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- PDB-2b7u: Ribosome inactivating protein type 1 from Charybdis maritima AGG -

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Basic information

Entry
Database: PDB / ID: 2b7u
TitleRibosome inactivating protein type 1 from Charybdis maritima AGG
ComponentsCHARYBDIN
KeywordsHYDROLASE / Ribosome inactivating protein
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / 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 type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 / Ribosome-inactivating protein, subdomain 2 / Ribosome-inactivating protein superfamily / Ribosome inactivating protein ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / 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
Ribosome-inactivating protein charybdin
Similarity search - Component
Biological speciesCharybdis maritima (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å
AuthorsGessmann, R. / Petratos, K.
CitationJournal: Febs J. / Year: 2006
Title: Isolation, characterization, sequencing and crystal structure of charybdin, a type 1 ribosome-inactivating protein from Charybdis maritima agg.
Authors: Touloupakis, E. / Gessmann, R. / Kavelaki, K. / Christofakis, E. / Petratos, K. / Ghanotakis, D.F.
History
DepositionOct 5, 2005Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 27, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Mar 7, 2018Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.detector
Revision 1.4Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Remark 650HELIX Determination Method: Author Determined

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: CHARYBDIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,4812
Polymers29,2851
Non-polymers1951
Water4,558253
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.240, 57.240, 51.088
Angle α, β, γ (deg.)90.00, 104.08, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein CHARYBDIN / Ribosome inactivating protein


Mass: 29285.281 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: The correct name of the source is CHARYBDIS MARITIMA AGG.
Source: (natural) Charybdis maritima (plant) / Tissue: BULB / References: UniProt: P84786, rRNA N-glycosylase
#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 253 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.41 Å3/Da / Density % sol: 49 %
Crystal growTemperature: 283 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 100mM Mes, 16% PEG 6000, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 283K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.99
DetectorDetector: CCD / Date: Feb 2, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99 Å / Relative weight: 1
ReflectionResolution: 1.6→49.63 Å / Num. obs: 35616 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 4.6 % / Biso Wilson estimate: 18.86 Å2 / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 18.1
Reflection shellResolution: 1.6→1.69 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.186 / Mean I/σ(I) obs: 5.9 / Rsym value: 0.186 / % possible all: 82.2

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5.2.0005refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: combined model from PARTS OF 12 RIP's

Resolution: 1.6→20 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.948 / SU B: 3.182 / SU ML: 0.052 / Cross valid method: THROUGHOUT / ESU R: 0.092 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.208 1785 5 %RANDOM
Rwork0.182 ---
all0.18648 ---
obs0.183 33815 97.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.74 Å20 Å2-0.42 Å2
2--0.37 Å20 Å2
3---0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.6→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2047 0 12 253 2312
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0222103
X-RAY DIFFRACTIONr_bond_other_d0.0010.021928
X-RAY DIFFRACTIONr_angle_refined_deg1.5981.9682847
X-RAY DIFFRACTIONr_angle_other_deg0.88634487
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4965250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.88223.786103
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.36215373
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.9921517
X-RAY DIFFRACTIONr_chiral_restr0.1630.2316
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022300
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02433
X-RAY DIFFRACTIONr_nbd_refined0.220.2485
X-RAY DIFFRACTIONr_nbd_other0.1940.22020
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21023
X-RAY DIFFRACTIONr_nbtor_other0.0830.21234
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2153
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.210
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2310.238
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0850.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1231.51350
X-RAY DIFFRACTIONr_mcbond_other0.2351.5507
X-RAY DIFFRACTIONr_mcangle_it1.66922038
X-RAY DIFFRACTIONr_scbond_it2.4463922
X-RAY DIFFRACTIONr_scangle_it3.5654.5809
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.601→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.204 96 -
Rwork0.178 1971 -
obs--77.59 %

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