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- PDB-6u14: VHH R303 C33A/C102A in complex withthe LRR domain of InlB -

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Basic information

Entry
Database: PDB / ID: 6u14
TitleVHH R303 C33A/C102A in complex withthe LRR domain of InlB
ComponentsVHH R303 C33A/C102A mutant
KeywordsIMMUNE SYSTEM / Nanobody / VHH / Internalin / Listeria / Disulfide bond
Biological speciesCamelus dromedarius (Arabian camel)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.3 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
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: VHH R303 C33A/C102A mutant
A: VHH R303 C33A/C102A mutant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,7335
Polymers31,4452
Non-polymers2883
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.280, 47.380, 99.340
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: Antibody VHH R303 C33A/C102A mutant


Mass: 15722.280 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Camelus dromedarius (Arabian camel) / Production host: Escherichia coli (E. coli)
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 1.77 Å3/Da / Density % sol: 30.48 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Bis-Tris pH 4.8 with 2 M Ammonium sulfate.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: May 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.3→34.284 Å / Num. obs: 53995 / % possible obs: 96.86 % / Redundancy: 4.7 % / Biso Wilson estimate: 12.2 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04984 / Rpim(I) all: 0.02511 / Rrim(I) all: 0.05612 / Net I/σ(I): 15.28
Reflection shellResolution: 1.3→1.346 Å / Rmerge(I) obs: 0.3365 / Mean I/σ(I) obs: 4.51 / Num. unique obs: 5298 / CC1/2: 0.919 / Rpim(I) all: 0.1652 / Rrim(I) all: 0.3765 / % possible all: 95.87

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DBA

6dba


Resolution: 1.3→34.284 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 16.7
RfactorNum. reflection% reflection
Rfree0.1789 2700 5 %
Rwork0.1593 --
obs0.1603 53993 96.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 75.55 Å2 / Biso mean: 20.5522 Å2 / Biso min: 6.35 Å2
Refinement stepCycle: final / Resolution: 1.3→34.284 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1839 0 15 301 2155
Biso mean--42.79 30.26 -
Num. residues----242
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.3-1.32360.25241400.2032265896
1.3236-1.34910.23171380.2015263096
1.3491-1.37660.21841390.1941264096
1.3766-1.40660.25261390.1884263196
1.4066-1.43930.23441390.1855265596
1.4393-1.47530.21061400.173266597
1.4753-1.51520.20751410.1734266397
1.5152-1.55980.1841420.1648269997
1.5598-1.61010.18831390.1586265697
1.6101-1.66770.19941420.159269897
1.6677-1.73440.18461410.1636267397
1.7344-1.81340.18151430.1558270597
1.8134-1.9090.1631410.1505269697
1.909-2.02850.18951430.1443270397
2.0285-2.18510.15251420.1412269497
2.1851-2.4050.14441440.1486275297
2.405-2.75290.1741450.1537274998
2.7529-3.46780.17511480.1557281098
3.4678-100.17191540.1631291697
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)
14.21594.6985-5.0486.5786-4.6616.4381-0.24930.53750.0848-0.27130.2090.34180.2841-0.3133-0.01680.1468-0.0113-0.01880.1116-0.02960.104-25.3256-0.0891-4.3273
24.82540.44573.93486.45980.92715.9480.1711-0.01810.0018-0.10050.0093-0.4314-0.24840.371-0.1460.1101-0.03060.03090.12550.01510.1216-2.2624-0.0216-6.8526
32.6313-0.3582-2.76072.7641-0.19962.9631-0.07910.1150.072-0.15050.11680.1219-0.1824-0.0121-0.09160.1457-0.0033-0.02780.08310.00810.0952-19.31943.9292-3.0657
43.7064-0.4074-0.09372.88310.18162.5246-0.0414-0.05720.1632-0.008-0.13190.419-0.2084-0.28290.06120.06960.0132-0.02390.0846-0.03120.1225-23.1087-1.06214.771
51.0966-1.5329-1.84288.04485.0664.424-0.1265-0.1256-0.17420.1793-0.03390.2550.06530.06430.12810.0537-0.0012-0.00560.07410.01250.079-15.9443-6.46655.7633
61.71050.2657-0.39093.75560.67464.36790.0055-0.14110.09830.0116-0.0314-0.0217-0.25060.35450.08480.1026-0.0209-0.03180.1243-0.01320.0718-11.8342.84159.1988
72.89270.2994-0.76911.43610.40251.8224-0.0439-0.13770.1185-0.03590.0118-0.0589-0.1990.07680.01810.1004-0.0069-0.02340.0630.00170.0596-14.1733-0.03470.5439
87.5653-3.7988-3.36282.6651.02415.6360.0181-0.55660.08230.5318-0.04760.0414-0.1631-0.20780.01030.1267-0.00630.00280.1378-0.03510.0782-24.9339-4.751312.3762
97.17471.6252-4.51111.0195-0.79154.1129-0.09780.2744-0.109-0.05840.0063-0.14130.0588-0.1450.10560.07740.0032-0.0050.0560.00650.0829-16.7975-7.0179-2.12
104.3998-3.2590.81934.3928-2.21613.49950.04970.2156-0.3403-0.1449-0.08990.08810.25810.11670.02640.10870.002-0.01580.1499-0.03830.0999-11.9561-4.88618.6186
113.90341.2544-1.04713.26210.27973.77680.02140.13550.102-0.07670.1053-0.065-0.11350.2449-0.08920.06760.0041-0.00910.1069-0.00050.0559-10.64493.990123.8544
123.00464.00110.92025.93392.09172.02020.0941-0.35320.16510.2658-0.24640.30370.2079-0.12560.11480.133-0.0030.01320.1721-0.00520.1152-16.8263-0.850430.6947
133.48641.2225-1.13214.57260.19552.4374-0.0612-0.2233-0.16770.41270.1082-0.15320.17740.3917-0.00180.14560.052-0.02980.21150.01230.1026-5.9695-2.240232.4777
142.97181.38890.22698.27820.49681.4669-0.102-0.0193-0.29240.00910.1190.03230.240.21990.01050.10120.03840.00140.1583-0.00520.0983-8.0481-4.754224.5188
152.1088-0.2303-0.82376.05813.28863.890.05150.0217-0.0835-0.0329-0.05440.0168-0.0069-0.06760.01150.0583-0.00070.00220.09180.00490.0585-16.99973.182926.7715
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'B' and (resid 1 through 8 )B1 - 8
2X-RAY DIFFRACTION2chain 'B' and (resid 9 through 17 )B9 - 17
3X-RAY DIFFRACTION3chain 'B' and (resid 18 through 26 )B18 - 26
4X-RAY DIFFRACTION4chain 'B' and (resid 27 through 40 )B27 - 40
5X-RAY DIFFRACTION5chain 'B' and (resid 41 through 53 )B41 - 53
6X-RAY DIFFRACTION6chain 'B' and (resid 54 through 73 )B54 - 73
7X-RAY DIFFRACTION7chain 'B' and (resid 74 through 99 )B74 - 99
8X-RAY DIFFRACTION8chain 'B' and (resid 100 through 107 )B100 - 107
9X-RAY DIFFRACTION9chain 'B' and (resid 108 through 123 )B108 - 123
10X-RAY DIFFRACTION10chain 'A' and (resid 2 through 17 )A2 - 17
11X-RAY DIFFRACTION11chain 'A' and (resid 18 through 39 )A18 - 39
12X-RAY DIFFRACTION12chain 'A' and (resid 40 through 53 )A40 - 53
13X-RAY DIFFRACTION13chain 'A' and (resid 54 through 73 )A54 - 73
14X-RAY DIFFRACTION14chain 'A' and (resid 74 through 91 )A74 - 91
15X-RAY DIFFRACTION15chain 'A' and (resid 92 through 122 )A92 - 122

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