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- PDB-1bry: BRYODIN TYPE I RIP -

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Basic information

Entry
Database: PDB / ID: 1bry
TitleBRYODIN TYPE I RIP
ComponentsBRYODIN I
KeywordsRIBOSOME-INACTIVATING PROTEIN / IMMUNOTOXIN / BRYODIN
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / 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 / 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
Ribosome-inactivating protein bryodin I
Similarity search - Component
Biological speciesBryonia dioica (red bryony)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsKlei, H.E. / Chang, C.Y.
Citation
Journal: Biochemistry / Year: 1997
Title: Molecular, biological, and preliminary structural analysis of recombinant bryodin 1, a ribosome-inactivating protein from the plant Bryonia dioica.
Authors: Gawlak, S.L. / Neubauer, M. / Klei, H.E. / Chang, C.Y. / Einspahr, H.M. / Siegall, C.B.
#1: Journal: Bioconjug.Chem. / Year: 1994
Title: Characterization of Ribosome-Inactivating Proteins Isolated from Bryonia Dioica and Their Utility as Carcinoma-Reactive Immunoconjugates
Authors: Siegall, C.B. / Gawlak, S.L. / Chace, D. / Wolff, E.A. / Mixan, B. / Marquardt, H.
History
DepositionFeb 14, 1997Processing site: BNL
Revision 1.0Mar 4, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 9, 2023Group: Database references / Other / Refinement description
Category: database_2 / pdbx_database_status / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site
Revision 1.4May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
Y: BRYODIN I
Z: BRYODIN I


Theoretical massNumber of molelcules
Total (without water)54,4062
Polymers54,4062
Non-polymers00
Water00
1
Y: BRYODIN I


Theoretical massNumber of molelcules
Total (without water)27,2031
Polymers27,2031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
Z: BRYODIN I


Theoretical massNumber of molelcules
Total (without water)27,2031
Polymers27,2031
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)65.720, 77.563, 115.601
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.962022, -0.161317, -0.220205), (0.202716, -0.118052, 0.972096), (-0.182811, -0.979817, -0.080867)
Vector: -18.81201, -2.78887, 120.38674)

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Components

#1: Protein BRYODIN I


Mass: 27202.820 Da / Num. of mol.: 2 / Fragment: RESIDUES 1 - 247
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bryonia dioica (red bryony)
Description: CDNA SEQUENCE ISOLATED FROM BRYONIA DIOICA LEAF MRNA
Organ: LEAF / Plasmid: PSE 13.0 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / Variant (production host): LAMBDA DE3 / References: UniProt: P33185, rRNA N-glycosylase

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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: 2.7 Å3/Da / Density % sol: 53 %
Description: TRICHOSANTHIN MODEL TRUNCATED WITH PROGRAM MUTATE (S.SHERIFF) TO SELECT COMMON ATOMS BASED ON SEQUENCE ALIGNMENT.
Crystal growpH: 6
Details: 0.1M MES (PH 6.0), 23% MEPEG5K, 0.2M AMMONIUM SULFATE, 0.1M LICL
Crystal grow
*PLUS
Method: unknown
Components of the solutions
*PLUS
Common name: PEG5000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jul 2, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.1→34 Å / Num. obs: 31074 / % possible obs: 89.1 % / Observed criterion σ(I): 0 / Redundancy: 3.6 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 25.9
Reflection shellResolution: 2.1→2.2 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.109 / Mean I/σ(I) obs: 8.7 / % possible all: 68.7

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Processing

Software
NameVersionClassification
X-PLOR3.1model building
X-PLOR3.1refinement
DENZOdata reduction
SCALEPACKdata scaling
X-PLOR3.1phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TCS

1tcs


Resolution: 2.1→8 Å / σ(F): 1
Details: NCS RESTRAINTS BETWEEN THE TWO MOLECULES IN THE ASYMMETRIC UNIT WERE USED FOR THE FIRST TWO REFINEMENT CYCLES BUT WERE REMOVED FOR ALL SUBSEQUENT CYCLES WHEN RFREE WAS SHOWN TO DECREASE BY ...Details: NCS RESTRAINTS BETWEEN THE TWO MOLECULES IN THE ASYMMETRIC UNIT WERE USED FOR THE FIRST TWO REFINEMENT CYCLES BUT WERE REMOVED FOR ALL SUBSEQUENT CYCLES WHEN RFREE WAS SHOWN TO DECREASE BY APPROXIMATELY THE SAME AMOUNT AS R WHEN THE RESTRAINTS WERE REMOVED.
RfactorNum. reflection% reflectionSelection details
Rfree0.298 -5 %RANDOM
Rwork0.237 ---
obs0.237 30733 88 %-
Displacement parametersBiso mean: 13 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3822 0 0 0 3822
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
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_deg1.4
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d23.9
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d1.4
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Version: 3.1 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_deg23.9
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_deg1.4

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