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- PDB-6dbd: Crystal Structure of VHH R326 -

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Basic information

Entry
Database: PDB / ID: 6dbd
TitleCrystal Structure of VHH R326
Componentsnanobody VHH R326
KeywordsIMMUNE SYSTEM / nanobody VHH Listeria
Function / homologyACETATE ION
Function and homology information
Biological speciesLama glama (llama)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.755 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
Revision 1.3Nov 6, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Jan 1, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry
Revision 1.6Oct 23, 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: nanobody VHH R326
B: nanobody VHH R326
C: nanobody VHH R326
D: nanobody VHH R326
hetero molecules


Theoretical massNumber of molelcules
Total (without water)56,7566
Polymers56,6744
Non-polymers822
Water8,341463
1
A: nanobody VHH R326


Theoretical massNumber of molelcules
Total (without water)14,1691
Polymers14,1691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: nanobody VHH R326
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,1922
Polymers14,1691
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: nanobody VHH R326


Theoretical massNumber of molelcules
Total (without water)14,1691
Polymers14,1691
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: nanobody VHH R326
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,2282
Polymers14,1691
Non-polymers591
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)97.701, 97.701, 243.800
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Components on special symmetry positions
IDModelComponents
11B-428-

HOH

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Components

#1: Antibody
nanobody VHH R326


Mass: 14168.574 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lama glama (llama) / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 463 / 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: 2.96 Å3/Da / Density % sol: 58.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.2 M ammonium sulfate, 0.1< sodium acetate, 22% PEG 4000

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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: 1.755→69.51 Å / Num. obs: 68308 / % possible obs: 98.4 % / Redundancy: 17.5 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 19.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
1.76-1.817.10.794.2193.4
7.85-69.5116.20.03937.1196.7

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Processing

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

6dba


Resolution: 1.755→48.85 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.96
RfactorNum. reflection% reflection
Rfree0.1819 3443 5.06 %
Rwork0.1595 --
obs0.1607 68035 97.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 109.76 Å2 / Biso mean: 36.5136 Å2 / Biso min: 14.29 Å2
Refinement stepCycle: final / Resolution: 1.755→48.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3305 0 8 463 3776
Biso mean--50.51 44.46 -
Num. residues----448
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0123360
X-RAY DIFFRACTIONf_angle_d1.0824562
X-RAY DIFFRACTIONf_chiral_restr0.067513
X-RAY DIFFRACTIONf_plane_restr0.007601
X-RAY DIFFRACTIONf_dihedral_angle_d10.9351963
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 25

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7554-1.77950.22791220.21172390251291
1.7795-1.80490.19771150.20352385250092
1.8049-1.83180.2211250.17712430255594
1.8318-1.86050.19991230.18412444256794
1.8605-1.8910.18061290.17412440256995
1.891-1.92360.21241440.17532451259595
1.9236-1.95860.18041350.16262483261896
1.9586-1.99620.19491410.15752538267998
1.9962-2.0370.17751430.15262557270098
2.037-2.08130.19141440.1552574271899
2.0813-2.12970.1771310.15112576270799
2.1297-2.18290.19161240.150226062730100
2.1829-2.2420.16451560.143225912747100
2.242-2.30790.17921500.15072587273799
2.3079-2.38240.18011450.14726272772100
2.3824-2.46760.18591250.152726002725100
2.4676-2.56640.1631400.153526502790100
2.5664-2.68320.16991340.155726212755100
2.6832-2.82460.22021390.155626522791100
2.8246-3.00150.17761550.161226352790100
3.0015-3.23330.15721480.161826762824100
3.2333-3.55850.17271260.154426992825100
3.5585-4.07330.17291530.144927072860100
4.0733-5.1310.15621480.131627542902100
5.131-48.86940.23621480.21822919306799
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)
13.9674-0.6008-2.08652.65571.49294.5784-0.07120.19890.1582-0.14340.11140.1556-0.0297-0.3146-0.06140.2584-0.06030.01450.21030.03410.26926.179451.21920.2394
24.2708-0.9372-1.63865.00271.10325.37920.05220.05670.38040.29260.3070.44270.1245-0.6523-0.30840.2182-00.03730.27450.06840.3223-3.294151.11227.7452
32.2627-0.0545-1.33385.27540.06673.0437-0.02130.06820.01180.03130.11130.0630.1276-0.2195-0.04810.2423-0.0466-0.02960.19820.01190.18092.974645.22938.5232
49.20722.99576.64823.99883.22375.18560.39550.1343-1.2038-0.08450.139-0.23561.5453-0.3149-0.4370.5856-0.08880.01150.2608-0.05240.40379.005635.9224-2.7087
55.2075-0.6503-2.63172.33060.37535.7661-0.02890.40830.1228-0.41610.2290.5495-0.1099-0.843-0.07780.2221-0.0581-0.05310.33640.09070.3139-2.203548.8397-0.686
69.56743.76687.05914.18633.56997.41150.0591-0.97310.58020.2268-0.1219-0.1085-0.9107-0.48120.10830.4670.0601-0.02440.3403-0.09480.2819-29.057239.612613.5959
73.38030.42870.33593.22060.30742.81120.0396-0.1294-0.17040.18140.1329-0.0545-0.3082-0.1241-0.14270.25150.0309-0.01950.16690.00990.1924-32.974930.57614.6811
85.41881.77910.84254.79320.05973.0714-0.1003-0.25020.26790.2811-0.005-0.0688-0.11160.01070.02720.2971-0.0205-0.06510.1618-0.02220.2144-22.768931.838813.5909
91.4331-0.5141.36272.67480.84712.04230.0228-0.50990.03460.4661-0.13450.2706-0.1057-0.157-0.06570.3134-0.00730.00370.2145-0.02390.2051-24.351425.589415.1795
107.08924.81080.80657.0571.31682.4167-0.0922-0.27690.12120.085-0.03960.054-0.33290.18430.05040.2292-0.0389-0.05230.15320.00430.2005-14.937427.86167.83
111.49660.2875-0.04281.32330.52431.77210.0858-0.1348-0.0195-0.0519-0.1722-0.0972-0.2191-0.06090.04370.254-0.0058-0.02430.1549-0.00240.2177-24.643328.15033.4925
127.46310.9556-5.85590.2457-0.75634.6056-0.2792-0.1397-0.70420.0180.0150.00620.37630.06520.18880.2709-0.0181-0.00940.20460.01710.2765-34.978917.85614.4845
137.05552.26652.20772.08370.23442.048-0.0869-0.19690.15240.24740.12010.0051-0.2864-0.03240.05920.2910.0409-0.02040.2238-0.00660.185-27.740829.864614.6443
148.15921.08371.62642.4027-0.33263.0715-0.5277-1.1120.90280.63030.142-0.0941-1.0272-0.08520.23450.5378-0.009-0.08390.3503-0.11720.2793-23.164835.408320.4788
157.0242.7692.4912.02024.63488.9617-0.185-0.1291-0.16120.04220.00920.6225-0.1138-0.4899-0.04390.2981-0.01660.00220.29090.06340.295-40.47823.44357.6296
161.92830.1532-0.32825.1014-1.92193.34850.06790.293-0.2735-0.2748-0.1601-0.14160.16830.3110.16970.2282-0.01020.01830.2609-0.05350.2285-6.165510.5525-4.3537
174.26571.1127-1.30663.0984-0.48784.4194-0.1722-0.13980.11270.22570.1561-0.02050.04990.1995-0.01310.26820.0243-0.01810.15590.0120.2207-7.666910.96017.3763
182.9911-0.45070.11332.8963-0.19771.98570.0129-0.2704-0.09340.2452-0.0759-0.3024-0.09160.30310.04090.2223-0.0288-0.04710.17290.00920.2074-10.515618.74646.0987
190.9161-1.17820.00964.6844-2.3022.07890.06420.2289-0.2057-0.2095-0.08280.22510.00880.13310.02630.2308-0.0268-0.00640.1768-0.03370.2427-13.574813.7147-1.593
208.90730.7944-0.00623.7911-0.262.85460.30440.49170.7571-0.3004-0.3693-0.3933-0.53040.29070.0790.3202-0.02650.01320.34850.07830.2851-6.556925.7081-9.2112
214.12981.2051-3.74084.2349-2.79749.4103-0.2272-0.2046-0.15920.46540.2571-0.25340.29650.21740.12930.29770.0209-0.03850.24250.00790.2573-2.34111.62437.9401
222.1924-0.3023-0.4843.7776-2.06894.2067-0.10290.4250.1696-0.3017-0.032-0.48320.1160.28410.14020.2028-0.03210.00860.3340.03170.2967-0.326815.575-2.7921
233.3656-1.39483.28241.80290.15935.062-0.1226-0.6332-0.4660.10430.23250.51530.725-0.4184-0.05640.4414-0.1114-0.12070.32840.10620.3639-3.288521.836727.5846
243.77413.6583-2.21467.7792-2.10286.10640.2630.7157-0.6543-0.26350.3353-0.31770.03080.8201-0.45780.21720.0547-0.11220.3845-0.11730.378916.449334.331330.4419
258.2065.20160.85414.97431.56641.97630.19820.07490.0086-0.00810.10370.22050.750.21-0.37930.3991-0.0345-0.15340.24890.0250.28863.405824.397624.0458
264.82922.5052.08614.67761.33624.66130.2028-0.2922-0.32570.0190.0113-0.0372-0.0571-0.3202-0.05630.2359-0.0899-0.07370.22740.04080.212-5.346429.951522.9424
274.68911.39991.82762.5947-0.33593.2321-0.0229-0.0106-0.0124-0.04280.0464-0.1129-0.22930.0149-0.02940.2579-0.0783-0.05780.17270.0210.1691-0.919336.253817.3285
285.98714.78241.50185.47521.3424.9661-0.25750.43830.1779-0.5320.35340.0540.01940.5044-0.13670.2845-0.039-0.04420.2414-0.01720.21176.798732.356718.0748
291.46980.23120.990.23660.91993.14980.05330.1096-0.0853-0.13890.2057-0.05020.10020.3181-0.15450.2436-0.0373-0.04950.2377-0.02060.21785.912933.397225.4902
306.50982.33245.33793.16641.89388.91940.652-0.9293-0.63660.3024-0.44860.21520.5347-0.947-0.45580.329-0.1069-0.06530.39830.07460.2909-11.04127.891726.1771
317.90755.17520.92193.70550.09584.5714-0.1750.2832-0.1207-0.16740.347-0.1157-0.3430.4515-0.08080.2212-0.0038-0.05280.2822-0.08080.240712.086135.671934.4971
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 27 )A1 - 27
2X-RAY DIFFRACTION2chain 'A' and (resid 28 through 38 )A28 - 38
3X-RAY DIFFRACTION3chain 'A' and (resid 39 through 81 )A39 - 81
4X-RAY DIFFRACTION4chain 'A' and (resid 82 through 89 )A82 - 89
5X-RAY DIFFRACTION5chain 'A' and (resid 90 through 116 )A90 - 116
6X-RAY DIFFRACTION6chain 'B' and (resid 1 through 7 )B1 - 7
7X-RAY DIFFRACTION7chain 'B' and (resid 8 through 27 )B8 - 27
8X-RAY DIFFRACTION8chain 'B' and (resid 28 through 39 )B28 - 39
9X-RAY DIFFRACTION9chain 'B' and (resid 40 through 52 )B40 - 52
10X-RAY DIFFRACTION10chain 'B' and (resid 53 through 59 )B53 - 59
11X-RAY DIFFRACTION11chain 'B' and (resid 60 through 81 )B60 - 81
12X-RAY DIFFRACTION12chain 'B' and (resid 82 through 89 )B82 - 89
13X-RAY DIFFRACTION13chain 'B' and (resid 90 through 98 )B90 - 98
14X-RAY DIFFRACTION14chain 'B' and (resid 99 through 109 )B99 - 109
15X-RAY DIFFRACTION15chain 'B' and (resid 110 through 116 )B110 - 116
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 27 )C1 - 27
17X-RAY DIFFRACTION17chain 'C' and (resid 28 through 38 )C28 - 38
18X-RAY DIFFRACTION18chain 'C' and (resid 39 through 63 )C39 - 63
19X-RAY DIFFRACTION19chain 'C' and (resid 64 through 81 )C64 - 81
20X-RAY DIFFRACTION20chain 'C' and (resid 82 through 89 )C82 - 89
21X-RAY DIFFRACTION21chain 'C' and (resid 90 through 103 )C90 - 103
22X-RAY DIFFRACTION22chain 'C' and (resid 104 through 116 )C104 - 116
23X-RAY DIFFRACTION23chain 'D' and (resid 1 through 7 )D1 - 7
24X-RAY DIFFRACTION24chain 'D' and (resid 8 through 17 )D8 - 17
25X-RAY DIFFRACTION25chain 'D' and (resid 18 through 26 )D18 - 26
26X-RAY DIFFRACTION26chain 'D' and (resid 27 through 45 )D27 - 45
27X-RAY DIFFRACTION27chain 'D' and (resid 46 through 63 )D46 - 63
28X-RAY DIFFRACTION28chain 'D' and (resid 64 through 73 )D64 - 73
29X-RAY DIFFRACTION29chain 'D' and (resid 74 through 97 )D74 - 97
30X-RAY DIFFRACTION30chain 'D' and (resid 98 through 109 )D98 - 109
31X-RAY DIFFRACTION31chain 'D' and (resid 110 through 117 )D110 - 117

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