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- PDB-6oca: Ricin A chain bound to VHH antibody V2G10 -

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Basic information

Entry
Database: PDB / ID: 6oca
TitleRicin A chain bound to VHH antibody V2G10
Components
  • Ricin A chain
  • VHH antibody V2G10
KeywordsTOXIN
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / negative regulation of translation
Similarity search - Function
Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesRicinus communis (castor bean)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.113 Å
AuthorsRudolph, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400021C United States
CitationJournal: J.Mol.Biol. / Year: 2020
Title: Intracellular Neutralization of Ricin Toxin by Single-domain Antibodies Targeting the Active Site.
Authors: Rudolph, M.J. / Czajka, T.F. / Davis, S.A. / Thi Nguyen, C.M. / Li, X.P. / Tumer, N.E. / Vance, D.J. / Mantis, N.J.
History
DepositionMar 22, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: Ricin A chain
C: VHH antibody V2G10
B: Ricin A chain
D: VHH antibody V2G10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)89,76911
Polymers89,1504
Non-polymers6197
Water3,621201
1
A: Ricin A chain
C: VHH antibody V2G10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0346
Polymers44,5752
Non-polymers4594
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Ricin A chain
D: VHH antibody V2G10
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,7345
Polymers44,5752
Non-polymers1603
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)193.962, 50.279, 111.671
Angle α, β, γ (deg.)90.000, 124.680, 90.000
Int Tables number5
Space group name H-MC121

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Components

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Protein / Antibody , 2 types, 4 molecules ABCD

#1: Protein Ricin A chain


Mass: 29676.428 Da / Num. of mol.: 2 / Fragment: Toxin catalytic subunit, residues 38-302
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody VHH antibody V2G10


Mass: 14898.465 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Production host: Escherichia coli (E. coli)

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Non-polymers , 4 types, 208 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.51 Å3/Da / Density % sol: 51.02 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 5 / Details: 100 mM MES (pH 5.0) and 20% PEG 6,000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 1, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
Reflection twinOperator: -h-2*l,-k,l / Fraction: 0.052
ReflectionResolution: 2.11→50 Å / Num. obs: 50806 / % possible obs: 99.2 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.115 / Rpim(I) all: 0.051 / Rrim(I) all: 0.126 / Χ2: 1.232 / Net I/σ(I): 4.7 / Num. measured all: 293951
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.11-2.154.31.50422470.3110.7911.7110.65288.4
2.15-2.195.11.18325390.4910.5721.320.65499.7
2.19-2.235.81.11525270.5860.5071.2280.646100
2.23-2.275.91.03725740.5910.4671.1410.683100
2.27-2.3260.8825000.7480.3930.9660.678100
2.32-2.3860.7325510.8020.3250.8010.692100
2.38-2.446.10.69625140.8350.3050.7620.7199.9
2.44-2.56.20.53625690.9020.2340.5870.67699.7
2.5-2.585.90.42225260.930.1880.4630.73299.8
2.58-2.665.50.3725540.9250.1730.410.78899.5
2.66-2.755.30.27324900.9590.1290.3030.88699
2.75-2.8660.23925740.9690.1060.2621.02100
2.86-2.996.40.20125550.980.0850.2191.211100
2.99-3.156.20.16825630.9840.0730.1841.45599.9
3.15-3.355.90.13325560.9920.0590.1461.6899.6
3.35-3.616.10.11225620.9920.0490.1222.12499.8
3.61-3.975.20.0925530.9930.0430.12.33199.7
3.97-4.545.90.07625990.9960.0330.0832.61599.8
4.54-5.726.10.0725760.9970.030.0772.37799.5
5.72-505.60.04926770.9990.0220.0541.7199.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.11 Å48.11 Å
Translation2.11 Å48.11 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIX(1.11.1_2575)refinement
PDB_EXTRACT3.24data extraction
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.113→48.157 Å / FOM work R set: 0.7527 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 31.43 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflection
Rfree0.2465 2496 4.91 %
Rwork0.2127 48258 -
obs0.2132 50791 99.06 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.904 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 138.61 Å2 / Biso mean: 58.91 Å2 / Biso min: 22.5 Å2
Baniso -1Baniso -2Baniso -3
1--4.8309 Å2-0 Å2-3.2122 Å2
2--7.4722 Å2-0 Å2
3----2.6413 Å2
Refinement stepCycle: final / Resolution: 2.113→48.157 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6126 0 31 201 6358
Biso mean--71.01 49.69 -
Num. residues----784
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026299
X-RAY DIFFRACTIONf_angle_d0.6228545
X-RAY DIFFRACTIONf_chiral_restr0.044941
X-RAY DIFFRACTIONf_plane_restr0.0021116
X-RAY DIFFRACTIONf_dihedral_angle_d13.492267
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.1165-2.15720.30541200.33782560268091
2.1572-2.20120.34721240.31142684280895
2.2012-2.2490.35081280.30442640276895
2.249-2.30130.30581550.29782672282795
2.3013-2.35880.35291430.35142642278594
2.3588-2.42250.30261510.28342666281795
2.4225-2.49370.32241280.26682704283295
2.4937-2.57410.31841500.26772657280794
2.5741-2.6660.33071400.29052646278694
2.666-2.77260.30081480.26272648279694
2.7726-2.89860.26611060.25522713281996
2.8986-3.05120.2781210.24332718283996
3.0512-3.24190.27641410.23842694283595
3.2419-3.49160.26891570.21352661281894
3.4916-3.84170.23221520.18792704285695
3.8417-4.39480.20961450.16342693283895
4.3948-5.52620.17631390.14922730286995
5.5262-24.32210.21621200.16682826294695
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
14.09732.1083-1.34335.8280.51713.1950.053-1.0715-0.07630.86140.16010.0943-0.2306-0.6675-0.23510.41510.1915-0.01280.97290.08880.289127.92825.676710.894
23.9887-1.2996-0.8662.89510.64344.0098-0.4033-0.7883-0.43540.34330.54450.22210.034-0.842-0.16120.33590.04590.00160.95040.21780.327125.49215.92556.5984
33.2254-0.5993-0.21072.1467-1.20711.6313-0.2117-0.5223-0.29120.15220.67970.45640.0077-1.3016-0.41950.24190.02390.00760.94140.2460.321317.044723.1894-3.9926
43.1127-1.77041.0713.60770.21853.6311-0.0423-0.3354-0.04470.02950.3578-0.28850.1173-0.1258-0.33030.1664-0.0030.0080.36480.04750.272837.856120.7251-4.0492
55.21831.85933.31040.87890.05547.93380.49960.8162-1.1758-0.6812-1.3992.12210.5915-0.66120.78920.5942-0.24190.110.675-0.27070.707630.1447-0.9453-31.3225
62.437-2.0916-1.67712.34533.27217.26920.22220.7081-0.7745-1.5678-0.14580.6388-0.5329-0.44940.03510.51660.013-0.11120.7571-0.270.586433.54235.0294-31.0646
73.4408-0.1913-1.97552.09891.67042.30070.02990.88130.9309-0.7643-0.75530.874-0.8039-0.32160.49331.12830.1854-0.07650.56930.03790.598432.55823.0291-24.3672
87.08933.00891.42648.09551.03954.075-0.17370.0134-0.0321-0.0655-0.12060.80980.5653-0.06930.36840.4697-0.09670.05330.4812-0.15460.387531.79866.8539-20.4682
92.0673.4602-0.61219.92641.04138.4849-0.24250.3167-0.56560.05030.4467-0.69890.8450.6061-0.23010.45380.10550.02570.4275-0.07460.412842.43397.9628-19.3106
106.56941.73630.38636.6431.28680.24970.2979-0.1659-1.36990.938-0.0523-0.66910.7437-0.0291-0.30240.82910.0736-0.08790.5926-0.09880.690641.125-1.5037-18.0689
115.7246-0.09841.25978.11941.24555.16140.10040.7617-0.3794-1.0868-0.1046-0.7573-0.28230.7432-0.01760.6413-0.03280.12360.5351-0.16180.399140.81926.365-27.5762
125.1725-2.37171.66662.0671.33645.04140.20740.6876-0.8675-0.775-0.1747-0.1733-0.07280.2505-0.01850.548-0.01210.06990.6256-0.22240.529637.37683.5433-28.8483
130.96650.90661.22547.15211.55444.9506-0.02360.3471-0.86550.634-0.4010.69531.333-0.84550.57120.6053-0.22180.14940.6289-0.19170.661632.27031.3669-19.7271
141.86561.40822.00778.28713.83023.7285-0.03950.0401-0.8014-0.1212-0.63251.38950.4365-1.08110.61020.4123-0.21220.09160.9561-0.29480.892326.25464.51-21.6702
154.9457-0.8021-0.87195.25410.50123.8855-0.099-0.3484-0.22670.6356-0.03720.49360.3501-0.21420.1370.2634-0.01560.03990.21690.00040.1669-4.607947.98753.4764
163.2101-0.1066-0.26392.8726-0.71023.1707-0.0351-0.10090.40990.1119-0.17350.7115-0.2074-0.70010.35870.23880.0549-0.01410.3237-0.11260.526-13.587255.626146.0305
175.391-0.1571-0.84154.3691-1.79125.5757-0.18530.1787-0.5927-0.0375-0.08971.252-0.146-0.64260.31370.31140.0067-0.03620.4709-0.16780.7777-20.709650.374141.153
187.2765-3.4342-1.83464.6108-0.15445.76950.13120.90480.3979-0.2361-0.28820.6486-0.8457-0.82040.22420.37940.0878-0.10950.35480.02310.4705-7.510364.724638.1902
192.39920.3616-0.49012.69551.45922.19920.01850.16420.0607-0.08710.0878-0.0069-0.11340.1084-0.12650.20830.0036-0.07140.22960.00410.17966.89853.006741.1064
203.90820.47480.74036.9982-2.31822.63590.097-0.2605-0.52540.2765-0.1784-0.24290.12050.01580.13190.30810.0185-0.02540.3634-0.05230.36416.761436.179747.1481
211.29660.79571.35680.50131.02863.89560.00460.4569-0.132-0.54570.03740.1323-0.34510.1780.23860.30190.0191-0.17721.3288-0.40330.4837-1.61534.013711.5784
222.24592.87481.48384.65492.40763.2343-0.20191.61910.154-0.65130.14970.2041-0.9059-0.23850.19050.5745-0.0045-0.02941.1962-0.04370.44252.92146.373315.165
235.55691.8471-1.183.48951.65231.74150.03151.26960.6524-0.5846-0.138-0.0178-0.85090.2995-0.21550.5854-0.054-0.06260.74680.0050.42947.534553.441724.3341
247.64024.15593.52485.29272.16532.80480.08150.39350.09260.13460.02310.38280.1326-0.3211-0.15940.29280.0308-0.03350.7743-0.19260.3416-2.749335.418723.7942
257.92124.20571.58137.0516-0.09463.21610.4040.615-0.61460.36390.0583-0.8366-0.0740.9255-0.33660.26920.1063-0.11620.8846-0.26410.473515.181939.666526.2053
261.30920.86120.15061.8664-0.05265.58750.49880.7197-1.55410.7039-0.3661-0.42381.00320.1899-0.24270.57150.0551-0.09440.8862-0.39130.78813.961925.517824.3594
271.4490.61731.65042.18242.2093.05530.20441.1526-0.3992-0.07970.0151-0.00480.13790.40510.02760.26820.0738-0.12311.1001-0.38050.26892.448635.747920.368
281.69243.03462.30165.50683.91754.68750.12740.6457-0.1141-0.0581-0.06350.2447-0.0089-0.11260.37870.16740.0579-0.11690.9913-0.3750.4017-5.576334.925819.1955
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:32)A5 - 32
2X-RAY DIFFRACTION2chain 'A' and (resseq 33:75)A33 - 75
3X-RAY DIFFRACTION3chain 'A' and (resseq 76:160)A76 - 160
4X-RAY DIFFRACTION4chain 'A' and (resseq 161:260)A161 - 260
5X-RAY DIFFRACTION5chain 'C' and (resseq 2:17)C2 - 17
6X-RAY DIFFRACTION6chain 'C' and (resseq 18:25)C18 - 25
7X-RAY DIFFRACTION7chain 'C' and (resseq 26:35)C26 - 35
8X-RAY DIFFRACTION8chain 'C' and (resseq 36:52)C36 - 52
9X-RAY DIFFRACTION9chain 'C' and (resseq 53:67)C53 - 67
10X-RAY DIFFRACTION10chain 'C' and (resseq 68:79)C68 - 79
11X-RAY DIFFRACTION11chain 'C' and (resseq 80:88)C80 - 88
12X-RAY DIFFRACTION12chain 'C' and (resseq 89:95)C89 - 95
13X-RAY DIFFRACTION13chain 'C' and (resseq 96:120)C96 - 120
14X-RAY DIFFRACTION14chain 'C' and (resseq 121:135)C121 - 135
15X-RAY DIFFRACTION15chain 'B' and (resseq 3:56)B3 - 56
16X-RAY DIFFRACTION16chain 'B' and (resseq 57:97)B57 - 97
17X-RAY DIFFRACTION17chain 'B' and (resseq 98:122)B98 - 122
18X-RAY DIFFRACTION18chain 'B' and (resseq 123:160)B123 - 160
19X-RAY DIFFRACTION19chain 'B' and (resseq 161:248)B161 - 248
20X-RAY DIFFRACTION20chain 'B' and (resseq 249:267)B249 - 267
21X-RAY DIFFRACTION21chain 'D' and (resseq 2:17)D2 - 17
22X-RAY DIFFRACTION22chain 'D' and (resseq 18:30)D18 - 30
23X-RAY DIFFRACTION23chain 'D' and (resseq 31:39)D31 - 39
24X-RAY DIFFRACTION24chain 'D' and (resseq 40:60)D40 - 60
25X-RAY DIFFRACTION25chain 'D' and (resseq 61:72)D61 - 72
26X-RAY DIFFRACTION26chain 'D' and (resseq 73:80)D73 - 80
27X-RAY DIFFRACTION27chain 'D' and (resseq 81:120)D81 - 120
28X-RAY DIFFRACTION28chain 'D' and (resseq 121:139)D121 - 139

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