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- PDB-6obe: Ricin A chain bound to VHH antibody V6H8 -

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Basic information

Entry
Database: PDB / ID: 6obe
TitleRicin A chain bound to VHH antibody V6H8
Components
  • Ricin A chain
  • VHH antibody V6H8
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
IMIDAZOLE / NICKEL (II) ION / Ricin
Similarity search - Component
Biological speciesRicinus communis (castor bean)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.732 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 20, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Oct 14, 2020Group: Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / pdbx_struct_conn_angle / struct_conn
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 / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.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_symmetry
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
B: VHH antibody V6H8
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,9938
Polymers42,6202
Non-polymers3736
Water7,386410
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: surface plasmon resonance
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3300 Å2
ΔGint2 kcal/mol
Surface area16190 Å2
Unit cell
Length a, b, c (Å)90.371, 90.371, 204.015
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
11A-302-

NI

21A-675-

HOH

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein Ricin A chain


Mass: 29676.428 Da / Num. of mol.: 1 / 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 V6H8


Mass: 12943.438 Da / Num. of mol.: 1
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, 416 molecules

#3: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / 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: 2.82 Å3/Da / Density % sol: 56.4 %
Crystal growTemperature: 295 K / Method: vapor diffusion / Details: 100 mM citric acid and 15% PEG

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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: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.73→50 Å / Num. obs: 52131 / % possible obs: 100 % / Redundancy: 20.2 % / Biso Wilson estimate: 20.35 Å2 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.038 / Rrim(I) all: 0.173 / Χ2: 1.094 / Net I/σ(I): 6.2 / Num. measured all: 1053545
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.73-1.7613.12.53825370.6860.7182.6390.569100
1.76-1.7915.32.225520.7880.5732.2750.587100
1.79-1.8317.21.88325540.8590.4621.940.611100
1.83-1.8618.81.69225540.8860.3981.7390.629100
1.86-1.9211.42525700.9460.3191.4610.681100
1.9-1.9521.71.04425460.9490.231.0690.782100
1.95-221.70.78725610.9710.1730.8060.73100
2-2.0521.70.64125730.9770.1410.6560.758100
2.05-2.1121.70.52125700.9870.1150.5340.858100
2.11-2.1821.70.38425620.9920.0850.3930.834100
2.18-2.2621.60.34326010.9920.0760.3511.032100
2.26-2.3521.60.26525590.9960.0580.2710.903100
2.35-2.4521.60.22126010.9960.0490.2270.913100
2.45-2.5821.60.17825970.9970.0390.1830.945100
2.58-2.7521.50.14126230.9970.0310.1441.088100
2.75-2.9621.30.1126190.9980.0240.1121.223100
2.96-3.2621.10.08726410.9990.0190.0891.601100
3.26-3.7320.70.07426780.9990.0170.0752.284100
3.73-4.69200.05627040.9990.0130.0582.35100
4.69-5019.20.0529290.9990.0120.0511.98499.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å44.12 Å
Translation2 Å44.12 Å

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Processing

Software
NameVersionClassificationNB
HKL-2000data reduction
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIX(1.7.1_743)refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.732→44.116 Å / FOM work R set: 0.8757 / SU ML: 0.43 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 18.81 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2079 2570 4.94 %
Rwork0.1706 49462 -
obs0.1725 52032 99.96 %
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 34.471 Å2 / ksol: 0.328 e/Å3
Displacement parametersBiso max: 97 Å2 / Biso mean: 28.09 Å2 / Biso min: 8.25 Å2
Baniso -1Baniso -2Baniso -3
1-1.3321 Å2-0 Å2-0 Å2
2--1.3321 Å2-0 Å2
3----2.6643 Å2
Refinement stepCycle: final / Resolution: 1.732→44.116 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3000 0 19 410 3429
Biso mean--24.95 37.52 -
Num. residues----382
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0113151
X-RAY DIFFRACTIONf_angle_d1.2644287
X-RAY DIFFRACTIONf_chiral_restr0.094470
X-RAY DIFFRACTIONf_plane_restr0.006569
X-RAY DIFFRACTIONf_dihedral_angle_d14.0521152
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 18 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.732-1.76530.34381480.299626542802
1.7653-1.80130.27731290.26527342863
1.8013-1.84050.27551250.234127272852
1.8405-1.88330.24391430.207526842827
1.8833-1.93040.22711380.180826852823
1.9304-1.98260.18421390.159726952834
1.9826-2.0410.22191370.149327192856
2.041-2.10680.18341510.153327032854
2.1068-2.18210.17521490.146326972846
2.1821-2.26950.16961360.149827312867
2.2695-2.37280.20571470.152727432890
2.3728-2.49790.22151410.166727172858
2.4979-2.65430.20521120.169227912903
2.6543-2.85930.21121450.169827422887
2.8593-3.14690.21081470.170927792926
3.1469-3.60210.2111480.167928032951
3.6021-4.53750.17941520.149228462998
4.5375-44.13070.21611830.184330123195
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)
12.38951.211-0.08853.3367-0.55122.7065-0.10420.1338-0.0172-0.18440.09040.22090.0448-0.2453-0.00460.1069-0.0498-0.02760.13140.03240.058211.0652.6979-5.2956
22.1198-0.5325-1.04030.8535-0.2642.08060.02940.19770.0356-0.01850.04870.0285-0.0254-0.1857-0.07820.112-0.0115-0.01530.09910.01990.067217.618860.4878-4.6468
31.0936-0.6184-0.26272.39670.09652.4663-0.03460.04320.11920.1510.1290.1862-0.2358-0.2164-0.0570.11730.01710.02960.09120.04920.108914.738167.55457.5203
43.07020.4939-0.91551.51290.17542.0732-0.0539-0.1326-0.05720.24150.12180.11450.1426-0.1392-0.07340.16890.00620.02760.1070.06470.119115.758551.86513.7286
54.70173.0835-0.95426.849-1.22771.0386-0.15780.1992-0.3268-0.09570.1024-0.0660.2776-0.0650.03910.1876-0.00820.01240.12050.01020.104320.770343.9353-1.1562
66.20713.0892-0.95723.5619-0.86631.5652-0.1291-0.2447-0.55440.18760.095-0.19740.3016-0.01720.02960.19690.0320.01820.12180.03180.117325.531743.49556.1233
72.5907-0.2031-0.22882.4224-0.10752.68220.0133-0.029-0.0892-0.05650.0073-0.23620.04650.37730.01580.11010.00260.00770.13120.00310.086237.002252.2893-6.1343
84.1564-2.12540.26611.1512-0.17521.55370.01570.82960.75730.1386-0.2394-0.13640.02830.10120.4560.2488-0.0284-0.12890.5194-0.1560.603545.586568.512312.3048
90.33490.5460.18222.6208-0.71980.69520.12380.2188-0.20920.0843-0.1432-0.44180.21750.4434-0.03150.54520.1717-0.39080.8524-0.18720.91564.158854.316918.3127
105.3991-5.58143.77536.1389-4.17413.87550.0586-0.16050.17680.2786-0.2379-0.32780.03430.30970.12370.40550.1456-0.29030.5242-0.19140.606850.939260.638419.4217
114.6538-0.4896-0.61280.2774-0.29380.6526-0.0233-0.17680.56970.16080.1927-0.6309-0.06230.1671-0.13050.19880.0972-0.09370.2893-0.12760.382341.009259.533512.301
126.45320.6503-6.93190.4218-0.60857.46910.00320.2951-0.37180.06490.0572-0.4439-0.1235-0.3643-0.06470.23170.1029-0.08320.3088-0.06520.539750.017550.94557.0251
138.4264-4.15770.98422.7694-0.36540.13520.17530.0177-0.7197-0.0818-0.1732-0.74820.38780.51490.00350.38310.1852-0.06670.38230.05750.469139.223648.208716.7918
144.679-1.7244-0.62632.3978-0.59092.6054-0.0775-0.5749-0.50860.4093-0.032-0.59650.2410.37280.16360.36840.2097-0.2210.5042-0.04630.48547.523352.804420.02
150.8823-0.0668-2.05090.0050.15524.7675-0.3269-0.7135-1.0080.11960.1531-0.06280.6310.74350.19570.47880.3136-0.14250.72-0.06110.983261.43747.402614.0541
162.2525-0.45660.55730.745-0.26260.7105-0.0665-0.00930.19160.15490.2521-0.67550.0670.3845-0.06610.11790.0292-0.03150.2612-0.140.37244.238260.12848.3585
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 3:32)A3 - 32
2X-RAY DIFFRACTION2chain 'A' and (resseq 33:75)A33 - 75
3X-RAY DIFFRACTION3chain 'A' and (resseq 76:122)A76 - 122
4X-RAY DIFFRACTION4chain 'A' and (resseq 123:174)A123 - 174
5X-RAY DIFFRACTION5chain 'A' and (resseq 175:194)A175 - 194
6X-RAY DIFFRACTION6chain 'A' and (resseq 195:210)A195 - 210
7X-RAY DIFFRACTION7chain 'A' and (resseq 211:267)A211 - 267
8X-RAY DIFFRACTION8chain 'B' and (resseq 0:7)B0 - 7
9X-RAY DIFFRACTION9chain 'B' and (resseq 8:15)B8 - 15
10X-RAY DIFFRACTION10chain 'B' and (resseq 17:25)B17 - 25
11X-RAY DIFFRACTION11chain 'B' and (resseq 26:39)B26 - 39
12X-RAY DIFFRACTION12chain 'B' and (resseq 40:52)B40 - 52
13X-RAY DIFFRACTION13chain 'B' and (resseq 53:60)B53 - 60
14X-RAY DIFFRACTION14chain 'B' and (resseq 61:83)B61 - 83
15X-RAY DIFFRACTION15chain 'B' and (resseq 84:90)B84 - 90
16X-RAY DIFFRACTION16chain 'B' and (resseq 91:117)B91 - 117

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