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- PDB-6z1y: Crystal structure of type-I ribosome-inactivating protein trichob... -

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Basic information

Entry
Database: PDB / ID: 6z1y
TitleCrystal structure of type-I ribosome-inactivating protein trichobakin (TBK)
ComponentsTrichobakin
KeywordsHYDROLASE / Trichobakin / Trichosantin / ribosome-inactivating protein / RIP
Function / homology
Function and homology information


rRNA N-glycosylase / rRNA N-glycosylase activity / 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
Biological speciesTrichosanthes sp. Bac Kan 8-98 (plant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsBoyko, K.M. / Nikolaeva, A.Y. / Britikov, V.V. / Bocharov, E.V. / Britikova, E.V. / Le, T.B.T. / Phan, C.V. / Popov, V.O. / Usanov, S.A.
Funding support Russian Federation, Belarus, 2items
OrganizationGrant numberCountry
Russian Science Foundation19-74-30014 Russian Federation
Not fundedBRFFR-VAST X17B-012Belarus
CitationJournal: To Be Published
Title: Crystal structure of type-I ribosome-inactivating protein trichobakin (TBK)
Authors: Britikov, V.V. / Britikova, E.V. / Bocharov, E.V. / Le, T.B.T. / Phan, C.V. / Nikolaeva, A.Y. / Boyko, K.M. / Arseniev, A.S. / Usanov, S.A.
History
DepositionMay 14, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 27, 2020Provider: repository / Type: Initial release
Revision 1.1Sep 23, 2020Group: Database references / Derived calculations
Category: pdbx_related_exp_data_set / pdbx_struct_conn_angle / struct_conn
Item: _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Trichobakin
B: Trichobakin
C: Trichobakin
D: Trichobakin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,55810
Polymers109,4204
Non-polymers1386
Water12,142674
1
A: Trichobakin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,3782
Polymers27,3551
Non-polymers231
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Trichobakin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4013
Polymers27,3551
Non-polymers462
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Trichobakin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,4244
Polymers27,3551
Non-polymers693
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Trichobakin


Theoretical massNumber of molelcules
Total (without water)27,3551
Polymers27,3551
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)71.720, 73.730, 88.070
Angle α, β, γ (deg.)90.000, 96.850, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ASPASPASNASNAA1 - 2422 - 243
21ASPASPASNASNBB1 - 2422 - 243
12METMETASNASNAA0 - 2421 - 243
22METMETASNASNCC0 - 2421 - 243
13VALVALASNASNAA2 - 2423 - 243
23VALVALASNASNDD2 - 2423 - 243
14ASPASPASNASNBB1 - 2422 - 243
24ASPASPASNASNCC1 - 2422 - 243
15VALVALASNASNBB2 - 2423 - 243
25VALVALASNASNDD2 - 2423 - 243
16VALVALMETMETCC2 - 2463 - 247
26VALVALMETMETDD2 - 2463 - 247

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
Trichobakin


Mass: 27355.059 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Trichosanthes sp. Bac Kan 8-98 (plant) / Gene: TBK / Production host: Escherichia coli (E. coli) / References: UniProt: Q9LRE3
#2: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 674 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.11 Å3/Da / Density % sol: 41.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 8mM sodium citrate pH 5.0, 10% KCl.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: KURCHATOV SNC / Beamline: K4.4 / Wavelength: 0.79475 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 12, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.79475 Å / Relative weight: 1
ReflectionResolution: 2→39.41 Å / Num. obs: 61634 / % possible obs: 99.8 % / Redundancy: 6 % / CC1/2: 0.992 / Rmerge(I) obs: 0.2 / Rpim(I) all: 0.087 / Rrim(I) all: 0.219 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2-2.055.90.72660245140.8460.3020.7642.298.9
8.94-39.415.60.05341047320.9980.0230.05813.399

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0258refinement
MOSFLMdata reduction
Aimless0.7.4data scaling
MOLREPphasing
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2JJR

2jjr


Resolution: 2→39.41 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 2.819 / SU ML: 0.082 / SU R Cruickshank DPI: 0.0426 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.043 / ESU R Free: 0.037 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2265 2986 4.8 %RANDOM
Rwork0.1722 ---
obs0.1748 58630 99.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.16 Å2 / Biso mean: 13.117 Å2 / Biso min: 0.5 Å2
Baniso -1Baniso -2Baniso -3
1-8.18 Å20 Å2-3.45 Å2
2--0.18 Å2-0 Å2
3----8.37 Å2
Refinement stepCycle: final / Resolution: 2→39.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7577 0 6 675 8258
Biso mean--5.01 19.02 -
Num. residues----981
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0137798
X-RAY DIFFRACTIONr_bond_other_d0.0010.0177272
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.64110624
X-RAY DIFFRACTIONr_angle_other_deg1.471.56316827
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6935987
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.78522.262389
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.882151295
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.6481550
X-RAY DIFFRACTIONr_chiral_restr0.0970.21100
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.028750
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021636
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A76960.1
12B76960.1
21A75950.11
22C75950.11
31A76210.1
32D76210.1
41B75920.11
42C75920.11
51B76670.1
52D76670.1
61C79730.09
62D79730.09
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 210 -
Rwork0.184 4287 -
all-4497 -
obs--98.79 %

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