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- PDB-4zt8: Structure of the complex of type 1 ribosome inactivating protein ... -

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Basic information

Entry
Database: PDB / ID: 4zt8
TitleStructure of the complex of type 1 ribosome inactivating protein from Momordica balsamina with a pyrimidine base, cytosine at 1.98 A resolution
ComponentsRibosome inactivating protein
KeywordsHYDROLASE
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / 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
6-AMINOPYRIMIDIN-2(1H)-ONE / rRNA N-glycosylase
Similarity search - Component
Biological speciesMomordica balsamina (balsam apple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsYamini, S. / Pandey, S. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: Biochem Biophys Rep / Year: 2015
Title: Binding and structural studies of the complexes of type 1 ribosome inactivating protein fromMomordica balsaminawith cytosine, cytidine, and cytidine diphosphate.
Authors: Yamini, S. / Pandey, S.N. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionMay 14, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 3, 2015Provider: repository / Type: Initial release
SupersessionAug 5, 2015ID: 4KJH
Revision 1.1Aug 5, 2015Group: Other
Revision 1.2Jul 27, 2016Group: Database references
Revision 1.3Jan 1, 2020Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.pdbx_database_id_PubMed / _citation.title ..._citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _pdbx_struct_oper_list.symmetry_operation
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / 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 / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Nov 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 1.6Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ribosome inactivating protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6105
Polymers27,0941
Non-polymers5164
Water3,963220
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area460 Å2
ΔGint2 kcal/mol
Surface area11250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)130.258, 130.258, 39.939
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-CYT / 6-AMINOPYRIMIDIN-2(1H)-ONE / CYTOSINE


Mass: 111.102 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H5N3O
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 220 / 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

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Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 48.89 %
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: May 1, 2013
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97 Å / Relative weight: 1
ReflectionResolution: 1.98→37.63 Å / Num. all: 16671 / Num. obs: 16671 / % possible obs: 99.9 % / Redundancy: 4.2 % / Rsym value: 0.073 / Net I/σ(I): 32.3
Reflection shellResolution: 1.98→2.01 Å / Rmerge(I) obs: 0.283 / Mean I/σ(I) obs: 4.2 / % possible all: 99.8

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
DENZOdata reduction
SCALEPACKdata scaling
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S9Q

3s9q


Resolution: 1.98→37.63 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.945 / SU B: 4.25 / SU ML: 0.119 / Cross valid method: THROUGHOUT / ESU R: 0.186 / ESU R Free: 0.156 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20423 890 5.1 %RANDOM
Rwork0.17766 ---
obs0.17959 16671 99.85 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.105 Å2
Baniso -1Baniso -2Baniso -3
1--0.69 Å2-0.69 Å20 Å2
2---0.69 Å2-0 Å2
3---2.25 Å2
Refinement stepCycle: 1 / Resolution: 1.98→37.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 34 220 2165
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0191979
X-RAY DIFFRACTIONr_bond_other_d0.0010.021910
X-RAY DIFFRACTIONr_angle_refined_deg1.0891.9822691
X-RAY DIFFRACTIONr_angle_other_deg0.7234367
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0465245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21923.92984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.15315322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.4341513
X-RAY DIFFRACTIONr_chiral_restr0.0570.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0212234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02456
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_it1.0712.885983
X-RAY DIFFRACTIONr_mcbond_other1.072.883982
X-RAY DIFFRACTIONr_mcangle_it1.8444.3181227
X-RAY DIFFRACTIONr_mcangle_other1.8444.3211228
X-RAY DIFFRACTIONr_scbond_it1.1483.081996
X-RAY DIFFRACTIONr_scbond_other1.1473.081997
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.9834.5471465
X-RAY DIFFRACTIONr_long_range_B_refined4.50124.0192433
X-RAY DIFFRACTIONr_long_range_B_other4.18323.6142360
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.98→2.032 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 63 -
Rwork0.24 1216 -
obs--99.84 %

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