[English] 日本語
Yorodumi
- PDB-4dj4: X-ray structure of mutant N211D of bifunctional nuclease TBN1 fro... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4dj4
TitleX-ray structure of mutant N211D of bifunctional nuclease TBN1 from Solanum lycopersicum (Tomato)
ComponentsNuclease
KeywordsHYDROLASE / mainly alpha helical / trinuclear metal centre / bi-functional / nuclease / 3'-nucleotidase / cytosol membrane associated
Function / homology
Function and homology information


Aspergillus nuclease S1 / single-stranded DNA endodeoxyribonuclease activity / DNA catabolic process / RNA endonuclease activity / nucleic acid binding / metal ion binding
Similarity search - Function
S1/P1 nuclease / S1/P1 Nuclease / P1 Nuclease / P1 Nuclease / Phospholipase C/P1 nuclease domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Aspergillus nuclease S1
Similarity search - Component
Biological speciesSolanum lycopersicum (tomato)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å
AuthorsKoval, T. / Stepankova, A. / Lipovova, P. / Podzimek, T. / Matousek, J. / Duskova, J. / Skalova, T. / Hasek, J. / Dohnalek, J.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2013
Title: Plant multifunctional nuclease TBN1 with unexpected phospholipase activity: structural study and reaction-mechanism analysis.
Authors: Koval, T. / Lipovova, P. / Podzimek, T. / Matousek, J. / Duskova, J. / Skalova, T. / Stepankova, A. / Hasek, J. / Dohnalek, J.
History
DepositionFeb 1, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 7, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 20, 2013Group: Database references
Revision 1.2Jan 31, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 2.0Jul 29, 2020Group: Atomic model / Data collection ...Atomic model / Data collection / Database references / Derived calculations / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / struct_asym / struct_conn / struct_ref_seq_dif / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.name / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_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.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _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.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_ref_seq_dif.details
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Sep 13, 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
Revision 2.2Nov 27, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Nuclease
B: Nuclease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,77615
Polymers63,2952
Non-polymers3,48113
Water3,045169
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1599 Å2
ΔGint-5 kcal/mol
Surface area22940 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.322, 113.322, 138.322
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number146
Space group name H-MH3

-
Components

-
Protein , 1 types, 2 molecules AB

#1: Protein Nuclease


Mass: 31647.520 Da / Num. of mol.: 2 / Mutation: N211D
Source method: isolated from a genetically manipulated source
Details: pLV07 is a derivative of plant binary vector pBinPLUS; TBN1 cDNA sequence is driven from 35S promoter of CaMV, and terminated by CaMV terminator. Expression casette is placed between left ...Details: pLV07 is a derivative of plant binary vector pBinPLUS; TBN1 cDNA sequence is driven from 35S promoter of CaMV, and terminated by CaMV terminator. Expression casette is placed between left and right borders of T-DNA.
Source: (gene. exp.) Solanum lycopersicum (tomato) / Strain: cv. Rutgers / Gene: tbn1 / Plasmid: pLV07 / Production host: Nicotiana benthamiana (plant) / References: UniProt: Q0KFV0

-
Sugars , 3 types, 4 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Polysaccharide alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 910.823 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3[DManpa1-6]DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE
#4: Polysaccharide alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1- ...alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 748.682 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DManpa1-3DManpb1-4DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/3,4,3/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3/a4-b1_b4-c1_c3-d1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}}}}}LINUCSPDB-CARE

-
Non-polymers , 4 types, 178 molecules

#5: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#6: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 169 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.7 Å3/Da / Density % sol: 54.45 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.16 M Magnesium chloride 0.08 M TRIS pH 8.5 19% w/v Polyethylene glycol 3,350 3.3% Butane-1,4-diol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 19, 2010 / Details: 2 mirrors and a double-crystal monochromator
RadiationMonochromator: KMC-1, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 2.35→35 Å / Num. obs: 26874 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3.7 / Redundancy: 5.7 % / Biso Wilson estimate: 46.6 Å2 / Rmerge(I) obs: 0.098 / Net I/σ(I): 17.7
Reflection shellResolution: 2.35→2.41 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.615 / Mean I/σ(I) obs: 2.3 / Num. unique all: 1524 / % possible all: 78.5

-
Processing

Software
NameVersionClassification
MxCuBEdata collection
MOLREPphasing
REFMAC5.6.0111refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3SNG

3sng


Resolution: 2.35→35 Å / Cor.coef. Fo:Fc: 0.953 / SU B: 4.736 / SU ML: 0.115 / Isotropic thermal model: isotropic / Cross valid method: Rfree throughout / σ(F): 0 / ESU R: 0.324
Stereochemistry target values: CCP4 stereochemistry library, version 6.2.0
Details: HYDROGENS HAVE BEEN GENERATED AND USED ONLY IN REFINEMENT. THE LAST STEPS OF REFINEMENT OF THIS STRUCTURE WERE DONE USING ALL REFLECTIONS. CALCULATION OF THE REPORTED VALUES OF RWORK AND ...Details: HYDROGENS HAVE BEEN GENERATED AND USED ONLY IN REFINEMENT. THE LAST STEPS OF REFINEMENT OF THIS STRUCTURE WERE DONE USING ALL REFLECTIONS. CALCULATION OF THE REPORTED VALUES OF RWORK AND RFREE PRECEDED THIS LAST STEP OF REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.2074 1349 5 %random
Rwork0.1834 ---
all0.18617 26873 --
obs0.18617 26873 97.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 40.612 Å2
Baniso -1Baniso -2Baniso -3
1--2.22 Å2-1.11 Å20 Å2
2---2.22 Å20 Å2
3---3.33 Å2
Refinement stepCycle: LAST / Resolution: 2.35→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4162 0 209 169 4540
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.024551
X-RAY DIFFRACTIONr_bond_other_d0.0010.023021
X-RAY DIFFRACTIONr_angle_refined_deg1.4641.9696197
X-RAY DIFFRACTIONr_angle_other_deg0.9853.0047262
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8775517
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.05624.148229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.31115721
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.7851524
X-RAY DIFFRACTIONr_chiral_restr0.0830.2694
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024917
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02955
LS refinement shellResolution: 2.352→2.413 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.267 66 -
Rwork0.234 1504 -
obs-1504 78.58 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more