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- PDB-4lgs: Ricin A chain bound to camelid nanobody (VHH4) -

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Basic information

Entry
Database: PDB / ID: 4lgs
TitleRicin A chain bound to camelid nanobody (VHH4)
Components
  • Camelid nanobody (VHH4)
  • Ricin
KeywordsHYDROLASE/IMMUNE SYSTEM / Ribosomal inhibiting protein 2 / 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 / Immunoglobulins / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesRicinus communis (castor bean)
Vicugna pacos (alpaca)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsRudolph, M.J. / Cheung, J. / Franklin, M. / Burshteyn, F. / Cassidy, M. / Gary, E. / Mantis, N.
CitationJournal: J.Mol.Biol. / Year: 2014
Title: Crystal Structures of Ricin Toxin's Enzymatic Subunit (RTA) in Complex with Neutralizing and Non-Neutralizing Single-Chain Antibodies.
Authors: Rudolph, M.J. / Vance, D.J. / Cheung, J. / Franklin, M.C. / Burshteyn, F. / Cassidy, M.S. / Gary, E.N. / Herrera, C. / Shoemaker, C.B. / Mantis, N.J.
History
DepositionJun 28, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jul 2, 2014Group: Database references
Revision 1.2Jul 30, 2014Group: Database references
Revision 1.3Aug 20, 2014Group: Database references
Revision 1.4Mar 15, 2017Group: Source and taxonomy
Revision 1.5Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ricin
B: Camelid nanobody (VHH4)


Theoretical massNumber of molelcules
Total (without water)43,3052
Polymers43,3052
Non-polymers00
Water32418
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1110 Å2
ΔGint-6 kcal/mol
Surface area17700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.391, 49.935, 114.442
Angle α, β, γ (deg.)90.000, 103.880, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-302-

HOH

21A-309-

HOH

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Components

#1: Protein Ricin / / Ricin A chain / rRNA N-glycosidase


Mass: 29432.139 Da / Num. of mol.: 1 / Fragment: UNP residues 39-301
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Plasmid: pUTA / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody Camelid nanobody (VHH4)


Mass: 13873.257 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vicugna pacos (alpaca) / Plasmid: MCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) Rosetta
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 18 / 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: 2.93 Å3/Da / Density % sol: 57.98 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 7.5
Details: 100 mM NaHepes, 20% PEG 8000, pH 7.5, VAPOR DIFFUSION, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.08 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 7, 2013
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 2.41→50 Å / Num. all: 19580 / Num. obs: 17642 / % possible obs: 90.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.1 % / Rmerge(I) obs: 0.093 / Χ2: 1.684 / Net I/σ(I): 10.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.41-2.451.90.7395191.45153
2.45-2.52.10.7675971.371159.9
2.5-2.542.30.6526271.463166.3
2.54-2.62.40.547531.39177.2
2.6-2.652.60.5837741.382180.9
2.65-2.712.70.5338331.51186.8
2.71-2.782.90.488941.395192.8
2.78-2.8630.4549541.381196.6
2.86-2.943.20.3889731.429199.3
2.94-3.043.30.3239721.491199
3.04-3.143.40.2699491.731199.6
3.14-3.273.40.2169711.689199.4
3.27-3.423.50.1619491.946199.1
3.42-3.63.40.1189891.816199.6
3.6-3.833.40.1039701.84199
3.83-4.123.40.0829671.97198.9
4.12-4.533.30.0649661.992198.3
4.53-5.193.40.0589941.9198.8
5.19-6.543.40.0579881.812199.2
6.54-503.30.04410031.616197.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 34.44 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation3.61 Å32.39 Å
Translation3.61 Å32.39 Å

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHASER2.1.4phasing
PHENIX1.7.1_743refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
DENZOdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→44.361 Å / Occupancy max: 1 / Occupancy min: 1 / FOM work R set: 0.7427 / SU ML: 0.73 / σ(F): 0 / Phase error: 31.29 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2478 689 5.01 %
Rwork0.2 --
obs0.2024 13754 98 %
all-14034 -
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.232 Å2 / ksol: 0.291 e/Å3
Displacement parametersBiso max: 209.42 Å2 / Biso mean: 74.4053 Å2 / Biso min: 33.62 Å2
Baniso -1Baniso -2Baniso -3
1-0.9577 Å2-0 Å2-17.3405 Å2
2---5.0167 Å20 Å2
3---4.059 Å2
Refinement stepCycle: LAST / Resolution: 2.7→44.361 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3052 0 0 18 3070
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0043118
X-RAY DIFFRACTIONf_angle_d0.8584234
X-RAY DIFFRACTIONf_chiral_restr0.064464
X-RAY DIFFRACTIONf_plane_restr0.004558
X-RAY DIFFRACTIONf_dihedral_angle_d14.1421125
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.7-2.90860.38741350.30512489262495
2.9086-3.20120.33411290.27172614274399
3.2012-3.66420.27531490.21052629277899
3.6642-4.61580.21391400.16412635277599
4.6158-44.36720.20591360.18022698283498
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)
17.34130.20292.45056.59142.71697.37040.0297-0.98080.0462-0.51-0.02480.49120.0956-1.1112-0.12680.2826-0.0243-0.06150.33790.04790.3758-13.473322.983749.6941
23.961-0.3021.1543.1373-1.32772.59770.50380.0316-0.93380.4642-0.341-0.34410.6386-0.2288-0.2490.5783-0.0001-0.31830.39060.00080.5838-12.007214.989543.4189
34.82882.42360.89093.2937-2.10456.2986-0.1120.4274-0.2701-0.39430.16840.16850.6825-0.2628-0.14160.5688-0.0205-0.30740.4774-0.06450.4863-14.686819.026629.7872
49.0564-2.56531.47694.4267-0.62776.9380.39460.8678-0.1835-0.4529-0.45980.0116-0.36470.5326-0.04190.3684-0.0399-0.0280.30940.06470.4194-5.018632.700634.1342
53.4492-0.98621.48181.9231-1.39775.5273-0.17140.11720.32710.0851-0.1927-0.6504-0.62570.39980.2120.2938-0.0238-0.01370.3608-0.03670.4712-1.356228.925244.6675
62.0551-1.1128-0.53144.5903-3.63043.36160.3703-0.0678-0.3576-0.4896-0.27170.00320.73320.4241-0.07410.53610.1149-0.27240.4519-0.1510.73038.025510.780646.6684
74.70450.27791.4740.94170.3933.27470.43940.7103-0.141-1.6401-0.272-0.26370.24980.6083-0.17011.13320.0618-0.35340.5232-0.09680.2902-14.553322.56912.2567
85.8535-4.91625.45018.1368-6.29497.45030.130.32741.04151.1831-0.4014-0.7019-0.83650.52770.33971.2153-0.016-0.40930.3353-0.02220.6033-25.529429.58875.1987
94.2521-3.47175.5788.033-0.49249.5573-0.2179-0.60550.16221.04130.0453-0.15010.1768-1.04510.00950.95270.0227-0.14040.4945-0.03830.3901-21.582319.602712.7088
109.1598-1.27345.22277.8252-2.22685.36240.4888-0.524-0.7187-0.67950.20490.62581.2606-0.8479-0.6080.8437-0.1391-0.11890.58340.06570.2987-25.434416.65276.7274
112.1381.51282.19266.68840.98132.2978-0.07421.1123-0.1075-1.8713-0.18360.19590.14880.8255-0.14690.77080.1498-0.04390.7176-0.18390.4024-14.265816.79773.7579
124.45230.23823.38562.9086-1.92375.9061-0.0642-1.4326-0.13190.144-0.59670.7831-0.7258-0.32760.17941.1307-0.0775-0.46870.4586-0.10260.5274-26.323324.120.6669
133.0646-1.6274-3.35623.8823-0.65526.9955-0.246-0.6498-0.01790.36670.3828-0.0972-1.0264-0.491-0.28340.6925-0.0018-0.20550.6579-0.03780.3874-19.270726.085218.4066
144.0982-4.2189-5.04554.40785.25466.27791.117-0.31221.3781-0.71220.2569-1.3627-1.06710.8953-0.86541.415-0.1097-0.42880.5711-0.04710.7295-14.846430.93738.3724
153.0585-1.0076-2.49887.0997-0.47395.6333-0.19961.29580.7126-0.2184-0.09720.4129-1.0378-1.0910.10760.85260.1064-0.22970.81190.11850.5697-28.163725.7259-7.1375
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 5:33)A5 - 33
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 34:76)A34 - 76
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 77:123)A77 - 123
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 124:161)A124 - 161
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 162:202)A162 - 202
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 203:266)A203 - 267
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 1:33)B1 - 33
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 34:44)B34 - 44
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 45:60)B45 - 60
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 61:73)B61 - 73
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 74:83)B74 - 83
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 84:98)B84 - 98
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 99:115)B99 - 115
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 116:122)B116 - 122
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 123:129)B123 - 129

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