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- PDB-6u12: VHH R303 C33A/C102A in complex withthe LRR domain of InlB -

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Basic information

Entry
Database: PDB / ID: 6u12
TitleVHH R303 C33A/C102A in complex withthe LRR domain of InlB
Components
  • InlB
  • VHH R303 C33A/C102A mutant
KeywordsIMMUNE SYSTEM / Nanobody / VHH / Internalin / Listeria / Disulfide bond
Function / homology
Function and homology information


entry of bacterium into host cell / peptidoglycan-based cell wall / InlB-mediated entry of Listeria monocytogenes into host cell / heparin binding / lipid binding / cell surface / extracellular region / metal ion binding / plasma membrane
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
Biological speciesListeria monocytogenes (bacteria)
Camelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsMendoza, M.N. / Jian, M. / Toride King, M. / Brooks, C.L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)SC3GM112532 United States
CitationJournal: Protein Sci. / Year: 2020
Title: Role of a noncanonical disulfide bond in the stability, affinity, and flexibility of a VHH specific for the Listeria virulence factor InlB.
Authors: Mendoza, M.N. / Jian, M. / King, M.T. / Brooks, C.L.
History
DepositionAug 15, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 12, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: InlB
B: VHH R303 C33A/C102A mutant


Theoretical massNumber of molelcules
Total (without water)41,4012
Polymers41,4012
Non-polymers00
Water7,278404
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)83.210, 83.210, 64.930
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein InlB


Mass: 25678.355 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q45GD4, UniProt: P0DQD3*PLUS
#2: Antibody VHH R303 C33A/C102A mutant


Mass: 15722.280 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 404 / 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: 2.71 Å3/Da / Density % sol: 54.69 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 0.49 M Sodium Phosphate monobasic monohydrate, 0.91 M Potassium Phosphate dibasic pH 6.8.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9794 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 14, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 1.56→64.92 Å / Num. obs: 62702 / % possible obs: 99.3 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.063 / Rpim(I) all: 0.027 / Rrim(I) all: 0.068 / Net I/σ(I): 13.5 / Num. measured all: 384474 / Scaling rejects: 931
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
1.56-1.63.70.6131610543020.5920.3350.7031.692.8
6.98-64.926.30.02847577530.9990.0120.03146.399.9

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Processing

Software
NameVersionClassification
Aimless0.7.1data scaling
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
xia2data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DBF

6dbf


Resolution: 1.56→51.19 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.48 / Phase error: 21.12
RfactorNum. reflection% reflection
Rfree0.1989 3134 5 %
Rwork0.1745 --
obs0.1758 62672 99.25 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.18 Å2 / Biso mean: 32.1161 Å2 / Biso min: 13.08 Å2
Refinement stepCycle: final / Resolution: 1.56→51.19 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2496 0 0 404 2900
Biso mean---41.27 -
Num. residues----327
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.56-1.58430.30041450.2915241290
1.5843-1.61030.24651290.2869259696
1.6103-1.6380.31081250.276272099
1.638-1.66780.28461520.2562269499
1.6678-1.69990.26471490.2452691100
1.6999-1.73460.26291010.23382773100
1.7346-1.77230.27111670.2232680100
1.7723-1.81350.22331520.21192704100
1.8135-1.85890.27391310.20372746100
1.8589-1.90920.24291470.19932696100
1.9092-1.96530.22621440.20152702100
1.9653-2.02880.21061460.18962748100
2.0288-2.10130.19531340.17292715100
2.1013-2.18540.171120.1742744100
2.1854-2.28490.19731400.16892710100
2.2849-2.40540.21111170.17172779100
2.4054-2.5560.15611510.16572710100
2.556-2.75340.17921610.1672715100
2.7534-3.03040.21881550.16392738100
3.0304-3.46890.20881370.1622735100
3.4689-4.37010.15311700.14372747100
4.3701-51.190.19321690.15722783100
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)
11.2786-0.49691.45714.77840.68082.13740.43850.2698-0.6404-0.3599-0.0960.52560.5856-0.1608-0.34650.2306-0.027-0.13250.382-0.02730.4514-47.0455-9.8584-9.5617
23.22870.60541.46551.37810.14062.38970.1036-0.1942-0.2379-0.04740.01870.59620.0797-0.3645-0.12960.1583-0.0012-0.02440.29420.01750.3549-47.4211-0.8587-5.9642
34.50671.13492.2419.16.35157.80970.2831-0.435-0.52580.4604-0.09020.23280.4213-0.5375-0.11450.1745-0.0459-0.01510.27210.09040.2926-40.4222-5.50444.4768
42.11620.3491.58243.8482-0.37184.01640.17460.1774-0.4833-0.16630.02950.11460.3037-0.0029-0.19130.10430.0074-0.0390.2436-0.04770.2589-34.2556-4.2642-3.6575
55.35260.2414-2.1296.19190.09254.93510.146-0.1968-0.47530.24370.15870.02330.1563-0.196-0.27090.1167-0.0235-0.05940.2256-0.02650.1993-28.9201-2.67964.1492
63.0003-1.59551.41964.4128-1.21873.53610.14530.1789-0.4474-0.2294-0.00030.02970.2408-0.1035-0.1510.1297-0.0326-0.02790.1709-0.04250.2397-23.8457-4.08451.1836
72.7041-0.8927-0.14352.33030.40832.07330.09290.134-0.2451-0.12860.024-0.12850.08460.0292-0.10490.12870.0109-0.02680.165-0.06550.1646-16.7194-0.56842.3929
85.2798-0.0487-1.34164.5201-1.17672.1694-0.0012-0.0273-0.1748-0.0350.031-0.18460.09620.0423-0.02610.161-0.0021-0.06270.1727-0.07410.1716-11.22962.99998.0745
93.2547-1.01461.42332.5537-1.00962.4244-0.0368-0.2297-0.17020.14390.1143-0.0802-0.1338-0.0356-0.06670.19720.0155-0.04340.1863-0.03960.1715-11.26025.008314.8197
102.7315-0.76920.56692.4879-1.96284.4092-0.1139-0.10210.07510.09010.1081-0.1492-0.0422-0.15420.0210.2428-0.0169-0.07960.1635-0.06330.1968-9.12799.790511.8966
114.556-0.0913-0.61884.162-2.21761.69170.12860.0487-0.23070.9086-0.06420.3261-0.234-0.19180.050.75220.28690.17310.3589-0.01920.2332-35.334523.414214.9072
123.41792.4883-0.46072.1081-1.27443.1981-0.7797-0.4421-0.1611.16380.90040.712-0.5046-0.6288-0.28940.49310.19960.15210.32350.12210.3656-37.014140.3041-0.0167
131.6869-1.11971.45593.2609-4.10565.1478-0.33390.01470.41521.41140.0116-0.3067-0.9271-0.21720.11040.75260.1634-0.06080.2763-0.07730.2305-31.313530.182510.7352
143.20590.285-0.68932.772-0.35222.7968-0.4538-0.6128-0.07540.76960.53350.2317-0.4184-0.4168-0.18280.28380.09220.01280.21180.00340.1606-29.101620.03749.5454
154.4023-1.20464.37837.0564-1.1124.37250.2932-0.0748-0.263-0.2805-0.00590.42980.4943-0.261-0.32090.1996-0.01870.00470.2436-0.00540.1742-30.745921.26121.1799
163.8326-0.79181.41883.019-0.54662.3443-0.2754-0.0020.4420.64610.1367-0.64-0.24320.12040.12670.31890.0344-0.07170.1631-0.02680.2175-24.703128.06084.0777
171.81960.81550.06183.03972.83433.1721-0.27660.49310.7913-0.74830.33390.4554-0.5005-0.1302-0.09280.3429-0.0232-0.06870.2680.08120.3461-34.749135.3462-5.6776
181.1028-0.1888-0.38673.8771-1.56961.5835-0.16890.11870.2250.50640.38560.5017-0.2842-0.227-0.15660.20420.05810.03840.21550.04880.2307-34.383420.88474.1865
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 37 through 51 )A37 - 51
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 83 )A52 - 83
3X-RAY DIFFRACTION3chain 'A' and (resid 84 through 94 )A84 - 94
4X-RAY DIFFRACTION4chain 'A' and (resid 95 through 124 )A95 - 124
5X-RAY DIFFRACTION5chain 'A' and (resid 125 through 136 )A125 - 136
6X-RAY DIFFRACTION6chain 'A' and (resid 137 through 158 )A137 - 158
7X-RAY DIFFRACTION7chain 'A' and (resid 159 through 193 )A159 - 193
8X-RAY DIFFRACTION8chain 'A' and (resid 194 through 212 )A194 - 212
9X-RAY DIFFRACTION9chain 'A' and (resid 213 through 224 )A213 - 224
10X-RAY DIFFRACTION10chain 'A' and (resid 225 through 243 )A225 - 243
11X-RAY DIFFRACTION11chain 'B' and (resid 1 through 7 )B1 - 7
12X-RAY DIFFRACTION12chain 'B' and (resid 8 through 17 )B8 - 17
13X-RAY DIFFRACTION13chain 'B' and (resid 18 through 25 )B18 - 25
14X-RAY DIFFRACTION14chain 'B' and (resid 26 through 39 )B26 - 39
15X-RAY DIFFRACTION15chain 'B' and (resid 40 through 53 )B40 - 53
16X-RAY DIFFRACTION16chain 'B' and (resid 54 through 83 )B54 - 83
17X-RAY DIFFRACTION17chain 'B' and (resid 84 through 91 )B84 - 91
18X-RAY DIFFRACTION18chain 'B' and (resid 92 through 123 )B92 - 123

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