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- PDB-1j4g: crystal structure analysis of the trichosanthin delta C7 -

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Basic information

Entry
Database: PDB / ID: 1j4g
Titlecrystal structure analysis of the trichosanthin delta C7
ComponentsTrichosanthin delta C7
KeywordsHYDROLASE / Antiviral / Protein synthesis inhibitor
Function / homology
Function and homology information


regulation of defense response to virus / 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 alpha-trichosanthin
Similarity search - Component
Biological speciesTrichosanthes kirilowii (Chinese cucumber)
MethodX-RAY DIFFRACTION / Resolution: 2 Å
AuthorsDing, Y. / Too, H.M. / Wang, Z.L. / Liu, Y.W. / Dong, Y.C. / Shaw, P.C. / Rao, Z.H.
CitationJournal: To be Published
Title: crystal structure analysis of the trichosanthin delta C7
Authors: Ding, Y. / Too, H.M. / Wang, Z.L. / Liu, Y.W. / Dong, Y.C. / Shaw, P.C. / Rao, Z.H.
History
DepositionSep 30, 2001Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 24, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 21, 2022Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / 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 / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 29, 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
A: Trichosanthin delta C7
B: Trichosanthin delta C7
C: Trichosanthin delta C7
D: Trichosanthin delta C7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3528
Polymers109,1924
Non-polymers1604
Water18,3571019
1
A: Trichosanthin delta C7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3382
Polymers27,2981
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Trichosanthin delta C7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3382
Polymers27,2981
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Trichosanthin delta C7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3382
Polymers27,2981
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Trichosanthin delta C7
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3382
Polymers27,2981
Non-polymers401
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.56, 74.40, 87.56
Angle α, β, γ (deg.)90, 96.96, 90
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Trichosanthin delta C7 / RIBOSOME-INACTIVATING PROTEIN ALPHA-TRICHOSANTHIN


Mass: 27297.965 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichosanthes kirilowii (Chinese cucumber)
Plasmid: pET8c / Production host: Escherichia coli (E. coli) / References: UniProt: P09989, rRNA N-glycosylase
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1019 / 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: 2.12 Å3/Da / Density % sol: 41.93 %
Crystal growTemperature: 291 K / Method: evaporation / pH: 6.5
Details: PEG8000, calcium acetate, sodium cacodylate, pH 6.5, EVAPORATION, temperature 291K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mg/mlprotein1drop
215 %PEG80001reservoir
30.2 M1reservoirCaAc2
40.1 Msodium cacodylate1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jul 28, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. all: 61794 / Num. obs: 59190 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.2 % / Biso Wilson estimate: 11.5 Å2 / Rmerge(I) obs: 0.082 / Net I/σ(I): 10.4
Reflection shellResolution: 2→2.13 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.225 / Num. unique all: 8268 / % possible all: 98.2
Reflection
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 40 Å / Num. obs: 19310 / % possible obs: 98.2 % / Num. measured all: 61794 / Rmerge(I) obs: 0.071
Reflection shell
*PLUS
Highest resolution: 1.8 Å / Lowest resolution: 1.87 Å / % possible obs: 95.8 % / Num. unique obs: 1950 / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 5.1

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 2→30 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber / Details: CNS
RfactorNum. reflection% reflection
Rfree0.235 5956 10 %
Rwork0.174 --
all-61794 -
obs-59190 95.8 %
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7460 0 4 1019 8483
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.014
X-RAY DIFFRACTIONc_angle_deg1.62
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.174
Solvent computation
*PLUS
Displacement parameters
*PLUS

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