[English] 日本語
Yorodumi
- PDB-4xgr: Crystal structure of addiction module from Mycobacterial species -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4xgr
TitleCrystal structure of addiction module from Mycobacterial species
Components
  • Antitoxin VapB30
  • Ribonuclease VapC30
KeywordsTOXIN/ANTITOXIN / Mycobacteria / addiction module / TOXIN-ANTITOXIN complex
Function / homology
Function and homology information


positive regulation of growth / negative regulation of growth / RNA nuclease activity / Hydrolases; Acting on ester bonds / magnesium ion binding
Similarity search - Function
Antitoxin VapB-like / Rv0623-like transcription factor / : / PIN domain / VapC family / 5'-nuclease / PIN domain / PIN-like domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Ribonuclease VapC30 / Antitoxin VapB30
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.7 Å
AuthorsLee, B.-J. / Lee, I.-G. / Lee, S.J.
CitationJournal: Nucleic Acids Res. / Year: 2015
Title: Structural and functional studies of the Mycobacterium tuberculosis VapBC30 toxin-antitoxin system: implications for the design of novel antimicrobial peptides
Authors: Lee, I.-G. / Lee, S.J. / Chae, S. / Lee, K.Y. / Kim, J.H. / Lee, B.-J.
History
DepositionJan 2, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Aug 12, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 16, 2015Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_reflns_twin / pdbx_struct_oper_list / struct_conn
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_reflns_twin.operator / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Ribonuclease VapC30
G: Ribonuclease VapC30
E: Ribonuclease VapC30
C: Ribonuclease VapC30
B: Antitoxin VapB30
H: Antitoxin VapB30
F: Antitoxin VapB30
D: Antitoxin VapB30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,20210
Polymers95,1538
Non-polymers492
Water99155
1
A: Ribonuclease VapC30
C: Ribonuclease VapC30
B: Antitoxin VapB30
D: Antitoxin VapB30
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,6256
Polymers47,5764
Non-polymers492
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7850 Å2
ΔGint-62 kcal/mol
Surface area13660 Å2
MethodPISA
2
G: Ribonuclease VapC30
E: Ribonuclease VapC30
H: Antitoxin VapB30
F: Antitoxin VapB30


Theoretical massNumber of molelcules
Total (without water)47,5764
Polymers47,5764
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6410 Å2
ΔGint-40 kcal/mol
Surface area13300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)96.310, 96.310, 233.033
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

-
Components

#1: Protein
Ribonuclease VapC30 / RNase VapC30 / Toxin VapC30


Mass: 14585.790 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: vapC30, Rv0624, MTCY20H10.05 / Production host: Escherichia coli (E. coli)
References: UniProt: P9WF77, Hydrolases; Acting on ester bonds
#2: Protein
Antitoxin VapB30


Mass: 9202.435 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria)
Strain: ATCC 25618 / H37Rv / Gene: vapB30, Rv0623 / Production host: Escherichia coli (E. coli) / References: UniProt: P9WJ35
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 55 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 3.31 Å3/Da / Density % sol: 62.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.2 M sodium acetate, 0.1 M sodium citrate at pH 5.5, and 5% (w/v) PEG4000

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 5C (4A) / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.524
11-h,-k,l20.476
ReflectionResolution: 2.7→48.15 Å / Num. obs: 34963 / % possible obs: 98.9 % / Redundancy: 6.7 % / Net I/σ(I): 37.037

-
Processing

Software
NameVersionClassification
REFMAC5.8.0103refinement
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementResolution: 2.7→48.15 Å / Cor.coef. Fo:Fc: 0.907 / Cor.coef. Fo:Fc free: 0.897 / SU B: 8.799 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.083 / ESU R Free: 0.062 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27757 1672 4.8 %RANDOM
Rwork0.24273 ---
obs0.24444 33219 98.82 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 59.969 Å2
Baniso -1Baniso -2Baniso -3
1-23.69 Å20 Å20 Å2
2--23.69 Å20 Å2
3----47.39 Å2
Refinement stepCycle: LAST / Resolution: 2.7→48.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4749 0 2 55 4806
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0194827
X-RAY DIFFRACTIONr_bond_other_d0.0020.024579
X-RAY DIFFRACTIONr_angle_refined_deg1.4211.976538
X-RAY DIFFRACTIONr_angle_other_deg0.979310474
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9835610
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38323.362229
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.17615710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.9791543
X-RAY DIFFRACTIONr_chiral_restr0.0710.2744
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.025501
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021094
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.6175.8892479
X-RAY DIFFRACTIONr_mcbond_other3.6185.8872478
X-RAY DIFFRACTIONr_mcangle_it5.5098.8183076
X-RAY DIFFRACTIONr_mcangle_other5.5088.823077
X-RAY DIFFRACTIONr_scbond_it3.4926.2092348
X-RAY DIFFRACTIONr_scbond_other3.4936.2052346
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.2519.193462
X-RAY DIFFRACTIONr_long_range_B_refined7.8147.2575490
X-RAY DIFFRACTIONr_long_range_B_other7.80747.275489
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.699→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 121 -
Rwork0.274 2453 -
obs--99.88 %

+
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