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- PDB-4f9n: Crystal structure of the complex of type I Ribosome inactivating ... -

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Basic information

Entry
Database: PDB / ID: 4f9n
TitleCrystal structure of the complex of type I Ribosome inactivating protein from Momordica balsamina with N7-methylated guanine at 2.65 A resolution
ComponentsRibosome inactivating protein
KeywordsHYDROLASE / N7-methylated guanine / Ligand binding
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
2-amino-7-methyl-1,7-dihydro-6H-purin-6-one / rRNA N-glycosylase
Similarity search - Component
Biological speciesMomordica balsamina (balsam apple)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.65 Å
AuthorsYamini, S. / Kushwaha, G.S. / Bhushan, A. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
CitationJournal: To be Published
Title: Crystal structure of the complex of type I Ribosome inactivating protein from Momordica balsamina with N7-methylated guanine at 2.65 A resolution
Authors: Yamini, S. / Kushwaha, G.S. / Bhushan, S. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionMay 19, 2012Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 20, 2012Provider: repository / Type: Initial release
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_validate_close_contact / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.auth_asym_id / _atom_site.auth_seq_id ..._atom_site.auth_asym_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_validate_close_contact.auth_asym_id_1 / _pdbx_validate_close_contact.auth_asym_id_2 / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Nov 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 2.2Oct 30, 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)27,6833
Polymers27,0941
Non-polymers5902
Water2,000111
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)131.428, 131.428, 39.808
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: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Chemical ChemComp-MY6 / 2-amino-7-methyl-1,7-dihydro-6H-purin-6-one


Mass: 165.153 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H7N5O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.44 Å3/Da / Density % sol: 49.63 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: PEG, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 21, 2009 / Details: MIRROR
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 2.65→19.76 Å / Num. all: 7364 / Num. obs: 7364 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 53.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.3
Reflection shellResolution: 2.65→2.74 Å / Rmerge(I) obs: 0.586 / Mean I/σ(I) obs: 2 / % possible all: 98.9

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
AUTOMARdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3S9Q

3s9q


Resolution: 2.65→19.61 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 2541410.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.196 401 5.4 %RANDOM
Rwork0.169 ---
all0.17 7364 --
obs0.169 7363 99.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 31.9142 Å2 / ksol: 0.258184 e/Å3
Displacement parametersBiso mean: 42.3 Å2
Baniso -1Baniso -2Baniso -3
1--8.79 Å2-1.45 Å20 Å2
2---8.79 Å20 Å2
3---17.57 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.26 Å
Luzzati d res low-5 Å
Luzzati sigma a0.45 Å0.42 Å
Refinement stepCycle: LAST / Resolution: 2.65→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 40 111 2062
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24.2
X-RAY DIFFRACTIONc_improper_angle_d0.96
X-RAY DIFFRACTIONc_mcbond_it1.381.5
X-RAY DIFFRACTIONc_mcangle_it2.32
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.412.5
LS refinement shellResolution: 2.65→2.74 Å / Rfactor Rfree error: 0.045 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.354 61 5 %
Rwork0.28 1147 -
obs--99.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2ion.paramion.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION5my6.parammy6.top

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