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- PDB-1hwp: EBULIN COMPLEXED WITH PTEROIC ACID, TRIGONAL CRYSTAL FORM -

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Basic information

Entry
Database: PDB / ID: 1hwp
TitleEBULIN COMPLEXED WITH PTEROIC ACID, TRIGONAL CRYSTAL FORM
Components(EBULIN) x 2
KeywordsHYDROLASE / Ribosome-inactivating protein / ricin-like / inhibitor
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / metabolic process / 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 conserved site / Ricin-type beta-trefoil lectin domain / Shiga/ricin ribosomal inactivating toxins active site signature. / Ribosome-inactivating protein type 1/2 / Ribosome-inactivating protein / Ribosome-inactivating protein, subdomain 1 ...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 / Ricin-type beta-trefoil lectin domain / 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 / Ricin-type beta-trefoil / Lectin domain of ricin B chain profile. / Ricin B, lectin domain / Ricin B-like lectins / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
beta-lactose / PTEROIC ACID / Ribosome-inactivating protein
Similarity search - Component
Biological speciesSambucus ebulus (plant)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.1 Å
AuthorsPascal, J.M. / Day, P.J. / Monzingo, A.F. / Ernst, S.R. / Robertus, J.D.
CitationJournal: Proteins / Year: 2001
Title: 2.8-A crystal structure of a nontoxic type-II ribosome-inactivating protein, ebulin l.
Authors: Pascal, J.M. / Day, P.J. / Monzingo, A.F. / Ernst, S.R. / Robertus, J.D. / Iglesias, R. / Perez, Y. / Ferreras, J.M. / Citores, L. / Girbes, T.
History
DepositionJan 9, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
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 / entity / entity_name_com / 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_molecule_features / 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 / _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_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Aug 9, 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

Downloads & links

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Assembly

Deposited unit
A: EBULIN
B: EBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,0985
Polymers57,8572
Non-polymers1,2413
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5180 Å2
ΔGint2 kcal/mol
Surface area19920 Å2
MethodPISA
2
A: EBULIN
B: EBULIN
hetero molecules

A: EBULIN
B: EBULIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,19610
Polymers115,7144
Non-polymers2,4826
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_556y,x,-z+11
Buried area12810 Å2
ΔGint7 kcal/mol
Surface area37390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.230, 74.230, 190.980
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 2 types, 2 molecules AB

#1: Protein EBULIN / EBULIN A CHAIN


Mass: 28478.982 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: N-GLYCOSIDASE / Source: (natural) Sambucus ebulus (plant) / Tissue: LEAF / References: UniProt: Q9AVR2, rRNA N-glycosylase
#2: Protein EBULIN / EBULIN B CHAIN


Mass: 29377.898 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: GALACTOSIDE SPECIFIC LECTIN / Source: (natural) Sambucus ebulus (plant) / Tissue: LEAF / References: UniProt: Q9AVR2, rRNA N-glycosylase

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Sugars , 2 types, 2 molecules

#3: Polysaccharide beta-D-galactopyranose-(1-4)-beta-D-glucopyranose / beta-lactose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: beta-lactose
DescriptorTypeProgram
DGalpb1-4DGlcpb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/2,2,1/[a2122h-1b_1-5][a2112h-1b_1-5]/1-2/a4-b1WURCSPDB2Glycan 1.1.0
[][b-D-Glcp]{[(4+1)][b-D-Galp]{}}LINUCSPDB-CARE
#4: Polysaccharide beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 586.542 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5]/1-1-2/a4-b1_b4-c1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{}}}}LINUCSPDB-CARE

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Non-polymers , 2 types, 21 molecules

#5: Chemical ChemComp-PT1 / PTEROIC ACID


Mass: 312.283 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H12N6O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 20 / Source method: isolated from a natural source / Formula: H2O

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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: 2.62 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 1.1 M Na,K Tartrate, 100 mM HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
13 mg/mlprotein1drop
21.1 MNa, K tartrate1reservoir
3100 mMHEPES1reservoir

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Data collection

DiffractionMean temperature: 150 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Oct 21, 1998
RadiationMonochromator: Double focusing mirrors, (Ni + Pt) + Ni filters
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 3.1→40 Å / Num. all: 11311 / Num. obs: 11311 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 1.95 % / Rmerge(I) obs: 0.118 / Net I/σ(I): 7.3
Reflection shellResolution: 3.1→3.21 Å / Rmerge(I) obs: 0.378 / % possible all: 98.1
Reflection shell
*PLUS
% possible obs: 98.1 % / Mean I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
SCALEPACKdata scaling
X-PLORmodel building
X-PLOR3.851refinement
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1HWO

1hwo


Resolution: 3.1→40 Å / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.317 519 5% of all reflections were flagged
Rwork0.219 --
all-11311 -
obs-10252 -
Refinement stepCycle: LAST / Resolution: 3.1→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4018 0 85 20 4123
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.054
X-RAY DIFFRACTIONx_dihedral_angle_d30.982
Software
*PLUS
Name: X-PLOR / Version: 3.851 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg30.982

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