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- PDB-4lhj: Ricin A chain bound to camelid nanobody (VHH5) -

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Basic information

Entry
Database: PDB / ID: 4lhj
TitleRicin A chain bound to camelid nanobody (VHH5)
Components
  • Camelid antibody
  • Ricin
KeywordsHYDROLASE/IMMUNE SYSTEM / Ribosome inhibiting protein / 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 / 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 / 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: 1.8 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
DepositionJul 1, 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 antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,9063
Polymers41,8712
Non-polymers351
Water3,981221
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)81.419, 103.782, 42.086
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212

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Components

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


Mass: 29032.738 Da / Num. of mol.: 1 / Fragment: UNP residues 39-297
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 antibody


Mass: 12838.080 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: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
Crystal growTemperature: 293 K / Method: vapor diffusion / pH: 4.5
Details: 100 mM NaAcetate, 200 mM NaCl, 40% PEG 300, 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
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: 1.8→50 Å / Num. all: 33873 / Num. obs: 33433 / % possible obs: 98.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Rmerge(I) obs: 0.064 / Χ2: 0.995 / Net I/σ(I): 7.8
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.8-1.833.80.4416880.475199.6
1.83-1.863.90.3916220.4961100
1.86-1.93.90.44116720.5381100
1.9-1.9440.24216670.707199.9
1.94-1.9840.2516520.6361100
1.98-2.0340.18216800.6811100
2.03-2.0840.17116600.735199.9
2.08-2.1340.14516790.832199.9
2.13-2.240.13216950.8491100
2.2-2.273.70.11716061.062196.6
2.27-2.353.90.11216680.896198.6
2.35-2.4440.09516670.9351100
2.44-2.5540.08316790.948199.9
2.55-2.6940.07616841.086199.9
2.69-2.863.90.07117111.2631100
2.86-3.083.90.06516931.562199.7
3.08-3.393.80.05617061.642199.4
3.39-3.883.60.04815611.61190
3.88-4.883.50.04117061.633197.6
4.88-503.60.03817371.533192.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 47.37 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å40.74 Å
Translation2.5 Å40.74 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: 1.8→40.709 Å / Occupancy max: 1 / Occupancy min: 0.34 / FOM work R set: 0.8042 / SU ML: 0.47 / σ(F): 0 / Phase error: 25.88 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2497 1700 5.1 %RANDOM
Rwork0.1956 ---
obs0.1983 33366 98.14 %-
all-33998 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 38.814 Å2 / ksol: 0.338 e/Å3
Displacement parametersBiso max: 87 Å2 / Biso mean: 34.2304 Å2 / Biso min: 14.28 Å2
Baniso -1Baniso -2Baniso -3
1-4.0789 Å2-0 Å20 Å2
2---10.2214 Å20 Å2
3---6.1425 Å2
Refinement stepCycle: LAST / Resolution: 1.8→40.709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2943 0 1 221 3165
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0173040
X-RAY DIFFRACTIONf_angle_d1.6314135
X-RAY DIFFRACTIONf_chiral_restr0.119459
X-RAY DIFFRACTIONf_plane_restr0.01545
X-RAY DIFFRACTIONf_dihedral_angle_d14.5021101
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.8-1.85080.34221480.28082472262094
1.8508-1.91050.32761200.281226842804100
1.9105-1.97880.3191450.255626282773100
1.9788-2.0580.27191430.217826352778100
2.058-2.15170.27161600.203726292789100
2.1517-2.26510.31641470.21772624277199
2.2651-2.4070.29781360.20552642277898
2.407-2.59280.2561620.203626452807100
2.5928-2.85370.23621490.186126882837100
2.8537-3.26640.22271290.176227212850100
3.2664-4.11470.21091100.16442581269194
4.1147-40.71990.22571510.19092717286895
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)
10.370.2086-0.38920.7614-0.15560.22650.0826-0.2301-0.43330.42510.071-0.10090.1254-0.39370.01310.3076-0.0241-0.04430.25560.02970.286234.0092-43.752423.3561
23.68410.42482.01324.01412.5248.73780.1135-0.2894-0.1790.14710.04060.54190.1274-0.5980.17680.1951-0.01960.02830.23390.01730.259728.75-35.282323.6234
31.962-0.21620.31473.3542.57445.2255-0.0572-0.22150.03050.39060.06180.14140.13890.1203-0.09010.1743-0.03530.00960.20720.02710.164638.0057-35.32230.6464
43.57-2.4683-0.56773.2294-0.69933.8449-0.1651-0.52230.07190.49970.1589-0.33980.16690.22090.05290.18490.0026-0.03750.2401-0.00980.196851.0742-39.779727.7431
53.71920.45910.07884.6754-1.02352.02780.04840.16080.0885-0.2482-0.0116-0.35950.00050.0364-0.03180.154-0.01240.03560.202-0.00580.150146.4486-33.96511.9774
67.7816-1.8638-0.74147.56940.67452.6545-0.13510.0729-0.0287-0.43560.0396-0.6147-0.00580.22020.01020.1662-0.04210.01740.17430.01390.190847.7146-35.071413.2338
71.9082-0.425-0.14953.08970.91265.17970.0584-0.05450.4896-0.02150.04390.066-0.7427-0.2139-0.1160.24130.01910.04210.181-0.0060.330534.9396-19.125223.254
84.3125-0.49511.32672.0312-9.38982.055-0.0712-0.0372-0.46541.14960.95671.3425-0.9777-0.7869-0.7270.38630.01550.14810.30380.03860.347919.65115.743420.8083
94.3217-2.23391.00585.0737-1.92227.738-0.12770.45730.39460.4326-0.0062-0.2937-1.36950.16330.34730.4338-0.0917-0.12610.29270.03240.259523.710724.33076.2822
104.3374-1.55890.99249.0078-2.32636.1982-0.1777-0.0736-0.78260.401-0.0628-0.22470.13010.10610.23110.1255-0.01880.04120.28110.04880.353826.87094.355617.1473
118.0844-4.313.92087.7851-2.41049.5314-0.1750.6363-0.5938-0.770.02391.0748-0.006-0.52450.17970.3012-0.0599-0.06150.3554-0.0090.314718.08297.82524.3038
129.9975-2.80163.967.9669-1.59899.7270.23360.6549-0.722-0.5915-0.27760.76410.3280.28730.13950.2886-0.02050.06530.1708-0.05940.301923.61014.60624.5892
135.329-3.45862.01169.4754-6.52018.85530.06730.2837-0.8242-1.4713-0.4094-0.92511.25390.69560.36430.43130.05120.21630.37610.01110.501730.73113.62642.5145
144.6209-0.8549-1.64318.1219-4.53188.11010.0164-0.1323-0.28780.2647-0.3725-1.0738-0.3140.88110.36410.142-0.0393-0.0040.2812-0.0190.367631.00619.42799.9922
151.29940.16020.2237.8242-4.35633.0056-0.1680.1579-0.1284-0.1668-0.1532-0.75760.03620.10880.3460.1362-0.00320.02280.2232-0.03770.214921.79533.776110.5913
161.61950.3122-0.5123.4558-0.59367.5152-0.13570.017-0.0442-0.05360.27150.51310.1002-0.478-0.14960.1257-0.0240.03530.2017-0.02480.234317.188310.542710.7888
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1CHAIN A AND (RESSEQ 5:18)A5 - 18
2X-RAY DIFFRACTION2CHAIN A AND (RESSEQ 19:33)A19 - 33
3X-RAY DIFFRACTION3CHAIN A AND (RESSEQ 34:76)A34 - 76
4X-RAY DIFFRACTION4CHAIN A AND (RESSEQ 77:123)A77 - 123
5X-RAY DIFFRACTION5CHAIN A AND (RESSEQ 124:157)A124 - 157
6X-RAY DIFFRACTION6CHAIN A AND (RESSEQ 158:175)A158 - 175
7X-RAY DIFFRACTION7CHAIN A AND (RESSEQ 176:263)A176 - 263
8X-RAY DIFFRACTION8CHAIN B AND (RESSEQ 1:7)B1 - 7
9X-RAY DIFFRACTION9CHAIN B AND (RESSEQ 8:17)B8 - 17
10X-RAY DIFFRACTION10CHAIN B AND (RESSEQ 18:32)B18 - 32
11X-RAY DIFFRACTION11CHAIN B AND (RESSEQ 33:44)B33 - 44
12X-RAY DIFFRACTION12CHAIN B AND (RESSEQ 45:52)B45 - 52
13X-RAY DIFFRACTION13CHAIN B AND (RESSEQ 53:63)B53 - 63
14X-RAY DIFFRACTION14CHAIN B AND (RESSEQ 64:82)B64 - 82
15X-RAY DIFFRACTION15CHAIN B AND (RESSEQ 83:107)B83 - 107
16X-RAY DIFFRACTION16CHAIN B AND (RESSEQ 108:120)B108 - 120

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