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- PDB-5j56: RTA-V1C7 -

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Basic information

Entry
Database: PDB / ID: 5j56
TitleRTA-V1C7
Components
  • Ricin
  • VHH single chain antibody V1C7
KeywordsHYDROLASE/IMMUNE SYSTEM / Ricin / RTA / single chain antibody (VHH) / 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: 1.8 Å
AuthorsRudolph, M.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201400021C United States
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Structural Analysis of Single Domain Antibodies Bound to a Second Neutralizing Hot Spot on Ricin Toxin's Enzymatic Subunit.
Authors: Rudolph, M.J. / Vance, D.J. / Cassidy, M.S. / Rong, Y. / Mantis, N.J.
History
DepositionApr 1, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 21, 2016Group: Database references
Revision 1.2Feb 1, 2017Group: Database references
Revision 1.3Apr 12, 2017Group: Source and taxonomy / Structure summary
Revision 1.4Sep 13, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.5Dec 11, 2019Group: Author supporting evidence / Derived calculations / Category: pdbx_audit_support / pdbx_struct_special_symmetry / Item: _pdbx_audit_support.funding_organization
Revision 1.6Mar 6, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: VHH single chain antibody V1C7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)44,5299
Polymers44,0462
Non-polymers4837
Water4,161231
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)64.768, 64.768, 215.016
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-307-

CL

21A-422-

HOH

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Components

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Protein / Antibody , 2 types, 2 molecules AB

#1: Protein Ricin /


Mass: 30067.953 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) / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase
#2: Antibody VHH single chain antibody V1C7


Mass: 13978.278 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 , 5 types, 238 molecules

#3: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#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-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#7: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 231 / 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: 3.05 Å3/Da / Density % sol: 59.74 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.6 / Details: 100 mM sodium acetate pH 4.6 and 8% PEG4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 1, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.8→49.729 Å / Num. obs: 49957 / % possible obs: 99.9 % / Redundancy: 7.9 % / Biso Wilson estimate: 34.76 Å2 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.022 / Rrim(I) all: 0.064 / Χ2: 0.681 / Net I/av σ(I): 30.69 / Net I/σ(I): 5.5 / Num. measured all: 393312
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allΧ2% possible allRrim(I) all
1.8-1.837.60.99623980.810.370.42599.9
1.83-1.867.60.86824840.8120.3250.42699.90.929
1.86-1.97.60.67224620.930.250.44199.90.719
1.9-1.947.70.51624620.9170.1920.45799.90.552
1.94-1.987.50.45924290.9540.1720.47299.90.491
1.98-2.037.40.34624920.9650.1310.4821000.371
2.03-2.086.90.31124630.9760.1230.50999.80.335
2.08-2.137.90.23924270.9870.0870.5041000.255
2.13-2.27.90.1924720.9880.0690.5399.90.203
2.2-2.277.90.16524820.9880.060.55999.80.176
2.27-2.357.80.13824660.9930.050.58199.80.148
2.35-2.447.70.12424980.9940.0450.6231000.132
2.44-2.557.30.10924760.9930.0420.67799.80.117
2.55-2.698.30.09125010.9960.0320.70199.80.096
2.69-2.868.40.07825130.9960.0270.7591000.083
2.86-3.088.30.06725090.9970.0240.8621000.071
3.08-3.3980.05925190.9980.0221.0299.80.063
3.39-3.888.90.05425630.9990.0191.1971000.057
3.88-4.888.20.04625860.9980.0171.17699.90.049
4.88-508.30.0427550.9970.0150.90599.90.043

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å49.73 Å
Translation2 Å49.73 Å

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
PHASER2.5.6phasing
PHENIX1.8.4_1496refinement
PDB_EXTRACT3.2data extraction
HKL-2000v1.0data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→49.729 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 22.61
RfactorNum. reflection% reflection
Rfree0.2096 2377 4.8 %
Rwork0.1734 --
obs0.1752 49537 99.82 %
Solvent computationShrinkage radii: 1.2 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 112.97 Å2 / Biso mean: 46.92 Å2 / Biso min: 26.11 Å2
Refinement stepCycle: final / Resolution: 1.8→49.729 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3001 0 22 231 3254
Biso mean--58.48 49.57 -
Num. residues----383
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183089
X-RAY DIFFRACTIONf_angle_d1.6094188
X-RAY DIFFRACTIONf_chiral_restr0.089457
X-RAY DIFFRACTIONf_plane_restr0.009551
X-RAY DIFFRACTIONf_dihedral_angle_d14.5851114
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 17 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.8-1.83670.3441460.300126772823
1.8367-1.87670.27451460.270727182864
1.8767-1.92030.24891570.242327042861
1.9203-1.96840.25881350.218327752910
1.9684-2.02160.19971250.208227362861
2.0216-2.08110.2721570.200727092866
2.0811-2.14820.27271300.198527422872
2.1482-2.2250.22761480.1927472895
2.225-2.31410.23341430.189427512894
2.3141-2.41940.23131330.179227282861
2.4194-2.5470.26741230.189927832906
2.547-2.70650.23671220.191327932915
2.7065-2.91550.20191620.184827582920
2.9155-3.20890.25521140.19628322946
3.2089-3.67310.20711320.183828162948
3.6731-4.62710.19551520.139728823034
4.6271-49.74820.15411520.141430093161
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)
110.2444-8.5169-5.86162.28496.6018.76210.1144-0.30780.9825-0.34570.5277-1.1671-0.62541.009-0.50070.3263-0.0653-0.03190.46770.00370.471238.926718.139110.0733
29.8341-2.7517-6.45687.73787.44249.1798-0.2106-0.96170.02691.02340.4137-0.65860.37571.0806-0.11530.2974-0.0032-0.10440.42560.05340.333937.356211.313916.3027
34.56313.2521-0.93816.0299-4.96498.56440.3164-0.80290.20711.5673-0.2233-0.1183-0.4030.4561-0.08020.6944-0.0156-0.06270.4785-0.12180.410226.974220.962427.5419
43.4868-1.4075-4.76382.94852.66558.79360.0696-0.2210.36130.05970.0638-0.103-0.18380.5315-0.13420.2194-0.0408-0.03820.2482-0.01170.283629.023123.08897.7568
52.3240.75840.30454.62460.48162.4187-0.06940.00980.40010.1897-0.02660.5683-0.3284-0.17710.14270.25480.0442-0.00810.2975-0.01780.293820.643422.14126.4432
61.3414-0.39590.06984.388-5.43259.28570.05740.0723-0.0171-0.0084-0.1586-0.2363-0.04670.27890.06380.19870.0213-0.02230.2618-0.03490.261527.020315.52641.2133
72.88360.3028-4.40436.31380.0746.6986-0.1527-0.1409-0.32920.00380.0529-0.54240.9240.840.15840.28440.1005-0.0140.357-0.02140.294730.37771.02639.2519
80.96930.2494-0.1093.05990.75696.6626-0.0019-0.11320.08160.2764-0.16460.4333-0.1611-0.5470.21730.23670.04620.02270.3586-0.0460.292816.66182.688123.5884
99.2069-4.2693-0.25272.36928.46789.5992-0.1016-0.30560.18020.9391-0.05060.3508-0.3617-0.360.08610.46770.02670.08030.38320.00850.257923.071211.333226.6053
109.7154.12062.02892.63534.10154.8926-1.18461.3017-0.493-1.82781.1054-0.34-0.510.0808-0.10470.7625-0.19120.10850.60660.05960.392433.30136.8392-28.8609
112.92221.93171.19720.9593-0.42637.1698-0.21730.5218-0.2184-0.13360.1305-0.04860.4626-0.07980.07770.3533-0.01610.08050.3274-0.00710.377741.57310.744-21.4456
124.43721.9579-0.36774.0907-0.52019.5402-0.48910.4098-0.4267-0.51050.35440.310.7528-1.14260.09570.41-0.10990.03650.4026-0.02760.33229.28014.5075-19.3822
134.77353.53873.16346.92044.2747.8729-0.37430.7153-0.0527-0.8530.33830.3907-0.1907-0.56490.09920.3378-0.057-0.03550.49010.02190.275528.187611.981-21.2688
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 141:180)A141 - 180
7X-RAY DIFFRACTION7chain 'A' and (resseq 181:201)A181 - 201
8X-RAY DIFFRACTION8chain 'A' and (resseq 202:248)A202 - 248
9X-RAY DIFFRACTION9chain 'A' and (resseq 249:259)A249 - 259
10X-RAY DIFFRACTION10chain 'B' and (resseq 0:17)B0 - 17
11X-RAY DIFFRACTION11chain 'B' and (resseq 18:31)B18 - 31
12X-RAY DIFFRACTION12chain 'B' and (resseq 32:95)B32 - 95
13X-RAY DIFFRACTION13chain 'B' and (resseq 96:128)B96 - 128

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