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- PDB-5u4l: RTA-V1C7_G29R-high-salt -

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Basic information

Entry
Database: PDB / ID: 5u4l
TitleRTA-V1C7_G29R-high-salt
Components
  • Ricin
  • V1C7 VHH antibody G29R variant
KeywordsHYDROLASE/IMMUNE SYSTEM / Ricin A chain / VHH 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
PHOSPHATE ION / Ricin
Similarity search - Component
Biological speciesRicinus communis (castor bean)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / 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 1.1Jan 17, 2018Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Dec 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 1.3Dec 11, 2019Group: 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

Downloads & links

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Assembly

Deposited unit
A: Ricin
B: V1C7 VHH antibody G29R variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,00711
Polymers45,4832
Non-polymers5249
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2780 Å2
ΔGint-48 kcal/mol
Surface area16500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.970, 64.970, 215.968
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-305-

CL

21A-307-

CL

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein Ricin /


Mass: 30340.205 Da / Num. of mol.: 1 / Fragment: residues 36-302
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 V1C7 VHH antibody G29R variant


Mass: 15142.449 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, 33 molecules

#3: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: PO4
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 24 / 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: 59.88 %
Crystal growTemperature: 295 K / Method: vapor diffusion / pH: 8.5
Details: 1.6 M ammonium dihydrogen phosphate, 20% glycerol, and 100 mM Tris pH 8.5

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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: Feb 22, 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: 19198 / % possible obs: 99.9 % / Redundancy: 10.3 % / Biso Wilson estimate: 63.74 Å2 / Rmerge(I) obs: 0.11 / Rpim(I) all: 0.036 / Rrim(I) all: 0.116 / Χ2: 1.882 / Net I/σ(I): 8.4 / Num. measured all: 197913
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.5-2.549.62.7939030.6510.9372.9491.341100
2.54-2.599.92.4749550.7090.8182.6081.369100
2.59-2.6410.32.1249330.7540.6862.2331.416100
2.64-2.6910.41.8449520.7940.5931.9381.477100
2.69-2.7510.61.4979180.8550.4751.5711.504100
2.75-2.8210.61.1819670.8990.3751.241.512100
2.82-2.8910.60.9619300.9440.3051.0091.583100
2.89-2.9610.50.7569750.9620.2410.7941.62100
2.96-3.0510.60.5618980.9760.1790.591.662100
3.05-3.1510.60.4139600.9860.1320.4341.619100
3.15-3.2610.70.2939550.9950.0930.3081.693100
3.26-3.3910.70.2159520.9940.0690.2261.725100
3.39-3.5510.70.1639660.9950.0520.1711.865100
3.55-3.7310.70.1219390.9980.0390.1272.0199.9
3.73-3.9710.50.0929570.9980.030.0972.223100
3.97-4.2710.40.0789800.9980.0250.0822.56699.9
4.27-4.79.90.0679820.9990.0230.0712.922100
4.7-5.389.70.0649870.9980.0220.0683.18599.9
5.38-6.789.90.0529990.9980.0170.0552.428100
6.78-509.30.03310900.9990.0110.0351.89598.8

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHENIX1.7.1_743refinement
PDB_EXTRACT3.22data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2AAI and 4LGR

2aai

4lgr


Resolution: 2.5→49.898 Å / SU ML: 0.7 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 32.41
RfactorNum. reflection% reflection
Rfree0.257 949 4.97 %
Rwork0.2092 --
obs0.2116 19094 99.49 %
Solvent computationShrinkage radii: 1.06 Å / VDW probe radii: 1.3 Å / Bsol: 57.94 Å2 / ksol: 0.348 e/Å3
Displacement parametersBiso max: 180.18 Å2 / Biso mean: 92.28 Å2 / Biso min: 53.86 Å2
Baniso -1Baniso -2Baniso -3
1-10.2234 Å2-0 Å2-0 Å2
2--10.2234 Å2-0 Å2
3----20.4467 Å2
Refinement stepCycle: final / Resolution: 2.5→49.898 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3026 0 24 24 3074
Biso mean--104.34 69.34 -
Num. residues----386
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0063119
X-RAY DIFFRACTIONf_angle_d0.9814234
X-RAY DIFFRACTIONf_chiral_restr0.071460
X-RAY DIFFRACTIONf_plane_restr0.005555
X-RAY DIFFRACTIONf_dihedral_angle_d14.3971125
LS refinement shell

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

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4973-2.6290.41281340.33832477261198
2.629-2.79370.39931320.319225432675100
2.7937-3.00940.3591590.296625332692100
3.0094-3.31220.30251540.252725622716100
3.3122-3.79130.25671160.218626122728100
3.7913-4.7760.23281190.162326382757100
4.776-49.90820.20631350.18592780291599
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)
11.94671.26170.82486.0648-2.44732.05290.152-0.67610.41561.2648-0.08470.8118-1.2195-0.7147-0.13021.70820.61460.08160.5426-0.14380.664432.957325.808449.3942
24.35642.814.53064.24010.3987.36020.1942-1.63890.3628-0.2693-0.05010.5205-0.2263-1.0614-0.16691.12830.19180.17751.1020.00810.662533.401313.445963.8094
33.94241.29650.33960.6899-0.00012.2094-0.3627-0.4893-0.2416-0.12680.41760.2499-0.5983-1.2283-0.03021.24510.31460.09660.55640.04650.535430.093313.546143.7285
47.05240.57360.60884.8240.09713.15830.4708-0.6449-0.86840.4822-0.32010.0161-0.1554-0.5951-0.12671.16720.00640.13550.3620.03010.483835.37666.857642.5343
50.51050.20610.38575.92641.1680.7896-0.73630.07280.0323-0.82810.40520.1927-1.352-0.40310.29521.45530.1475-0.00150.2533-0.01870.583937.132915.315434.8321
63.2847-0.46840.53940.56950.30461.3789-0.5733-0.2773-0.0545-0.27290.1759-0.2806-0.28550.16020.33641.47080.11180.05420.4088-0.03190.528251.213217.836454.5296
76.41744.81181.64855.73351.48890.45420.0484-1.28150.17750.7358-0.35950.26570.4077-0.23220.30791.69940.14380.26260.43770.01120.564943.20814.872662.8116
87.6613-1.58570.95612.237-0.63791.5749-0.44131.66590.2206-0.3310.20020.1961-0.3678-1.05010.34431.282-0.0071-0.25471.0217-0.10190.496534.951824.736610.976
94.043-0.2323-3.85743.77693.32686.1870.41411.48481.0322-0.4216-0.7114-0.8304-0.8544-0.1820.33271.21650.0334-0.09430.77070.27750.858647.716327.31237.2699
107.5068-3.81230.77653.54991.03113.2734-0.50270.0830.01910.48160.15090.22670.6681-0.28570.39171.3589-0.1096-0.19850.6226-0.03080.616334.402325.884118.3937
119.22110.68551.73764.37745.74637.61650.37820.8631-1.26951.1313-0.29720.38190.96451.01370.00371.1472-0.1073-0.0320.6708-0.13150.672644.255813.087513.5792
128.7592-2.98362.29252.21611.976.966-0.87831.00390.4431.62240.28010.1534-0.09271.11430.16761.4672-0.208-0.23830.4380.12060.794148.664924.481421.4333
134.6683-6.1348-1.92818.37821.3434.8417-0.33180.3011.6453-0.28420.5461-0.8776-1.6134-0.6833-0.01131.45-0.0282-0.29320.68650.10160.720942.418631.522714.6445
149.1442-0.30471.36312.3347-0.475.115-0.67621.7261-0.28760.92860.5116-0.46360.12761.04030.17411.10270.0802-0.07540.7124-0.15190.601546.783719.057710.7901
155.23171.1266-2.5214.89961.15666.08660.8221-0.0208-0.31570.5419-0.0161-0.0349-0.574-0.10740.0831.88060.25450.11340.43630.00740.609540.89717.249124.9355
163.0418-1.79921.88492.13910.11212.5676-0.56110.5617-0.94480.21230.5510.00330.51470.231-0.06991.2522-0.0108-0.0080.6659-0.08470.670235.190116.79216.9249
170.16530.25911.05585.79390.15387.1403-0.4920.3243-0.0170.2543-0.46860.09120.3021-0.47561.05711.25040.0119-0.01181.1881-0.15380.592349.89319.46130.5506
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 33:56)A33 - 56
3X-RAY DIFFRACTION3chain 'A' and (resseq 57:97)A57 - 97
4X-RAY DIFFRACTION4chain 'A' and (resseq 98:140)A98 - 140
5X-RAY DIFFRACTION5chain 'A' and (resseq 141:174)A141 - 174
6X-RAY DIFFRACTION6chain 'A' and (resseq 175:248)A175 - 248
7X-RAY DIFFRACTION7chain 'A' and (resseq 249:259)A249 - 259
8X-RAY DIFFRACTION8chain 'B' and (resseq -2:12)B-2 - 12
9X-RAY DIFFRACTION9chain 'B' and (resseq 13:24)B13 - 24
10X-RAY DIFFRACTION10chain 'B' and (resseq 25:42)B25 - 42
11X-RAY DIFFRACTION11chain 'B' and (resseq 43:54)B43 - 54
12X-RAY DIFFRACTION12chain 'B' and (resseq 55:77)B55 - 77
13X-RAY DIFFRACTION13chain 'B' and (resseq 78:87)B78 - 87
14X-RAY DIFFRACTION14chain 'B' and (resseq 88:104)B88 - 104
15X-RAY DIFFRACTION15chain 'B' and (resseq 105:111)B105 - 111
16X-RAY DIFFRACTION16chain 'B' and (resseq 112:121)B112 - 121
17X-RAY DIFFRACTION17chain 'B' and (resseq 122:128)B122 - 128

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