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- PDB-5gz7: Crystal Structure of the complex of Ribosome Inactivating Protein... -

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Basic information

Entry
Database: PDB / ID: 5gz7
TitleCrystal Structure of the complex of Ribosome Inactivating Protein with 1,2-ethanediol at 1.95 Angstrom resolution
ComponentsRibosome inactivating protein
KeywordsHYDROLASE
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / toxin activity / negative regulation of translation / nucleotide binding
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
Biological speciesMomordica balsamina (balsam apple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsTiwari, P. / Pandey, S.N. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To Be Published
Title: Crystal Structure of the complex of Ribosome Inactivating Protein with 1,2-ethanediol at 1.95 Angstrom resolution.
Authors: Tiwari, P. / Pandey, S.N. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionSep 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_prerelease_seq / pdbx_struct_oper_list / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Ribosome inactivating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5615
Polymers27,0941
Non-polymers4674
Water4,810267
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)130.197, 130.197, 40.656
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

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Components

#1: Protein Ribosome inactivating protein


Mass: 27093.756 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Momordica balsamina (balsam apple) / References: UniProt: D9J2T9, rRNA N-glycosylase
#2: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 267 / 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: 2.32 Å3/Da / Density % sol: 47 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7 / Details: 14% PEG 6000, 0.1M Sodium Phosphate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.97 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 30, 2016 / Details: MIRROR
RadiationMonochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.95→65.1 Å / Num. obs: 17664 / % possible obs: 99.3 % / Redundancy: 6.6 % / Rsym value: 0.12 / Net I/σ(I): 0.14
Reflection shellResolution: 1.95→1.98 Å / % possible all: 91.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ZZ6
Resolution: 1.95→65.1 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / SU B: 5.157 / SU ML: 0.135 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.21354 870 4.7 %RANDOM
Rwork0.1562 ---
obs0.15881 17664 99.19 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.359 Å2
Baniso -1Baniso -2Baniso -3
1--0.98 Å2-0.49 Å20 Å2
2---0.98 Å20 Å2
3---3.19 Å2
Refinement stepCycle: 1 / Resolution: 1.95→65.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 30 267 2208
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191971
X-RAY DIFFRACTIONr_bond_other_d0.0020.021905
X-RAY DIFFRACTIONr_angle_refined_deg1.791.9792681
X-RAY DIFFRACTIONr_angle_other_deg1.01434364
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1645245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.82823.92984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.02315322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.1541513
X-RAY DIFFRACTIONr_chiral_restr0.1030.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0212224
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02449
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.3072.624983
X-RAY DIFFRACTIONr_mcbond_other2.3062.621982
X-RAY DIFFRACTIONr_mcangle_it3.2893.9231227
X-RAY DIFFRACTIONr_mcangle_other3.2893.9251228
X-RAY DIFFRACTIONr_scbond_it3.6513.108988
X-RAY DIFFRACTIONr_scbond_other3.6443.108988
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6254.4811455
X-RAY DIFFRACTIONr_long_range_B_refined8.16323.882422
X-RAY DIFFRACTIONr_long_range_B_other7.78422.2912278
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.952→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.312 51 -
Rwork0.323 1218 -
obs--91.62 %

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