[English] 日本語
Yorodumi
- PDB-4jd6: Crystal structure of Mycobacterium tuberculosis Eis in complex wi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 4jd6
TitleCrystal structure of Mycobacterium tuberculosis Eis in complex with coenzyme A and tobramycin
ComponentsEnhanced intracellular survival protein
KeywordsTRANSFERASE / GNAT / aminoglycoside acetyltransferase
Function / homology
Function and homology information


effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host inflammatory response / symbiont-mediated suppression of host defense-related programmed cell death / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / symbiont-mediated perturbation of host innate immune response / Suppression of autophagy / symbiont-mediated perturbation of host programmed cell death / bacterial extracellular vesicle / biological process involved in interaction with host ...effector-mediated defense to host-produced reactive oxygen species / symbiont-mediated perturbation of host inflammatory response / symbiont-mediated suppression of host defense-related programmed cell death / aminoglycoside antibiotic catabolic process / aminoglycoside N-acetyltransferase activity / symbiont-mediated perturbation of host innate immune response / Suppression of autophagy / symbiont-mediated perturbation of host programmed cell death / bacterial extracellular vesicle / biological process involved in interaction with host / host cell cytoplasmic vesicle / N-acetyltransferase activity / peptide-lysine-N-acetyltransferase activity / Transferases; Acyltransferases; Transferring groups other than aminoacyl groups / host extracellular space / response to antibiotic / identical protein binding / cytosol
Similarity search - Function
N-acetyltransferase Eis / Enhanced intracellular survival protein domain / Eis-like, acetyltransferase domain / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) ...N-acetyltransferase Eis / Enhanced intracellular survival protein domain / Eis-like, acetyltransferase domain / Sterol carrier protein domain / Acetyltransferase (GNAT) domain / Acetyltransferase (GNAT) domain / SCP2 sterol-binding domain / Nonspecific Lipid-transfer Protein; Chain A / SCP2 sterol-binding domain superfamily / Gcn5-related N-acetyltransferase (GNAT) / Gcn5-related N-acetyltransferase (GNAT) domain profile. / GNAT domain / Acyl-CoA N-acyltransferase / Aminopeptidase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
COENZYME A / TOBRAMYCIN / : / N-acetyltransferase Eis
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.5 Å
AuthorsBiswas, T. / Chen, W. / Garneau-Tsodikova, S. / Tsodikov, O.V.
CitationJournal: Chembiochem / Year: 2013
Title: Chemical and structural insights into the regioversatility of the aminoglycoside acetyltransferase eis.
Authors: Houghton, J.L. / Biswas, T. / Chen, W. / Tsodikov, O.V. / Garneau-Tsodikova, S.
History
DepositionFeb 23, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 23, 2013Provider: repository / Type: Initial release
Revision 1.1Mar 19, 2014Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Enhanced intracellular survival protein
B: Enhanced intracellular survival protein
C: Enhanced intracellular survival protein
D: Enhanced intracellular survival protein
E: Enhanced intracellular survival protein
F: Enhanced intracellular survival protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)285,50514
Polymers279,9656
Non-polymers5,5408
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area32620 Å2
ΔGint-46 kcal/mol
Surface area87640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.226, 154.908, 115.286
Angle α, β, γ (deg.)90.00, 104.70, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(0.939627, -0.295545, 0.172494), (0.010099, -0.479903, -0.877264), (0.342051, 0.826043, -0.447945)-5.24804, 30.35813, 45.86308
3given(0.943183, 0.015473, 0.331913), (-0.281381, -0.494083, 0.822622), (0.176721, -0.869277, -0.461657)-10.76475, -24.86138, 48.13255
4given(-0.996587, 0.079451, 0.022402), (0.078397, 0.825973, 0.558231), (0.025849, 0.558082, -0.829383)23.0836, -20.10835, 62.56199
5given(-0.929559, 0.27104, -0.249915), (0.268976, 0.034988, -0.962511), (-0.252135, -0.961932, -0.105427)31.68841, 30.29649, 40.74357
6given(-0.955774, -0.072602, -0.285), (-0.065516, -0.892141, 0.44698), (-0.286712, 0.445884, 0.847929)33.13609, -14.62191, 8.61691

-
Components

#1: Protein
Enhanced intracellular survival protein


Mass: 46660.840 Da / Num. of mol.: 6 / Mutation: C204A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: RVBD_2416c / Production host: Escherichia coli (E. coli) / References: UniProt: I6X469, UniProt: P9WFK7*PLUS
#2: Chemical
ChemComp-COA / COENZYME A


Mass: 767.534 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C21H36N7O16P3S
#3: Chemical ChemComp-TOY / TOBRAMYCIN / 4-AMINO-2-[4,6-DIAMINO-3-(3-AMINO-6-AMINOMETHYL-5-HYDROXY-TETRAHYDRO-PYRAN-2-YLOXY)-2-HYDROXY-CYCLOHEXYLOXY]-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-3,5-DIOL


Mass: 467.514 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H37N5O9 / Comment: antibiotic*YM
Nonpolymer detailsThe phosphopantetheinyl arms of CoA molecules were poorly resolved in chains A, D, E, F and were ...The phosphopantetheinyl arms of CoA molecules were poorly resolved in chains A, D, E, F and were placed in the partial electron density based on their conformation in the other monomers and consistent with the previously observed position of the phosphopantetheinyl arm of CoA molecules mound to Eis in entry 3R1K. Similarly, the tobramycin molecule bound to monomer B was placed and refined in partial, but strong, omit density based on the position of the tobramycin molecule in the binding site of monomer A.

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.54 Å3/Da / Density % sol: 51.51 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: TOB (1 mM) and CoA (1 mM)); reservoir solution (Tris-HCl (100 mM, pH 8.5) and PEG 8,000 (13% w/v)), VAPOR DIFFUSION, HANGING DROP, temperature 295K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 11, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.5→50 Å / Num. obs: 33556 / % possible obs: 100 % / Observed criterion σ(I): 2.3

-
Processing

Software
NameVersionClassification
HKL-2000data collection
PHASERphasing
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.5→40 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.901 / SU B: 42.469 / SU ML: 0.626 / Cross valid method: THROUGHOUT / ESU R Free: 0.733 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.27574 1769 5 %RANDOM
Rwork0.24423 ---
obs0.24583 33556 99.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 126.345 Å2
Baniso -1Baniso -2Baniso -3
1-10.69 Å20 Å211.58 Å2
2---8.93 Å20 Å2
3---4.12 Å2
Refinement stepCycle: LAST / Resolution: 3.5→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms18300 0 352 0 18652
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.01919144
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.11.98826090
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.6552364
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.83721.348846
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.334152898
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.36115240
X-RAY DIFFRACTIONr_chiral_restr0.1220.22936
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.02114586
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 3.5→3.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.386 140 -
Rwork0.365 2408 -
obs--100 %

+
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://pdbjlvh1.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