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- PDB-4nec: Conversion of a Disulfide Bond into a Thioacetal Group during Ech... -

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Basic information

Entry
Database: PDB / ID: 4nec
TitleConversion of a Disulfide Bond into a Thioacetal Group during Echinomycin Biosynthesis
Components
  • Echinomycin
  • Putative SAM-dependent methyltransferase
KeywordsTRANSFERASE/ANTIBIOTIC / Methyltransferase / SAM-dependent methyltransferase / TRANSFERASE-ANTIBIOTIC complex
Function / homology
Function and homology information


methyltransferase activity / methylation
Similarity search - Function
Methyltransferase domain 25 / Methyltransferase domain / Vaccinia Virus protein VP39 / S-adenosyl-L-methionine-dependent methyltransferase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Echinomycin / ACETATE ION / TRIETHYLENE GLYCOL / 2-CARBOXYQUINOXALINE / S-ADENOSYL-L-HOMOCYSTEINE / : / Class I SAM-dependent methyltransferase
Similarity search - Component
Biological speciesStreptomyces lasaliensis (bacteria)
Streptomyces echinatus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsHotta, K. / Keegan, R.M. / Ranganathan, S. / Fang, M. / Bibby, J. / Winn, M.D. / Sato, M. / Lian, M. / Watanabe, K. / Rigden, D.J. / Kim, C.-Y.
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2014
Title: Conversion of a disulfide bond into a thioacetal group during echinomycin biosynthesis.
Authors: Hotta, K. / Keegan, R.M. / Ranganathan, S. / Fang, M. / Bibby, J. / Winn, M.D. / Sato, M. / Lian, M. / Watanabe, K. / Rigden, D.J. / Kim, C.Y.
History
DepositionOct 29, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jan 15, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 22, 2014Group: Structure summary
Revision 1.2Aug 24, 2022Group: Advisory / Database references / Derived calculations
Category: citation / citation_author ...citation / citation_author / database_2 / pdbx_struct_conn_angle / pdbx_validate_polymer_linkage / struct_conn / struct_ref_seq_dif / struct_site
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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_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.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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Apr 3, 2024Group: Data collection / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_conn
Item: _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative SAM-dependent methyltransferase
E: Echinomycin
B: Putative SAM-dependent methyltransferase
F: Echinomycin
C: Putative SAM-dependent methyltransferase
G: Echinomycin
D: Putative SAM-dependent methyltransferase
H: Echinomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,69428
Polymers117,2758
Non-polymers6,41920
Water5,765320
1
A: Putative SAM-dependent methyltransferase
E: Echinomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,2488
Polymers29,3192
Non-polymers9296
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1960 Å2
ΔGint-21 kcal/mol
Surface area11510 Å2
MethodPISA
2
B: Putative SAM-dependent methyltransferase
F: Echinomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,1106
Polymers29,3192
Non-polymers7924
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-6 kcal/mol
Surface area11560 Å2
MethodPISA
3
C: Putative SAM-dependent methyltransferase
G: Echinomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0746
Polymers29,3192
Non-polymers7564
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1830 Å2
ΔGint-13 kcal/mol
Surface area11210 Å2
MethodPISA
4
D: Putative SAM-dependent methyltransferase
H: Echinomycin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,2618
Polymers29,3192
Non-polymers3,9436
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-1 kcal/mol
Surface area11180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.187, 146.880, 58.187
Angle α, β, γ (deg.)90.00, 102.63, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein / Protein/peptide , 2 types, 8 molecules ABCDEFGH

#1: Protein
Putative SAM-dependent methyltransferase


Mass: 28509.682 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces lasaliensis (bacteria) / Gene: ecm18 / Plasmid: pKW469 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q0X0A7
#2: Protein/peptide
Echinomycin


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 809.008 Da / Num. of mol.: 4 / Source method: obtained synthetically
Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ...Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
Source: (synth.) Streptomyces echinatus (bacteria) / References: NOR: NOR01126, Echinomycin

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Non-polymers , 7 types, 340 molecules

#3: Chemical
ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE


Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H20N6O5S
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#6: Chemical
ChemComp-QUI / 2-CARBOXYQUINOXALINE


Type: Cyclic depsipeptide / Class: Antibiotic / Mass: 174.156 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C9H6N2O2
Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ...Details: ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE. BICYCLIZATION IS ACHIEVED BY LINKING THE N- AND THE C- TERMINI, AND A THIOACETAL BOND BETWEEN RESIDUES 3 AND 7. THE TWO QUINOXALINE CHROMOPHORES ARE LINKED TO THE D-SERINE RESIDUES, RESIDUES 1 AND 5.
References: Echinomycin
#7: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#8: Chemical ChemComp-15P / POLYETHYLENE GLYCOL (N=34) / PEG 1500


Mass: 1529.829 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C69H140O35 / Comment: precipitant*YM
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 320 / Source method: isolated from a natural source / Formula: H2O

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Details

Compound detailsTHE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. ...THE ECHINOMYCIN IS A BICYCLIC OCTADEPSIPEPTIDE, A MEMBER OF THE QUINOXALINE CLASS OF ANTIBIOTICS. HERE, ECHINOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND TWO LIGANDS (HET) QUI.

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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: 2.07 Å3/Da / Density % sol: 40.55 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 0.1M sodium cacodylate pH 6.1, 0.2M sodium acetate trihydrate, 30% (w/v) PEG 8000, 14% (v/v) ethylene glycol, 2.7% (w/v) sucrose, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 10, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.53
11L, -K, H20.47
ReflectionResolution: 1.5→48.96 Å / Num. obs: 151355 / % possible obs: 99.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 22 Å2 / Rmerge(I) obs: 0.114 / Net I/σ(I): 5.4

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
AMPLEphasing
REFMAC5.8.0049refinement
Aimlessdata scaling
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: AMPLE generated Ensemble model from ROSETTA decoys

Resolution: 1.5→45.42 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.957 / SU B: 1.563 / SU ML: 0.028 / Isotropic thermal model: ANISOTROPIC / Cross valid method: THROUGHOUT / ESU R: 0.016 / ESU R Free: 0.014 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19016 7689 5.1 %RANDOM
Rwork0.15042 ---
obs0.15248 143561 99.68 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 18.066 Å2
Baniso -1Baniso -2Baniso -3
1-2.57 Å20 Å2-5.44 Å2
2---0.5 Å2-0 Å2
3----2.06 Å2
Refinement stepCycle: LAST / Resolution: 1.5→45.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7392 0 245 320 7957
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0197894
X-RAY DIFFRACTIONr_bond_other_d0.0010.027268
X-RAY DIFFRACTIONr_angle_refined_deg1.172.01710763
X-RAY DIFFRACTIONr_angle_other_deg0.709316682
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.525962
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.64522.988338
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.151151119
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3571569
X-RAY DIFFRACTIONr_chiral_restr0.0610.21179
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0218971
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021770
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_it1.3621.7733849
X-RAY DIFFRACTIONr_mcbond_other1.3621.7733847
X-RAY DIFFRACTIONr_mcangle_it1.7292.6654802
X-RAY DIFFRACTIONr_mcangle_other1.7292.6654803
X-RAY DIFFRACTIONr_scbond_it1.4911.9114045
X-RAY DIFFRACTIONr_scbond_other1.491.9114046
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other1.7772.825958
X-RAY DIFFRACTIONr_long_range_B_refined2.45414.9559165
X-RAY DIFFRACTIONr_long_range_B_other2.45214.9559165
X-RAY DIFFRACTIONr_rigid_bond_restr0.807315155
X-RAY DIFFRACTIONr_sphericity_free23.373585
X-RAY DIFFRACTIONr_sphericity_bonded7.748515204
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.271 533 -
Rwork0.19 10562 -
obs--99.11 %

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