[English] 日本語
Yorodumi
- PDB-4fbb: Structure of mutant RIP from barley seeds in complex with adenine... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4fbb
TitleStructure of mutant RIP from barley seeds in complex with adenine (AMP-incubated)
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: 1.8 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
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)119,8067
Polymers119,4014
Non-polymers4053
Water22,4651247
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


Theoretical massNumber of molelcules
Total (without water)29,8501
Polymers29,8501
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.252, 142.456, 85.064
Angle α, β, γ (deg.)90.00, 127.52, 90.00
Int Tables number5
Space group name H-MC121

-
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.: 3 / Source method: obtained synthetically / Formula: C5H5N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1247 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.43 %
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

-
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: Dec 16, 2011
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: 1.8→50 Å / Num. all: 113785 / Num. obs: 113785 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rmerge(I) obs: 0.039 / Net I/σ(I): 17.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
1.8-1.833.90.338199
1.83-1.8640.314199.3
1.86-1.94.10.249199.4
1.9-1.944.10.197199.4
1.94-1.984.10.161199.6
1.98-2.034.10.138199.6
2.03-2.084.20.124199.6
2.08-2.134.20.105199.7
2.13-2.24.20.091199.8
2.2-2.274.20.076199.8
2.27-2.354.20.069199.9
2.35-2.444.20.06199.9
2.44-2.554.20.0531100
2.55-2.694.20.045199.9
2.69-2.864.30.0391100
2.86-3.084.30.0341100
3.08-3.394.30.029199.9
3.39-3.884.30.026199.9
3.88-4.884.20.024199.6
4.88-504.10.023196.9

-
Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
PHENIX1.7.3_928refinement
PDB_EXTRACT3.11data extraction
HKL-2000data collection
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→31.495 Å / Occupancy max: 1 / Occupancy min: 0.91 / SU ML: 0.24 / σ(F): 1.34 / Phase error: 26.57 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2497 1998 1.76 %
Rwork0.2103 --
obs0.2111 113733 99.47 %
all-113736 -
Solvent computationShrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60 Å2 / ksol: 0.4 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-3.6975 Å20 Å23.5022 Å2
2---1.8459 Å2-0 Å2
3----0.3364 Å2
Refinement stepCycle: LAST / Resolution: 1.8→31.495 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8328 0 30 1247 9605
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0078557
X-RAY DIFFRACTIONf_angle_d1.06511653
X-RAY DIFFRACTIONf_dihedral_angle_d13.3123084
X-RAY DIFFRACTIONf_chiral_restr0.071332
X-RAY DIFFRACTIONf_plane_restr0.0051511
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84480.31251380.26957851X-RAY DIFFRACTION98
1.8448-1.89470.32671430.27137944X-RAY DIFFRACTION99
1.8947-1.95040.29931390.24637942X-RAY DIFFRACTION99
1.9504-2.01340.29291540.23827998X-RAY DIFFRACTION100
2.0134-2.08530.28981290.23717938X-RAY DIFFRACTION100
2.0853-2.16880.3091460.23467978X-RAY DIFFRACTION100
2.1688-2.26750.25971500.2248017X-RAY DIFFRACTION100
2.2675-2.3870.28381480.22617983X-RAY DIFFRACTION100
2.387-2.53650.25791330.22938029X-RAY DIFFRACTION100
2.5365-2.73220.2791480.22218004X-RAY DIFFRACTION100
2.7322-3.0070.26071420.21158012X-RAY DIFFRACTION100
3.007-3.44160.20311450.19568041X-RAY DIFFRACTION100
3.4416-4.33430.20991400.1778029X-RAY DIFFRACTION100
4.3343-31.49990.23061430.1947969X-RAY DIFFRACTION98

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more