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- PDB-4fba: Structure of mutant RIP from barley seeds in complex with adenine -

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Basic information

Entry
Database: PDB / ID: 4fba
TitleStructure of mutant RIP from barley seeds in complex with adenine
ComponentsProtein synthesis inhibitor I
KeywordsHYDROLASE / Ribosome Inactivating Protein / rRNA N-glycosylase activity / ribosome
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / defense response to fungus / toxin activity / killing of cells of another organism / negative regulation of translation / cytoplasm
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. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 ...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. / 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 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENINE / Protein synthesis inhibitor I
Similarity search - Component
Biological speciesHordeum vulgare (barley)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsLee, B.-G. / Kim, M.K. / Suh, S.W. / Song, H.K.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2012
Title: Structures of the ribosome-inactivating protein from barley seeds reveal a unique activation mechanism.
Authors: Lee, B.G. / Kim, M.K. / Kim, B.W. / Suh, S.W. / Song, H.K.
History
DepositionMay 22, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 31, 2012Provider: repository / Type: Initial release
Revision 1.1Jan 23, 2013Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein synthesis inhibitor I
B: Protein synthesis inhibitor I
C: Protein synthesis inhibitor I
D: Protein synthesis inhibitor I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,9418
Polymers119,4014
Non-polymers5414
Water24,5361362
1
A: Protein synthesis inhibitor I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9852
Polymers29,8501
Non-polymers1351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Protein synthesis inhibitor I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9852
Polymers29,8501
Non-polymers1351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Protein synthesis inhibitor I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9852
Polymers29,8501
Non-polymers1351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Protein synthesis inhibitor I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,9852
Polymers29,8501
Non-polymers1351
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)130.968, 142.412, 84.751
Angle α, β, γ (deg.)90.00, 127.52, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
Protein synthesis inhibitor I / Ribosome-inactivating protein I / rRNA N-glycosidase


Mass: 29850.240 Da / Num. of mol.: 4 / Mutation: E196A, K197A, K198A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Hordeum vulgare (barley) / Gene: RIP30 / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P22244, rRNA N-glycosylase
#2: Chemical
ChemComp-ADE / ADENINE


Mass: 135.127 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C5H5N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1362 / 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: 2.63 Å3/Da / Density % sol: 53.14 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.2
Details: 0.1M phosphate-citrate, 0.2M NaCl, 20%(w/v) PEG 8000, pH 4.2, vapor diffusion, hanging drop, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Photon Factory / Beamline: BL-17A / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 27, 2010
RadiationMonochromator: Numerical link type Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. all: 99910 / Num. obs: 99910 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.8 % / Rmerge(I) obs: 0.069
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.85-1.923.50.44193.7
1.92-1.993.60.317194.1
1.99-2.083.60.253194.6
2.08-2.193.70.191195.8
2.19-2.333.80.15197
2.33-2.513.90.12197.9
2.51-2.7640.09198.5
2.76-3.164.10.065198.8
3.16-3.994.10.047199
3.99-504.10.035198.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.85→47.654 Å / Occupancy max: 1 / Occupancy min: 0.41 / SU ML: 0.21 / σ(F): 1.37 / Phase error: 20.64 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2022 2013 2.02 %
Rwork0.1709 --
obs0.1715 99861 96.09 %
all-99864 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 43.29 Å2 / ksol: 0.35 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.9902 Å20 Å27.194 Å2
2--3.8471 Å2-0 Å2
3----5.7105 Å2
Refinement stepCycle: LAST / Resolution: 1.85→47.654 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8328 0 40 1362 9730
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068610
X-RAY DIFFRACTIONf_angle_d0.97711731
X-RAY DIFFRACTIONf_dihedral_angle_d12.2393099
X-RAY DIFFRACTIONf_chiral_restr0.0651335
X-RAY DIFFRACTIONf_plane_restr0.0051521
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.9010.32851320.25466137X-RAY DIFFRACTION84
1.901-1.95240.26081330.21456760X-RAY DIFFRACTION94
1.9524-2.00990.23531440.18946873X-RAY DIFFRACTION94
2.0099-2.07470.23351380.18716819X-RAY DIFFRACTION94
2.0747-2.14890.22611560.18096929X-RAY DIFFRACTION95
2.1489-2.23490.23551420.17216958X-RAY DIFFRACTION96
2.2349-2.33660.18161430.16917033X-RAY DIFFRACTION97
2.3366-2.45980.23521490.177099X-RAY DIFFRACTION98
2.4598-2.61390.21851510.17687160X-RAY DIFFRACTION98
2.6139-2.81570.20221410.17317156X-RAY DIFFRACTION99
2.8157-3.0990.23071430.17627196X-RAY DIFFRACTION99
3.099-3.54740.19621480.16467217X-RAY DIFFRACTION99
3.5474-4.46880.16741480.14527224X-RAY DIFFRACTION99
4.4688-47.66950.15971450.16667287X-RAY DIFFRACTION99

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