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- PDB-6dbg: Crystal Structure of VHH R303 in complex with InlB-LRR-IR -

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Basic information

Entry
Database: PDB / ID: 6dbg
TitleCrystal Structure of VHH R303 in complex with InlB-LRR-IR
Components
  • Internalin B
  • VHH R303
KeywordsIMMUNE SYSTEM / nanobody VHH Listeria Internalin B
Function / homology
Function and homology information


peptidoglycan-based cell wall / InlB-mediated entry of Listeria monocytogenes into host cell / heparin binding / lipid binding / extracellular region / plasma membrane / cytoplasm
Similarity search - Function
GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal ...GW domain / GW domain superfamily / GW (Gly-Tryp) dipeptide domain / GW domain profile. / Listeria/Bacterioides repeat / Listeria-Bacteroides repeat domain superfamily / Listeria-Bacteroides repeat domain (List_Bact_rpt) / Leucine-rich repeat-containing adjacent domain / LRR adjacent / Internalin, N-terminal / Bacterial adhesion/invasion protein N terminal / : / Copper resistance protein CopC/internalin, immunoglobulin-like / Leucine rich repeat 4 / Leucine Rich repeats (2 copies) / Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) / Ribonuclease Inhibitor / Leucine-rich repeat, SDS22-like subfamily / 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 / Immunoglobulin E-set / Alpha Beta
Similarity search - Domain/homology
Internalin B / Internalin B
Similarity search - Component
Biological speciesListeria monocytogenes (bacteria)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.51 Å
AuthorsBrooks, C.L. / Toride King, M. / Huh, I.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)SC3GM112532 United States
CitationJournal: J. Biol. Chem. / Year: 2018
Title: Structural basis of VHH-mediated neutralization of the food-borne pathogenListeria monocytogenes.
Authors: King, M.T. / Huh, I. / Shenai, A. / Brooks, T.M. / Brooks, C.L.
History
DepositionMay 3, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2018Provider: repository / Type: Initial release
Revision 1.1Jul 25, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_DOI ..._citation.journal_abbrev / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Sep 12, 2018Group: Data collection / Database references / Source and taxonomy
Category: citation / citation_author / entity_src_gen
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID / _citation_author.name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name
Revision 1.3Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 20, 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: Internalin B
B: Internalin B
C: VHH R303
D: VHH R303


Theoretical massNumber of molelcules
Total (without water)99,1644
Polymers99,1644
Non-polymers00
Water19,5461085
1
A: Internalin B

D: VHH R303


Theoretical massNumber of molelcules
Total (without water)49,5822
Polymers49,5822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
2
B: Internalin B
C: VHH R303


Theoretical massNumber of molelcules
Total (without water)49,5822
Polymers49,5822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)49.890, 66.950, 73.830
Angle α, β, γ (deg.)116.670, 97.730, 95.080
Int Tables number1
Space group name H-MP1

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Components

#1: Protein Internalin B


Mass: 33795.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Gene: inlB, lmo0434 / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: C6ZUN6, UniProt: P0DQD2*PLUS
#2: Antibody VHH R303


Mass: 15786.411 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Plasmid: pSJF2H / Production host: Escherichia coli (E. coli) / Strain (production host): TG1
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1085 / 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: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 0.1 M Sodium Citrate Tribasic Dihydrate, 34 % Jeffamine ED-2001

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: May 9, 2017
Details: Vertical Focusing Mirror: ultra-low expansion (ULE) titanium siliicate flat mirror with Pt, Uncoated, and Pd strips
RadiationMonochromator: ACCEL/BRUKER double crystal monochromator (DCM), featuring indirectly cryo-cooled first crystal and sagittally focusing second crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.51→43.201 Å / Num. obs: 122420 / % possible obs: 93.51 % / Redundancy: 2.9 % / Net I/σ(I): 15.91
Reflection shellResolution: 1.51→1.56 Å

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
PDB_EXTRACT3.24data extraction
xia2data reduction
pointlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DBA, 2UZX

6dba

2uzx


Resolution: 1.51→43.201 Å / SU ML: 0.14 / Cross valid method: THROUGHOUT / σ(F): 1.97 / Phase error: 17.8
RfactorNum. reflection% reflection
Rfree0.1804 6121 5 %
Rwork0.1604 --
obs0.1614 122399 93.52 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 92.91 Å2 / Biso mean: 25.8283 Å2 / Biso min: 10.13 Å2
Refinement stepCycle: final / Resolution: 1.51→43.201 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6203 0 0 1085 7288
Biso mean---33.47 -
Num. residues----812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0126379
X-RAY DIFFRACTIONf_angle_d1.0998700
X-RAY DIFFRACTIONf_chiral_restr0.0641034
X-RAY DIFFRACTIONf_plane_restr0.0081119
X-RAY DIFFRACTIONf_dihedral_angle_d12.7943860
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.51-1.52720.25642010.23253837403894
1.5272-1.54510.24432080.2063933414194
1.5451-1.5640.21352030.19883868407194
1.564-1.58380.22352070.19533917412494
1.5838-1.60460.24232050.1873912411794
1.6046-1.62660.22212060.18893903410995
1.6266-1.64980.21272030.18463860406394
1.6498-1.67450.2052080.18063951415994
1.6745-1.70060.20982050.16883884408994
1.7006-1.72850.21942050.17423905411094
1.7285-1.75830.20362070.17043936414395
1.7583-1.79030.18522040.16763869407394
1.7903-1.82470.2222060.17373918412495
1.8247-1.8620.21312080.18193953416194
1.862-1.90250.22552060.17423915412194
1.9025-1.94670.21912040.163865406994
1.9467-1.99540.18642030.15673860406392
1.9954-2.04930.1862050.15363893409895
2.0493-2.10960.17122030.14833860406393
2.1096-2.17770.17212050.14713887409293
2.1777-2.25560.15882050.14453893409894
2.2556-2.34590.1672010.14543833403493
2.3459-2.45260.14842040.14853869407393
2.4526-2.58190.17752040.15073870407493
2.5819-2.74370.17852020.15723835403793
2.7437-2.95550.18252040.16573885408993
2.9555-3.25280.18562000.16043806400693
3.2528-3.72320.15012000.15413796399691
3.7232-4.690.1422000.14323806400692
4.69-43.21910.19121990.17013759395891
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)
10.76210.45010.87970.79660.89573.96930.00090.13580.0435-0.07470.0640.0684-0.26450.0807-0.06440.17180.0310.00710.1413-0.00270.1386-37.8447-27.907529.0786
23.83761.61580.23433.96150.26254.46780.09750.02820.04930.0238-0.05420.2268-0.2731-0.3074-0.01440.16360.03080.02540.1095-0.02420.0807-39.9496-24.45844.5609
30.5219-0.0115-0.02041.14730.34481.2823-0.0116-0.0024-0.0379-0.12620.0177-0.01380.0435-0.0537-0.01210.1211-0.00990.00750.13180.00040.1297-36.2575-20.235159.7095
41.7876-1.38870.29668.2144-1.39762.0601-0.0912-0.15250.25980.43770.0358-0.0739-0.291-0.2485-0.0120.17450.0314-0.01750.2176-0.04050.1698-34.38971.140476.999
52.22712.246-0.44456.3611-1.77520.9496-0.0116-0.22560.09220.3368-0.0595-0.4226-0.26670.11660.05830.1865-0.0043-0.05830.1988-0.03510.1891-26.2854-5.950779.4892
61.2745-0.09870.26617.6821-1.20781.3133-0.1424-0.08970.23550.11080.1169-0.2645-0.28110.0236-0.00250.1660.0031-0.04990.1797-0.02170.1991-26.9563-1.949374.2961
71.3285-1.14540.08199.2325-0.33851.562-0.0537-0.03320.0870.02810.0712-0.3432-0.10430.02270.00240.10750.0003-0.03340.1514-0.00650.1045-28.4948-7.606769.4453
83.4643-2.24591.75154.4233-2.5256.2478-0.0221-0.25370.22110.0398-0.0377-0.3463-0.52810.36790.04570.1869-0.0542-0.02220.18780.00040.1709-40.6322-26.8438122.5937
90.8919-0.30530.820.7301-0.69983.9363-0.0105-0.08760.0890.07360.0239-0.0304-0.1587-0.1522-0.02350.1489-0.0114-0.00250.1240.00190.1293-46.9642-28.2849113.6236
104.4189-1.6378-0.03852.81440.10924.7284-0.03650.02520.14470.00040.02-0.2039-0.33090.16360.0230.1366-0.0123-0.00280.12240.02610.0708-44.9771-24.26299.8525
110.7775-0.1746-0.07051.651-0.53491.3861-0.0334-0.0644-0.00890.09460.023-0.1514-0.02340.12090.02250.12550.0127-0.01220.15130.00390.1224-45.3307-21.712390.571
120.62560.0812-0.0072.0619-0.61620.9363-0.01590.05560.00810.0210.02780.03270.0347-0.0414-0.01010.09440.0024-0.00960.15550.00290.1107-52.2342-20.762279.7445
130.89-0.057-0.00756.28370.21521.2643-0.06570.16150.2142-0.51160.1722-0.0537-0.25490.27970.03340.2046-0.03580.0040.23120.03790.189-54.0345-1.331567.0645
145.094-5.7541-1.2357.29631.64670.47650.07760.2649-0.1317-0.3251-0.11380.4265-0.0993-0.0645-0.00940.1693-0.0063-0.05560.21820.02060.1867-60.7098-8.890864.4278
151.0607-0.69850.04866.1561-0.28910.9982-0.10060.03740.1726-0.09840.16210.3191-0.1329-0.055-0.04240.14470.0017-0.03710.21320.01880.171-60.8579-4.449369.408
161.14950.4908-0.24272.0721-0.75471.1774-0.0007-0.00460.11080.04860.03130.3713-0.0824-0.0413-0.04070.1448-0.0179-0.03030.19560.02260.131-58.591-10.79574.7195
172.2042.35190.21135.60652.20662.6224-0.0519-0.1944-0.32630.0725-0.11341.16010.2758-0.45910.16560.1737-0.07530.02470.37780.08310.456-75.4976-45.177495.3469
184.0777-0.2863-0.75530.9826-1.57153.8331-0.2988-0.0522-0.07980.04790.20970.83170.0585-0.6678-0.19820.1899-0.0190.01520.31660.03680.2983-74.468-40.007292.2708
193.81840.852-0.52195.1658-2.39324.5878-0.0632-0.1880.18850.20680.19890.4886-0.1277-0.4201-0.07970.08990.01470.02570.190.00680.1812-66.1763-34.47593.3715
202.88330.2933-0.71663.65590.06683.8189-0.0185-0.1266-0.20750.0148-0.0615-0.05770.15480.20460.03830.1048-0.0144-0.00250.14720.03420.1769-61.3129-40.67990.7395
215.2776-1.95561.20196.1181-1.9155.5322-0.04350.1749-0.4019-0.0908-0.09480.23190.3977-0.12880.10760.1315-0.02960.0120.18260.01450.2253-65.5213-45.257787.4057
226.476-4.29011.55193.7615-3.27256.0230.1583-0.0258-0.4114-0.0827-0.04430.92750.5277-0.71320.11180.1472-0.07320.00090.28760.05480.2754-71.9928-42.096688.2397
231.48391.64-0.51493.87730.09391.74970.0109-0.1914-0.14770.1677-0.00720.27240.2072-0.14210.01350.1446-0.00140.01450.21920.05630.2046-64.3929-40.267697.4226
243.46170.4105-0.40750.37761.04083.66110.0381-0.2878-0.30030.38350.02040.44410.5303-0.41930.15810.3523-0.07530.33720.33220.12080.6421-73.9615-53.6869100.4904
251.2244-1.3738-0.90186.0448-0.332.91220.20190.0576-0.4642-0.0328-0.0821-0.4794-0.18371.1187-0.07590.11380.043-0.0010.4853-0.14290.4916-56.3437-38.022850.6556
262.6727-0.301-0.51091.7711-0.01493.0751-0.08140.1152-0.0721-0.01730.1922-0.23960.05480.3853-0.06240.0823-0.03480.02650.1853-0.05280.22-66.7523-30.517351.3043
271.9069-0.2172-0.07854.42370.85043.08380.0750.2554-0.6011-0.18470.0314-0.04010.22260.1196-0.04820.13020.0143-0.01170.167-0.09690.3201-69.5953-41.091852.0447
284.43963.44111.68363.73553.20557.38120.0436-0.1783-0.38630.2134-0.0533-0.2789-0.25830.5015-0.16010.1328-0.0207-0.00910.2325-0.03260.3157-62.2304-34.888560.1001
291.6089-0.5335-0.29291.6247-0.25512.05340.03070.1702-0.3126-0.20080.0385-0.37180.15110.4139-0.06540.14940.00650.03680.2264-0.0970.3095-64.4816-38.196748.4324
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 36 through 123 )A36 - 123
2X-RAY DIFFRACTION2chain 'A' and (resid 124 through 148 )A124 - 148
3X-RAY DIFFRACTION3chain 'A' and (resid 149 through 244 )A149 - 244
4X-RAY DIFFRACTION4chain 'A' and (resid 245 through 261 )A245 - 261
5X-RAY DIFFRACTION5chain 'A' and (resid 262 through 281 )A262 - 281
6X-RAY DIFFRACTION6chain 'A' and (resid 282 through 304 )A282 - 304
7X-RAY DIFFRACTION7chain 'A' and (resid 305 through 321 )A305 - 321
8X-RAY DIFFRACTION8chain 'B' and (resid 36 through 50 )B36 - 50
9X-RAY DIFFRACTION9chain 'B' and (resid 51 through 123 )B51 - 123
10X-RAY DIFFRACTION10chain 'B' and (resid 124 through 148 )B124 - 148
11X-RAY DIFFRACTION11chain 'B' and (resid 149 through 192 )B149 - 192
12X-RAY DIFFRACTION12chain 'B' and (resid 193 through 244 )B193 - 244
13X-RAY DIFFRACTION13chain 'B' and (resid 245 through 261 )B245 - 261
14X-RAY DIFFRACTION14chain 'B' and (resid 262 through 281 )B262 - 281
15X-RAY DIFFRACTION15chain 'B' and (resid 282 through 304 )B282 - 304
16X-RAY DIFFRACTION16chain 'B' and (resid 305 through 321 )B305 - 321
17X-RAY DIFFRACTION17chain 'C' and (resid 2 through 17 )C2 - 17
18X-RAY DIFFRACTION18chain 'C' and (resid 18 through 25 )C18 - 25
19X-RAY DIFFRACTION19chain 'C' and (resid 26 through 39 )C26 - 39
20X-RAY DIFFRACTION20chain 'C' and (resid 44 through 60 )C44 - 60
21X-RAY DIFFRACTION21chain 'C' and (resid 61 through 76 )C61 - 76
22X-RAY DIFFRACTION22chain 'C' and (resid 77 through 83 )C77 - 83
23X-RAY DIFFRACTION23chain 'C' and (resid 84 through 116 )C84 - 116
24X-RAY DIFFRACTION24chain 'C' and (resid 117 through 123 )C117 - 123
25X-RAY DIFFRACTION25chain 'D' and (resid 2 through 25 )D2 - 25
26X-RAY DIFFRACTION26chain 'D' and (resid 26 through 39 )D26 - 39
27X-RAY DIFFRACTION27chain 'D' and (resid 40 through 67 )D40 - 67
28X-RAY DIFFRACTION28chain 'D' and (resid 68 through 76 )D68 - 76
29X-RAY DIFFRACTION29chain 'D' and (resid 77 through 123 )D77 - 123

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