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- PDB-3n31: Crystal Structure of the complex of type I ribosome inactivating ... -

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Basic information

Entry
Database: PDB / ID: 3n31
TitleCrystal Structure of the complex of type I ribosome inactivating protein with fucose at 2.1A resolution
ComponentsRibosome inactivating proteinRibosome-inactivating protein
KeywordsHYDROLASE / RIP / RNA N-glycosidase / Plant protein / fucose
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
alpha-D-fucopyranose / rRNA N-glycosylase
Similarity search - Component
Biological speciesMomordica balsamina (balsam apple)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.11 Å
AuthorsKushwaha, G.S. / Pandey, N. / Perbandt, M. / Betzel, C. / 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 with fucose at 2.1A resolution
Authors: Kushwaha, G.S. / Pandey, N. / Perbandt, M. / Betzel, C. / Sinha, M. / Kaur, P. / Sharma, S. / Singh, T.P.
History
DepositionMay 19, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 30, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / diffrn_source / 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 / struct_asym / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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 1, 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

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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)27,7744
Polymers27,0941
Non-polymers6813
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)129.153, 129.153, 39.366
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 / 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*PLUS, 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: Sugar ChemComp-FCA / alpha-D-fucopyranose / alpha-D-fucose / 6-deoxy-alpha-D-galactopyranose / D-fucose / fucose / Fucose


Type: D-saccharide, alpha linking / Mass: 164.156 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C6H12O5
IdentifierTypeProgram
DFucpaCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
a-D-fucopyranoseCOMMON NAMEGMML 1.0
a-D-FucpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
FucSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsTHE SEQUENCE GIVEN FOR MOMORDICA BALSAMINA IS CORRECT, ITS GENBANK ACCESSION NO. IS HM367595.

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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: 2.33 Å3/Da / Density % sol: 47.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 14% PEG6000, 0.1M Sodium Phosphate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8148 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Oct 28, 2008 / Details: mirror
RadiationMonochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8148 Å / Relative weight: 1
ReflectionResolution: 2.1→64.58 Å / Num. all: 14192 / Num. obs: 14192 / % possible obs: 97.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 35.2 Å2 / Rsym value: 0.05 / Net I/σ(I): 14.2
Reflection shellResolution: 2.1→2.22 Å / Mean I/σ(I) obs: 4.7 / Rsym value: 0.175 / % possible all: 92.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0109refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AHA
Resolution: 2.11→64.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.93 / SU B: 4.754 / SU ML: 0.126 / Cross valid method: THROUGHOUT / ESU R: 0.257 / ESU R Free: 0.197 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22627 703 5.1 %RANDOM
Rwork0.17395 ---
all0.17847 14192 --
obs0.17638 13134 97.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.838 Å2
Baniso -1Baniso -2Baniso -3
1--2.5 Å2-1.25 Å20 Å2
2---2.5 Å20 Å2
3---3.76 Å2
Refinement stepCycle: LAST / Resolution: 2.11→64.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1911 0 45 175 2131
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0221993
X-RAY DIFFRACTIONr_angle_refined_deg2.2281.9922716
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2555245
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.70123.92984
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.69615322
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.0851513
X-RAY DIFFRACTIONr_chiral_restr0.1360.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0211480
X-RAY DIFFRACTIONr_mcbond_it1.2471.51227
X-RAY DIFFRACTIONr_mcangle_it2.13221988
X-RAY DIFFRACTIONr_scbond_it3.7123766
X-RAY DIFFRACTIONr_scangle_it5.6934.5728
LS refinement shellResolution: 2.105→2.16 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.315 58 -
Rwork0.235 873 -
obs--89.09 %

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