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- PDB-1rzo: Agglutinin from Ricinus communis with galactoaza -

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Basic information

Entry
Database: PDB / ID: 1rzo
TitleAgglutinin from Ricinus communis with galactoaza
Components(Agglutinin) x 2
KeywordsHYDROLASE / RIBOSOME-INACTIVATING PROTEIN / IMMUNOTOXIN / AGGLUTININ RICIN
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / defense response / toxin activity / carbohydrate binding / negative regulation of translation / nucleotide binding / endoplasmic reticulum
Similarity search - Function
Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / 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 ...Ricin (A Subunit), domain 2 / Ricin (A Subunit), domain 2 / Ricin (A subunit); domain 1 / Ricin (A subunit), domain 1 / Ricin-type beta-trefoil lectin domain / 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 / 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-D-galactopyranose / Agglutinin
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.63 Å
AuthorsGabdoulkhakov, A.G. / Savochkina, Y. / Konareva, N. / Krauspenhaar, R. / Stoeva, S. / Nikonov, S.V. / Voelter, W. / Betzel, C. / Mikhailov, A.M.
CitationJournal: To be Published
Title: Structure-function investigation complex of Agglutinin from Ricinus communis with galactoaza
Authors: Gabdoulkhakov, A.G. / Savochkina, Y. / Konareva, N. / Krauspenhaar, R. / Stoeva, S. / Nikonov, S.V. / Voelter, W. / Betzel, C. / Mikhailov, A.M.
History
DepositionDec 26, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 28, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 5, 2016Group: Database references
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / diffrn_source ...chem_comp / diffrn_source / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _diffrn_source.pdbx_synchrotron_site / _entity.pdbx_description / _pdbx_entity_nonpoly.name
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Aug 23, 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: Agglutinin
B: Agglutinin
C: Agglutinin
D: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,81925
Polymers116,8764
Non-polymers2,94221
Water7,314406
1
A: Agglutinin
B: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,09514
Polymers58,4382
Non-polymers1,65712
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-92 kcal/mol
Surface area20810 Å2
MethodPISA
2
C: Agglutinin
D: Agglutinin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,72311
Polymers58,4382
Non-polymers1,2859
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5130 Å2
ΔGint-56 kcal/mol
Surface area21550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.630, 97.630, 207.827
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

#1: Protein Agglutinin / / RCA / rRNA N-glycosidase


Mass: 29306.100 Da / Num. of mol.: 2 / Fragment: A chain / Source method: isolated from a natural source / Source: (natural) Ricinus communis (castor bean) / References: UniProt: P06750, rRNA N-glycosylase
#2: Protein Agglutinin / / RCA


Mass: 29132.029 Da / Num. of mol.: 2 / Fragment: B chain / Source method: isolated from a natural source / Source: (natural) Ricinus communis (castor bean) / References: UniProt: P06750
#3: Sugar
ChemComp-GAL / beta-D-galactopyranose / beta-D-galactose / D-galactose / galactose / Galactose


Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C6H12O6
IdentifierTypeProgram
DGalpbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
b-D-galactopyranoseCOMMON NAMEGMML 1.0
b-D-GalpIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GalSNFG CARBOHYDRATE SYMBOLGMML 1.0
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 406 / 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: 4.89 Å3/Da / Density % sol: 74.85 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 1,7 amonium sulphate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.801 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 10, 2002 / Details: mirrors
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.801 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 67524 / % possible obs: 99.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.86 % / Biso Wilson estimate: 66.7 Å2 / Rmerge(I) obs: 0.06 / Rsym value: 0.055 / Net I/σ(I): 14.74
Reflection shellResolution: 2.63→2.82 Å / Redundancy: 3.84 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 4.87 / Num. unique all: 11437 / Rsym value: 0.24 / % possible all: 98.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2AAI

2aai


Resolution: 2.63→26.11 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1719369.57 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.276 6600 10.1 %RANDOM
Rwork0.225 ---
all0.227 ---
obs0.225 65481 99.6 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 68.6547 Å2 / ksol: 0.313748 e/Å3
Displacement parametersBiso mean: 61.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.48 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.71 Å0.64 Å
Refinement stepCycle: LAST / Resolution: 2.63→26.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8171 0 182 406 8759
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d24
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it8.611.5
X-RAY DIFFRACTIONc_mcangle_it12.752
X-RAY DIFFRACTIONc_scbond_it10.432
X-RAY DIFFRACTIONc_scangle_it14.52.5
LS refinement shellResolution: 2.63→2.79 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.465 1096 10.1 %
Rwork0.42 9866 -
obs-9779 99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2GLB.PARAMGLB.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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