (human)
#2: Polysaccharide beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose- ...beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose


Type: oligosaccharide / Mass: 707.630 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGalpb1-4DGlcpNAcb1-3DGalpb1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1a_1-5][a2112h-1b_1-5][a2122h-1b_1-5_2*NCC/3=O]/1-2-3-2/a4-b1_b3-c1_c4-d1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][b-D-Galp]{[(3+1)][b-D-GlcpNAc]{[(4+1)][b-D-Galp]{}}}}LINUCSPDB-CARE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 799 / 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: 2.43 Å3/Da / Density % sol: 49.38 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 7.5 mg/mL O13 protein, 1.25 mM LnNT, 20% Peg4000, 0.2 M ammonium sufate, 0.1 M sodium acetate, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 25, 2015
RadiationMonochromator: Double crystal cryo-cooled Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 2.04→46.81 Å / Num. obs: 46172 / % possible obs: 90.4 % / Redundancy: 7.2 % / Biso Wilson estimate: 15.54 Å2 / Rmerge(I) obs: 0.22 / Net I/σ(I): 6.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Diffraction-ID% possible all
2.04-2.0820.61811170.491144.4
2.08-2.112.20.4890.576152.8
2.11-2.152.40.5430.572164.4
2.15-2.22.60.5140.602172.1
2.2-2.252.90.4860.637182.6
2.25-2.33.30.4940.648191.3
2.3-2.353.80.510.636197.6
2.35-2.424.60.5190.734199.7
2.42-2.495.80.5060.8331100
2.49-2.577.50.4680.9331100
2.57-2.669.60.4490.9711100
2.66-2.779.90.4110.9781100
2.77-2.899.90.3280.9851100
2.89-3.059.90.2970.9891100
3.05-3.249.80.240.9881100
3.24-3.499.80.1940.9891100
3.49-3.849.80.1620.9911100
3.84-4.399.70.1250.9941100
4.39-5.539.50.1260.9931100
5.53-46.818.90.1010.9961100

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Processing

Software
NameVersionClassification
DENZOdata collection
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACT3.22data extraction
DENZOdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5UEI

5uei


Resolution: 2.04→46.809 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.68
RfactorNum. reflection% reflection
Rfree0.2241 2281 4.96 %
Rwork0.1945 --
obs0.1959 46005 90.23 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 84.93 Å2 / Biso mean: 17.3641 Å2 / Biso min: 1.34 Å2
Refinement stepCycle: final / Resolution: 2.04→46.809 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5558 0 144 799 6501
Biso mean--18.46 25 -
Num. residues----723
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0045841
X-RAY DIFFRACTIONf_angle_d0.7567988
X-RAY DIFFRACTIONf_chiral_restr0.043967
X-RAY DIFFRACTIONf_plane_restr0.004999
X-RAY DIFFRACTIONf_dihedral_angle_d14.8983641
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDRmsType
11A3369X-RAY DIFFRACTION9.163TORSIONAL
12B3369X-RAY DIFFRACTION9.163TORSIONAL
13C3369X-RAY DIFFRACTION9.163TORSIONAL
21A78X-RAY DIFFRACTION9.163TORSIONAL
22B78X-RAY DIFFRACTION9.163TORSIONAL
23C78X-RAY DIFFRACTION9.163TORSIONAL
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 16

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.04-2.08440.2793730.27141340141345
2.0844-2.13290.3391850.2691663174856
2.1329-2.18620.28771000.2632028212868
2.1862-2.24530.25571470.24582396254381
2.2453-2.31140.2751680.23352697286592
2.3114-2.3860.23161520.22112959311199
2.386-2.47130.26061360.214329973133100
2.4713-2.57020.25421710.202229863157100
2.5702-2.68720.26441690.200829803149100
2.6872-2.82880.2141360.205530383174100
2.8288-3.0060.25231600.208330043164100
3.006-3.23810.22961470.202330533200100
3.2381-3.56380.19581480.176730663214100
3.5638-4.07920.17831750.156230503225100
4.0792-5.13840.17971450.145731533298100
5.1384-46.82150.18981690.178833143483100
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)
10.33630.1711-0.19420.7306-0.05820.5156-0.05860.12860.0393-0.20830.07890.0786-0.0383-0.05360.00030.1171-0.008-0.00450.1370.00910.12413.445530.2716-20.5389
20.70460.29250.40410.4634-0.29750.5769-0.00370.0214-0.0377-0.07550.018-0.07070.06250.013-00.0735-0.00080.01230.0925-0.02070.094210.587318.2504-8.4414
30.5101-0.0031-0.20210.1419-0.08540.39330.03470.1238-0.06660.0203-0.102-0.05430.0659-0.2117-0.04090.0873-0.005900.0977-0.01970.091714.354211.50521.9074
40.2668-0.16020.17920.6428-0.40910.37780.05770.03040.02530.0439-0.0424-0.0682-0.03520.05440.0130.1018-0.0051-0.00320.09010.00080.093718.782412.655312.0586
50.48980.01550.00330.38260.2220.19130.0627-0.0674-0.14510.04660.016-0.33490.07630.22220.00330.15180.00930.0070.1455-0.00350.206424.8098-29.6786-11.075
61.2668-0.52540.39620.7747-0.27220.7709-0.03730.00410.00670.0130.0263-0.0232-0.00610.0110.03980.1065-0.02320.01370.0567-0.00620.05311.8937-13.9798-14.1539
70.00380.00550.02740.02490.00840.0111-0.22150.0557-0.5549-0.18930.1579-0.12140.3790.0335-00.2945-0.02710.00880.25770.01420.287651.5789-5.3305-11.0905
80.4345-0.0640.10660.13870.09980.24550.0192-0.1231-0.1410.1022-0.07010.25030.1257-0.13990.03910.1905-0.04270.03390.2678-0.01230.228541.8636-1.0128-17.0764
90.1762-0.0679-0.06560.3032-0.21380.22610.0332-0.16350.06340.05160.04120.04510.0302-0.22140.00050.14860.0151-0.00330.26-0.01030.220839.44628.6607-22.798
100.06610.0455-0.0740.1162-0.1520.2206-0.04430.0310.30230.04520.15950.1457-0.2227-0.36140.00360.20040.0590.01560.3069-0.02030.354137.787516.2936-25.7236
11-0.0081-0.01140.02330.0221-0.04410.0471-0.0711-0.4282-0.0752-0.08050.38380.2044-0.0782-0.08580.00210.2030.0064-0.02670.3408-0.01380.302836.128813.0666-36.1507
120.160.0138-0.0570.1614-0.13130.1616-0.01120.06530.2438-0.02990.07410.0432-0.1506-0.2780.00050.22960.0222-0.02690.2718-0.00530.258140.938520.4915-35.149
130.15250.2912-0.22460.4165-0.02450.46330.06250.18970.1182-0.0306-0.01020.0266-0.2127-0.0630.00410.18850.021-0.01020.22770.02670.265446.345621.63-41.7572
140.00670.0059-0.0058-0.0105-0.01220.0134-0.15070.2689-0.04320.0530.15510.0879-0.0796-0.15050.00040.16710.0092-0.01550.24750.01180.220549.387417.4089-49.0872
150.0194-0.0347-0.02980.06990.06390.04470.0545-0.07890.2875-0.2299-0.07530.034-0.3253-0.2869-0.00030.20340.0548-0.01550.39880.07030.289638.096326.8181-53.5017
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 22 through 94 )A22 - 94
2X-RAY DIFFRACTION2chain 'A' and (resid 95 through 163 )A95 - 163
3X-RAY DIFFRACTION3chain 'A' and (resid 164 through 189 )A164 - 189
4X-RAY DIFFRACTION4chain 'A' and (resid 190 through 262 )A190 - 262
5X-RAY DIFFRACTION5chain 'B' and (resid 22 through 75 )B22 - 75
6X-RAY DIFFRACTION6chain 'B' and (resid 76 through 262 )B76 - 262
7X-RAY DIFFRACTION7chain 'C' and (resid 22 through 34 )C22 - 34
8X-RAY DIFFRACTION8chain 'C' and (resid 35 through 94 )C35 - 94
9X-RAY DIFFRACTION9chain 'C' and (resid 95 through 132 )C95 - 132
10X-RAY DIFFRACTION10chain 'C' and (resid 133 through 151 )C133 - 151
11X-RAY DIFFRACTION11chain 'C' and (resid 152 through 163 )C152 - 163
12X-RAY DIFFRACTION12chain 'C' and (resid 164 through 189 )C164 - 189
13X-RAY DIFFRACTION13chain 'C' and (resid 190 through 231 )C190 - 231
14X-RAY DIFFRACTION14chain 'C' and (resid 232 through 247 )C232 - 247
15X-RAY DIFFRACTION15chain 'C' and (resid 248 through 262 )C248 - 262

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