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- PDB-6dbe: Crystal Structure of VHH R330 -

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Basic information

Entry
Database: PDB / ID: 6dbe
TitleCrystal Structure of VHH R330
Componentsnanobody VHH R303
KeywordsIMMUNE SYSTEM / nanobody VHH Listeria
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 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 / 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 / _citation_author.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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: nanobody VHH R303
B: nanobody VHH R303
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0343
Polymers30,7962
Non-polymers2381
Water3,009167
1
A: nanobody VHH R303


Theoretical massNumber of molelcules
Total (without water)15,3981
Polymers15,3981
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: nanobody VHH R303
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,6362
Polymers15,3981
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)58.615, 58.615, 100.527
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Antibody nanobody VHH R303


Mass: 15397.870 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pSJF2H / Production host: Escherichia coli (E. coli) / Strain (production host): TG1
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 1.62 Å3/Da / Density % sol: 24.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 0.1M HEPES, 25% PEG 3350

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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: Dec 12, 2012
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: 1.65→50.76 Å / Num. obs: 24176 / % possible obs: 98.4 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.65-1.693.90.4973.8195.1
7.38-50.763.20.0511.4173.9

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
xia2data scaling
PDB_EXTRACT3.24data extraction
xia2data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DBA

6dba


Resolution: 1.65→45.313 Å / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 20.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2227 1233 5.1 %
Rwork0.185 --
obs0.1868 24176 97.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.65→45.313 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1752 0 15 167 1934
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011830
X-RAY DIFFRACTIONf_angle_d1.1522484
X-RAY DIFFRACTIONf_dihedral_angle_d12.5771077
X-RAY DIFFRACTIONf_chiral_restr0.06258
X-RAY DIFFRACTIONf_plane_restr0.007318
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.65-1.71610.29111320.24852441X-RAY DIFFRACTION95
1.7161-1.79420.2611550.21622526X-RAY DIFFRACTION100
1.7942-1.88880.24341510.19192564X-RAY DIFFRACTION100
1.8888-2.00710.20031390.17862564X-RAY DIFFRACTION100
2.0071-2.16210.26111440.17892562X-RAY DIFFRACTION100
2.1621-2.37970.24471230.18672594X-RAY DIFFRACTION100
2.3797-2.7240.21611430.18752573X-RAY DIFFRACTION99
2.724-3.43170.20271230.17422634X-RAY DIFFRACTION98
3.4317-45.32990.20941230.1832485X-RAY DIFFRACTION90
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)
10.3508-0.2266-0.26280.1616-0.08570.4180.0396-0.09310.03350.0261-0.0480.0056-0.0170.27710.00010.1927-0.0084-0.00240.1780.00720.196119.210547.023310.2189
20.97911.07081.49222.93061.24323.6788-0.6203-0.5954-0.6799-0.2999-0.65060.0647-0.2082-0.5374-1.01930.24620.15010.0510.3896-0.00320.45743.421853.627611.7752
31.00060.5176-0.06250.2094-0.05840.3046-0.15310.11890.07120.19680.12670.10340.1687-0.097-0.02180.21050.0117-0.01120.1403-0.0230.181413.09637.23785.1802
40.10150.29470.03030.61870.11190.67780.3090.218-0.4792-0.45410.10630.25550.49190.28310.07090.1860.0013-0.04180.1920.0390.196314.862543.80060.4282
50.4979-0.56170.18891.2038-0.12660.11380.0007-0.1067-0.38920.18960.18380.1509-0.06750.44880.00150.22540.0327-0.04030.30470.02860.19224.903842.98626.6464
60.4667-0.2481-0.28460.73270.15760.53460.0563-0.032-0.02120.1080.07590.2886-0.1029-0.0204-0.00030.2030.00640.00740.14080.00310.174513.753647.987610.9779
70.9195-0.16430.04260.38080.0799-0.0148-0.05520.0986-0.0701-0.26550.3542-0.00420.1381-0.07180.19310.2811-0.0546-0.00850.20150.02980.1853-5.900219.935410.2955
80.8572-0.4711-0.37911.31910.64370.62040.0553-0.3510.22180.43610.0961-0.3559-0.0372-0.16530.07150.26240.0081-0.00680.2004-0.00880.1738-3.422730.547413.8293
92.0382-0.23550.39480.37590.04880.1108-0.3801-0.79570.3492-0.6226-0.3291-0.20690.06080.3048-0.11230.33290.0455-0.00240.28080.12710.566111.392420.289912.4567
100.89280.6005-0.24010.3751-0.26120.5937-0.18210.07850.2490.17580.2258-0.3207-0.1218-0.08750.00290.21090.01420.00550.12060.03060.1631.858434.62165.1251
110.39640.44190.36530.50310.34591.0042-0.05980.25960.3799-0.0345-0.11770.1054-0.0006-0.6683-0.04930.29520.0017-0.01050.18680.0410.1501-2.994229.72122.1119
120.3071-0.19620.12990.07890.02480.2121-0.1053-0.22140.13430.3080.2120.41650.0518-0.56930.05860.26210.04980.00260.32650.03890.2504-9.831431.76818.6216
131.04440.1574-0.03191.2198-0.18890.43620.0054-0.05790.0168-0.04150.1513-0.377-0.0058-0.20720.14110.2922-0.0069-0.03120.14890.0120.17321.122923.65568.9961
141.5308-0.7422-0.54830.38360.30580.21820.2545-0.26180.6753-0.0738-0.2722-0.3244-0.0709-0.23530.0350.33220.00410.0110.2628-0.01980.32091.941835.492221.1425
150.94790.1124-0.16360.0492-0.03640.1590.4123-0.3853-0.740.0241-0.3058-0.06640.08570.08320.11510.3382-0.0547-0.09190.1457-0.00540.2861-1.039913.51667.8286
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 39 )
2X-RAY DIFFRACTION2chain 'A' and (resid 40 through 45 )
3X-RAY DIFFRACTION3chain 'A' and (resid 46 through 60 )
4X-RAY DIFFRACTION4chain 'A' and (resid 61 through 73 )
5X-RAY DIFFRACTION5chain 'A' and (resid 74 through 83 )
6X-RAY DIFFRACTION6chain 'A' and (resid 84 through 117 )
7X-RAY DIFFRACTION7chain 'B' and (resid 2 through 17 )
8X-RAY DIFFRACTION8chain 'B' and (resid 18 through 39 )
9X-RAY DIFFRACTION9chain 'B' and (resid 40 through 45 )
10X-RAY DIFFRACTION10chain 'B' and (resid 46 through 64 )
11X-RAY DIFFRACTION11chain 'B' and (resid 65 through 72 )
12X-RAY DIFFRACTION12chain 'B' and (resid 73 through 83 )
13X-RAY DIFFRACTION13chain 'B' and (resid 84 through 100 )
14X-RAY DIFFRACTION14chain 'B' and (resid 101 through 111 )
15X-RAY DIFFRACTION15chain 'B' and (resid 112 through 118 )

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