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- PDB-1br6: RICIN A CHAIN (RECOMBINANT) COMPLEX WITH PTEROIC ACID -

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Basic information

Entry
Database: PDB / ID: 1br6
TitleRICIN A CHAIN (RECOMBINANT) COMPLEX WITH PTEROIC ACID
ComponentsPROTEIN (RICIN)
KeywordsHYDROLASE / GLYCOSIDASE
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / AMP binding / defense response / toxin activity / carbohydrate binding / killing of cells of another organism / 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 / 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 / Few Secondary Structures / Irregular / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
PTEROIC ACID / Ricin
Similarity search - Component
Biological speciesRicinus communis (castor bean)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsHollis, T. / Yan, X. / Svinth, M. / Day, P. / Monzingo, A.F. / Milne, G.W.A. / Robertus, J.D.
Citation
Journal: J.Mol.Biol. / Year: 1997
Title: Structure-based identification of a ricin inhibitor.
Authors: Yan, X. / Hollis, T. / Svinth, M. / Day, P. / Monzingo, A.F. / Milne, G.W. / Robertus, J.D.
#1: Journal: Protein Sci. / Year: 1993
Title: The Structure of Recombinant Ricin a Chain at 2.3 Angstroms
Authors: Mlsna, D. / Monzingo, A.F. / Katzin, B.J. / Ernst, S. / Robertus, J.D.
#2: Journal: Proteins / Year: 1991
Title: Structure of Ricin A-Chain at 2.5 Angstroms
Authors: Katzin, B.J. / Collins, E.J. / Robertus, J.D.
History
DepositionAug 27, 1998Deposition site: BNL / Processing site: RCSB
Revision 1.0Sep 2, 1998Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 9, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN (RICIN)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,3802
Polymers30,0681
Non-polymers3121
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)38.992, 64.366, 49.442
Angle α, β, γ (deg.)90.00, 107.98, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein PROTEIN (RICIN) / E.C.3.2.2.22 / RTA


Mass: 30067.953 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ricinus communis (castor bean) / Organ: SEED / Production host: Escherichia coli (E. coli) / References: UniProt: P02879, rRNA N-glycosylase
#2: Chemical ChemComp-PT1 / PTEROIC ACID


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


Mass: 18.015 Da / Num. of mol.: 41 / 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: 2.25 Å3/Da / Density % sol: 37.3 %
Crystal growpH: 8.9 / Details: pH 8.9
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: Robertus, J.D., (1987) J. Biol. Chem., 262, 19.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
12-2.5 mg/mlprotein1drop
275 mMTris-HCl1reservoir
31 mMEDTA1reservoir
410 mMbeta-mercaptoethanol1reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: SDMS / Detector: AREA DETECTOR / Date: Aug 15, 1995
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.23→20 Å / Num. obs: 10999 / % possible obs: 96 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.0612 / Net I/σ(I): 11.3
Reflection shellResolution: 2.23→2.4 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.135 / Mean I/σ(I) obs: 4.2 / % possible all: 78

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Processing

Software
NameVersionClassification
X-PLORmodel building
X-PLOR3.1refinement
UCSD-systemdata reduction
UCSD-systemdata scaling
X-PLORphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RTC

1rtc


Resolution: 2.3→5 Å / Data cutoff high absF: 0 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / σ(F): 0
RfactorNum. reflection% reflection
Rwork0.18 --
obs0.18 9321 99.4 %
Refine analyzeLuzzati d res low obs: 0 Å
Refinement stepCycle: LAST / Resolution: 2.3→5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2122 0 23 41 2186
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.014
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg3.243
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d26.27
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.431
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_mcangle_it1.52
X-RAY DIFFRACTIONx_scbond_it21.5
X-RAY DIFFRACTIONx_scangle_it22
LS refinement shellResolution: 2.3→2.39 Å / Total num. of bins used: 8
RfactorNum. reflection% reflection
Rwork0.224 1111 -
obs--95.4 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PARAM19X.PROTOPH19X.PRO
X-RAY DIFFRACTION2PARAM.WATTOPH.WAT
X-RAY DIFFRACTION3PARAM.PT1TOPH.PT1
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.3 Å / Lowest resolution: 5 Å / σ(F): 0 / Rfactor obs: 0.18 / Rfactor Rwork: 0.18
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg26.27
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.431
X-RAY DIFFRACTIONx_mcbond_it1.51.5
X-RAY DIFFRACTIONx_scbond_it21.5
X-RAY DIFFRACTIONx_mcangle_it1.52
X-RAY DIFFRACTIONx_scangle_it22
LS refinement shell
*PLUS
Rfactor Rwork: 0.224

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