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- PDB-5u4m: RTA-V1C7-G29R-no_salt -

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Basic information

Entry
Database: PDB / ID: 5u4m
TitleRTA-V1C7-G29R-no_salt
Components
  • Ricin
  • V1C7 VHH antibody
KeywordsHYDROLASE/IMMUNE SYSTEM / Ricin A Chain / VHH camelid antibody / HYDROLASE-IMMUNE SYSTEM complex
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 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / 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 / Ricin-type beta-trefoil lectin domain / Ribosome-inactivating protein conserved site / Shiga/ricin ribosomal inactivating toxins active site signature. / 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 / Resolution: 2.5 Å
AuthorsRudolph, M.J. / Mantis, N.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400021C United States
CitationJournal: Proteins / Year: 2017
Title: Using homology modeling to interrogate binding affinity in neutralization of ricin toxin by a family of single domain antibodies.
Authors: Bazzoli, A. / Vance, D.J. / Rudolph, M.J. / Rong, Y. / Angalakurthi, S.K. / Toth 4th., R.T. / Middaugh, C.R. / Volkin, D.B. / Weis, D.D. / Karanicolas, J. / Mantis, N.J.
History
DepositionDec 5, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 13, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 26, 2018Group: Data collection / 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 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin
B: V1C7 VHH antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,7793
Polymers42,7442
Non-polymers351
Water84747
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1480 Å2
ΔGint-12 kcal/mol
Surface area16900 Å2
Unit cell
Length a, b, c (Å)64.912, 64.912, 215.419
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-301-

CL

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Components

#1: Protein Ricin /


Mass: 28638.256 Da / Num. of mol.: 1 / Fragment: residues 40-294
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 V1C7 VHH antibody


Mass: 14105.445 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)
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 47 / 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: 3.07 Å3/Da / Density % sol: 59.87 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 4.6 / Details: 8% PEG 4000 and 100 mM sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 23, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 19235 / % possible obs: 99.9 % / Redundancy: 10.2 % / Biso Wilson estimate: 57.56 Å2 / Rmerge(I) obs: 0.08 / Rpim(I) all: 0.026 / Rrim(I) all: 0.084 / Χ2: 1.344 / Net I/σ(I): 8.6 / Num. measured all: 195749
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsCC1/2Diffraction-ID% possible all
2.5-2.548.10.7390.925199.7
2.54-2.598.90.7380.9431100
2.59-2.649.80.6610.9541100
2.64-2.6910.20.6370.971100
2.69-2.7510.70.510.9771100
2.75-2.8210.60.3960.9851100
2.82-2.8910.60.3490.9891100
2.89-2.9610.60.2850.9941100
2.96-3.0510.60.2160.9951100
3.05-3.1510.50.1760.9961100
3.15-3.2610.70.1360.9981100
3.26-3.3910.70.1170.9971100
3.39-3.5510.70.0980.9971100
3.55-3.7310.70.0830.9981100
3.73-3.9710.60.0690.9991100
3.97-4.2710.50.0660.9991100
4.27-4.710.20.0660.9981100
4.7-5.389.90.0680.9981100
5.38-6.789.80.0540.9981100
6.78-509.30.0350.999199.3

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementResolution: 2.5→49.836 Å / SU ML: 0.65 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 29
RfactorNum. reflection% reflection
Rfree0.2465 945 4.98 %
Rwork0.2024 --
obs0.2046 18990 99.77 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Bsol: 36.601 Å2 / ksol: 0.303 e/Å3
Displacement parametersBiso max: 237.34 Å2 / Biso mean: 75.88 Å2 / Biso min: 42.63 Å2
Baniso -1Baniso -2Baniso -3
1-7.6565 Å2-0 Å2-0 Å2
2--7.6565 Å2-0 Å2
3----15.3131 Å2
Refinement stepCycle: final / Resolution: 2.5→49.836 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3014 0 1 47 3062
Biso mean--61.69 59.78 -
Num. residues----384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0033080
X-RAY DIFFRACTIONf_angle_d0.7534181
X-RAY DIFFRACTIONf_chiral_restr0.056457
X-RAY DIFFRACTIONf_plane_restr0.003550
X-RAY DIFFRACTIONf_dihedral_angle_d13.0161113
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 7 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
2.5001-2.63190.34291370.287924932630
2.6319-2.79680.35351350.281925182653
2.7968-3.01270.3191540.271525182672
3.0127-3.31580.32481500.245725272677
3.3158-3.79550.27561170.225625992716
3.7955-4.78130.2011170.155726262743
4.7813-49.8460.19491350.178127642899
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)
17.4584-0.86830.08447.05910.80295.56110.0633-0.0423-0.950.0753-0.98970.43440.2886-0.64280.10450.1299-0.02520.02091.04460.01030.658226.044394.0642225.4404
27.1608-1.39384.58653.6255-1.60238.4042-0.3391-1.2229-0.7840.42880.27270.4876-1.0629-0.7905-0.03980.55320.22240.12251.31410.04770.407327.4007100.9268231.6802
31.81872.47791.80624.13464.50355.76520.5685-0.37060.0042.0207-0.55360.22960.646-0.30510.06971.042-0.18660.04750.98340.17250.488237.799692.0219243.3213
43.0831-1.40982.51057.0322-2.38435.31210.0653-0.462-0.21140.1664-0.1005-0.09260.2245-0.62430.02310.40560.06410.02350.86010.02920.305135.769889.1725223.1685
52.83881.6496-1.2615.2603-0.99826.3191-0.1151-0.0419-0.4910.53470.1757-0.57350.3557-0.1104-0.04940.33120.1699-0.05470.60320.0650.377344.205890.1903221.8975
64.989-0.68521.90355.49763.30774.67240.26960.1295-0.0235-0.4808-0.39370.3378-0.3153-1.16590.11630.37540.14590.02120.6540.08950.268337.774196.0533214.209
73.89762.61243.38324.96780.33754.4779-0.0429-0.40530.522-0.0438-0.48660.3822-0.5295-1.36730.35770.53820.2360.02270.9336-0.04910.306834.8084107.6083228.7026
82.2522.91820.27083.57941.85884.6306-0.0526-0.26340.18050.1221-0.4647-0.4806-0.29390.24170.44760.39220.2610.02880.8060.10660.34346.0822110.2079235.843
96.6025-0.1575-0.36322.02711.46511.93720.3208-0.5836-0.47541.2233-0.80760.45210.55810.08910.34070.69040.15080.040.85780.15250.364541.6227101.1531242.0338
107.42553.8483-4.29055.6547-4.0456.7853-0.32070.37770.1832-1.40470.50530.8304-0.0545-0.11080.13141.04720.0371-0.15961.0886-0.19990.295728.824499.7938189.5959
112.81660.5959-0.58375.5465-4.81024.1651-1.51832.19550.9572-1.03441.22270.5427-1.2-0.7671-0.23531.2532-0.0793-0.21731.0898-0.01980.529932.4465111.5706186.8509
126.79132.34820.29334.01781.93541.2705-0.32920.2744-0.3673-0.6322-0.11080.08340.68090.28390.32510.78620.0923-0.06470.8359-0.09820.365627.046599.2269197.7939
132.7277-1.15720.70845.06133.26342.9262-0.12980.5172-1.04060.37330.5166-0.7178-0.15020.79290.12740.83860.22930.06641.1822-0.16640.625543.3543102.0305192.7343
147.05534.84312.35275.49943.19766.0124-1.6316-0.10580.3967-1.15310.87580.1676-0.8673-0.04390.69630.79450.2268-0.16750.7035-0.04040.491832.4961110.2256198.7822
153.36632.47020.59217.2525-2.60868.1617-0.40050.1475-0.1189-0.94130.2412-0.5980.06481.05310.16260.63770.13080.06930.91230.0090.367137.9344102.619192.824
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resseq 5:17)A5 - 17
2X-RAY DIFFRACTION2chain 'A' and (resseq 18:32)A18 - 32
3X-RAY DIFFRACTION3chain 'A' and (resseq 33:56)A33 - 56
4X-RAY DIFFRACTION4chain 'A' and (resseq 57:97)A57 - 97
5X-RAY DIFFRACTION5chain 'A' and (resseq 98:140)A98 - 140
6X-RAY DIFFRACTION6chain 'A' and (resseq 141:174)A141 - 174
7X-RAY DIFFRACTION7chain 'A' and (resseq 175:193)A175 - 193
8X-RAY DIFFRACTION8chain 'A' and (resseq 194:248)A194 - 248
9X-RAY DIFFRACTION9chain 'A' and (resseq 249:259)A249 - 259
10X-RAY DIFFRACTION10chain 'B' and (resseq -1:12)B-1 - 12
11X-RAY DIFFRACTION11chain 'B' and (resseq 13:24)B13 - 24
12X-RAY DIFFRACTION12chain 'B' and (resseq 25:42)B25 - 42
13X-RAY DIFFRACTION13chain 'B' and (resseq 43:54)B43 - 54
14X-RAY DIFFRACTION14chain 'B' and (resseq 55:87)B55 - 87
15X-RAY DIFFRACTION15chain 'B' and (resseq 88:127)B88 - 127

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