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- PDB-4lgr: Ricin A chain bound to camelid nanobody (VHH3) -

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Basic information

Entry
Database: PDB / ID: 4lgr
TitleRicin A chain bound to camelid nanobody (VHH3)
Components
  • Camelid nanobody (VHH3)
  • Ricin
KeywordsHYDROLASE/IMMUNE SYSTEM / Ribosome 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: 1.65 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 (VHH3)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,40117
Polymers41,6772
Non-polymers72415
Water4,612256
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2970 Å2
ΔGint-137 kcal/mol
Surface area17090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.345, 77.423, 121.805
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Antibody , 2 types, 2 molecules AB

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


Mass: 28638.256 Da / Num. of mol.: 1 / Fragment: UNP residues 40-294
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 (VHH3)


Mass: 13038.324 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

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Non-polymers , 5 types, 271 molecules

#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACY / ACETIC ACID / Acetic acid


Mass: 60.052 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H4O2
#5: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


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


Mass: 18.015 Da / Num. of mol.: 256 / 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: 3.47 Å3/Da / Density % sol: 64.56 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 100 mM NaAcetate, 200 mM Zinc Acetate, 10% PEG 3000, pH 4.5, 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
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.08 Å / Relative weight: 1
ReflectionResolution: 1.65→50 Å / Num. all: 70517 / Num. obs: 66357 / % possible obs: 94.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Rmerge(I) obs: 0.088 / Χ2: 1.649 / Net I/σ(I): 10.5
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.65-1.682.60.51621810.756163.6
1.68-1.7130.53625440.776172.9
1.71-1.743.60.60527740.798179.9
1.74-1.784.30.63429460.793184.7
1.78-1.825.10.60130980.814188.9
1.82-1.865.80.57633770.846195.8
1.86-1.96.40.46634300.909198.8
1.9-1.966.90.38134720.967199.7
1.96-2.017.20.30434971.072199.7
2.01-2.087.30.25534821.189199.8
2.08-2.157.30.21435151.239199.8
2.15-2.247.30.16735001.4199.9
2.24-2.347.30.14235411.552199.9
2.34-2.467.30.12734941.71199.8
2.46-2.627.20.10135261.802199.9
2.62-2.827.10.08835522.157199.8
2.82-3.116.90.07635492.618199.8
3.11-3.556.70.0635732.916199.7
3.55-4.486.40.04736092.89199.7
4.48-506.40.04536972.954197.2

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 30.61 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å43.22 Å
Translation2.5 Å43.22 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: 1.65→43.22 Å / Occupancy max: 1 / Occupancy min: 0.35 / FOM work R set: 0.864 / SU ML: 0.43 / σ(F): 0 / Phase error: 20.17 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2042 2736 5.07 %RANDOM
Rwork0.1795 ---
obs0.1808 53968 99.04 %-
all-54491 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 37.131 Å2 / ksol: 0.361 e/Å3
Displacement parametersBiso max: 93.37 Å2 / Biso mean: 30.5012 Å2 / Biso min: 10.71 Å2
Baniso -1Baniso -2Baniso -3
1--4.9556 Å2-0 Å20 Å2
2---8.2229 Å20 Å2
3---13.1785 Å2
Refinement stepCycle: LAST / Resolution: 1.65→43.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2924 0 27 256 3207
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073028
X-RAY DIFFRACTIONf_angle_d0.9794110
X-RAY DIFFRACTIONf_chiral_restr0.068454
X-RAY DIFFRACTIONf_plane_restr0.004543
X-RAY DIFFRACTIONf_dihedral_angle_d12.6611092
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.8310.2821250.25362323244892
1.831-1.86430.25931320.2372470260297
1.8643-1.90020.27591360.20562527266399
1.9002-1.9390.20831330.18912534266799
1.939-1.98110.21641530.165225552708100
1.9811-2.02720.2181450.173325132658100
2.0272-2.07790.22231420.174425332675100
2.0779-2.13410.24171300.178125842714100
2.1341-2.19690.19291300.16825722702100
2.1969-2.26780.18141430.169625722715100
2.2678-2.34890.21281020.169726052707100
2.3489-2.44290.19631440.176925412685100
2.4429-2.55410.19681480.176725692717100
2.5541-2.68870.18751120.180426032715100
2.6887-2.85710.20291400.188325812721100
2.8571-3.07770.22741470.195226172764100
3.0777-3.38730.20021500.18225852735100
3.3873-3.87720.17561370.174826112748100
3.8772-4.88370.16711430.147526402783100
4.8837-43.23260.24191440.2012697284197
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)
11.88290.34810.08524.05810.47020.9293-0.0148-0.34120.14280.6653-0.070.607-0.0112-0.11690.07110.20760.01760.08220.214-0.01840.1918-10.18980.257636.5015
22.97791.4682-1.14775.27261.56473.3601-0.0618-0.07560.17250.03080.036-0.1782-0.1260.10880.02880.09230.01-0.01520.1314-0.00960.09561.10.061524.7287
34.9333-0.354-0.34292.1452-0.04611.8978-0.00640.2988-0.1625-0.2488-0.05270.20760.0985-0.07750.04090.1581-0.0045-0.01560.1161-0.02630.0898-7.3143-9.223717.0049
43.4992-1.4903-0.37065.02411.53152.08060.02880.00990.1919-0.0685-0.1770.8306-0.1229-0.43360.13280.1340.01210.02160.2352-0.02210.3321-24.42710.199426.9092
51.3718-0.2783-1.24112.01161.62653.43350.19990.13110.1667-0.81860.0141-0.9878-0.0065-0.0468-0.17250.26370.01510.07130.3415-0.06540.222315.6473-22.618-2.4885
62.67631.1574-2.96764.85531.45925.12880.23720.27610.6179-0.870.5423-1.1644-0.65370.3281-0.67920.2307-0.04320.09430.3009-0.00040.318616.0727-10.76222.3868
79.20943.8802-1.43657.28465.01625.84220.27120.0373-0.1533-0.1188-0.53640.4806-0.2124-0.3290.2790.20280.03630.0280.2067-0.0150.13377.4837-16.87014.6117
88.90176.60697.25542.03268.0699.6371-0.06150.1842-0.12510.0194-0.36750.69270.1338-0.54520.29410.2730.00580.0130.3187-0.06380.3654.0087-20.53014.8216
97.0816-1.66581.65557.04492.55056.561-0.1955-0.5571-0.30230.584-0.0370.4061.05230.02270.23650.3140.01310.09440.25830.02510.137110.6988-17.807914.3726
107.67960.97691.0449.51341.17326.66590.1289-0.34850.4981-0.08790.1747-0.820.210.7487-0.23570.1730.04110.06190.2938-0.04660.249417.7903-16.24296.9851
113.7128-4.0337-0.63587.89694.93255.37870.05310.046-0.34430.294-0.15380.30590.3060.09540.07130.1655-0.02790.07690.2327-0.01540.171510.0183-23.87382.7812
126.4229-1.8608-2.78258.27717.37466.78330.19320.83180.51-1.2881-0.3575-0.2962-1.19650.08420.18210.30360.01310.03130.21470.06240.17283.5121-0.96247.0462
137.0275-1.02861.1072.00468.05339.14540.38930.8104-0.0222-1.5912-0.361-0.0318-0.7438-0.2528-0.03520.45490.05650.03270.3180.02440.18276.5145-11.0218-2.2196
142.7991-0.33691.1742.0821-1.38132.0456-0.04530.1742-0.41530.4594-0.10330.37520.7394-0.13810.11530.412-0.0190.14270.4125-0.07640.239612.2941-35.1879-5.8992
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 5:56)A5 - 56
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 57:122)A57 - 122
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 123:174)A123 - 174
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 175:259)A175 - 259
5X-RAY DIFFRACTION5CHAIN B AND (RESSEQ 2:17)B2 - 17
6X-RAY DIFFRACTION6CHAIN B AND (RESSEQ 18:32)B18 - 32
7X-RAY DIFFRACTION7CHAIN B AND (RESSEQ 33:39)B33 - 39
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 40:52)B40 - 52
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 53:63)B53 - 63
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 64:82)B64 - 82
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 83:98)B83 - 98
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 99:106)B99 - 106
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 107:112)B107 - 112
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 113:123)B113 - 123

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