[English] 日本語
Yorodumi
- PDB-1w3m: Crystal structure of tsushimycin -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1w3m
TitleCrystal structure of tsushimycin
ComponentsTSUSHIMYCIN
KeywordsANTIBIOTIC / AMPHOMYCIN / DAPTOMYCIN / LIPOPETIDE / ANTIBACTERIAL
Function / homologyTsushimycin / ETHANOL / Delta-3isotetradecenoic acid / :
Function and homology information
Biological speciesACTINOPLANES FRIULIENSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIRECT METHODS / Resolution: 1 Å
AuthorsBunkoczi, G. / Vertesy, L. / Sheldrick, G.M.
CitationJournal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2005
Title: Structure of the lipopeptide antibiotic tsushimycin.
Authors: Bunkoczi, G. / Vertesy, L. / Sheldrick, G.M.
History
DepositionJul 16, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 27, 2005Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Structure summary / Version format compliance
Revision 1.2Nov 30, 2012Group: Other
Revision 1.3Oct 31, 2018Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Experimental preparation / Refinement description
Category: citation / exptl_crystal_grow ...citation / exptl_crystal_grow / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / refine
Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.title / _exptl_crystal_grow.method / _refine.pdbx_starting_model
Revision 1.4May 22, 2019Group: Data collection / Derived calculations / Refinement description
Category: refine / struct_conn
Item: _refine.pdbx_ls_cross_valid_method / _struct_conn.pdbx_leaving_atom_flag

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: TSUSHIMYCIN
B: TSUSHIMYCIN
C: TSUSHIMYCIN
D: TSUSHIMYCIN
E: TSUSHIMYCIN
F: TSUSHIMYCIN
G: TSUSHIMYCIN
H: TSUSHIMYCIN
I: TSUSHIMYCIN
J: TSUSHIMYCIN
K: TSUSHIMYCIN
L: TSUSHIMYCIN
A: Delta-3isotetradecenoic acid
B: Delta-3isotetradecenoic acid
C: Delta-3isotetradecenoic acid
D: Delta-3isotetradecenoic acid
E: Delta-3isotetradecenoic acid
F: Delta-3isotetradecenoic acid
G: Delta-3isotetradecenoic acid
H: Delta-3isotetradecenoic acid
I: Delta-3isotetradecenoic acid
J: Delta-3isotetradecenoic acid
K: Delta-3isotetradecenoic acid
L: Delta-3isotetradecenoic acid
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,22576
Polymers13,36912
Non-polymers4,85664
Water3,441191
1
A: TSUSHIMYCIN
K: TSUSHIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,00012
Polymers2,2282
Non-polymers77110
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: TSUSHIMYCIN
G: TSUSHIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,27918
Polymers2,2282
Non-polymers1,05116
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: TSUSHIMYCIN
E: TSUSHIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,04413
Polymers2,2282
Non-polymers81611
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: TSUSHIMYCIN
L: TSUSHIMYCIN
hetero molecules


  • defined by author
  • 2.92 kDa, 2 polymers
Theoretical massNumber of molelcules
Total (without water)2,91810
Polymers2,2282
Non-polymers6908
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
F: TSUSHIMYCIN
J: TSUSHIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)3,00412
Polymers2,2282
Non-polymers77610
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
H: TSUSHIMYCIN
I: TSUSHIMYCIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)2,97911
Polymers2,2282
Non-polymers7519
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)33.488, 36.386, 37.511
Angle α, β, γ (deg.)65.64, 68.35, 69.88
Int Tables number1
Space group name H-MP1
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.3552, -0.75065, -0.5571), (-0.77579, -0.09577, 0.62368), (-0.52152, 0.65373, -0.54833)82.05582, 35.98845, 59.05227
2given(-0.81266, -0.5135, 0.27549), (-0.49858, 0.36799, -0.78486), (0.30165, -0.77518, -0.55507)69.89073, 58.21224, 57.79856
3given(-0.84322, 0.17118, -0.50959), (0.01711, -0.93892, -0.34371), (-0.5373, -0.29854, 0.78879)78.82603, 74.39417, 5.95721
4given(-0.50836, -0.2611, -0.82061), (-0.27743, -0.85246, 0.4431), (-0.81523, 0.45292, 0.36092)85.248, 52.608, 26.074
5given(0.80673, -0.04182, 0.58944), (0.46947, 0.65113, -0.59634), (-0.35887, 0.75781, 0.54492)-22.00171, 31.17325, 0.99058
6given(-0.99432, -0.06728, 0.08244), (-0.05047, -0.38392, -0.92198), (0.09368, -0.92091, 0.37835)65.2345, 79.23154, 29.58139
7given(0.84496, 0.45038, -0.28845), (-0.06506, 0.62188, 0.78041), (0.53086, -0.64065, 0.55476)26.45153, -0.72958, 18.52659
8given(0.50195, 0.3628, 0.78513), (0.86124, -0.12632, -0.49224), (-0.07941, 0.92326, -0.37587)-2.4707, 41.46967, 28.98703
9given(0.45405, 0.88434, -0.10857), (0.38389, -0.0842, 0.91953), (0.80404, -0.45919, -0.37772)-17.956, 8.812, 33.255
10given(0.26426, 0.81621, 0.51378), (0.80946, -0.47733, 0.34195), (0.52435, 0.32552, -0.78683)-17.874, 11.285, 27.106
11given(-0.40685, -0.91349, 0.00258), (-0.91324, 0.4068, 0.02229), (-0.02141, 0.00671, -0.99975)64.96851, 44.05581, 88.93584

-
Components

-
Protein/peptide , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein/peptide
TSUSHIMYCIN / FRIULIMICIN / AMPHOMYCIN / A1437 B


Type: Lipopeptide / Class: Antibiotic / Mass: 1114.121 Da / Num. of mol.: 12 / Source method: isolated from a natural source
Details: TSUSHIMYCIN IS A CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) ASP1 N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE RING. RESIDUE 2 AND 11 FORM A PEPTIDE BOND. A TETRADECENOIC FATTY ...Details: TSUSHIMYCIN IS A CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) ASP1 N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE RING. RESIDUE 2 AND 11 FORM A PEPTIDE BOND. A TETRADECENOIC FATTY ACID IS LINKED TO THE RESIDUE 1
Source: (natural) ACTINOPLANES FRIULIENSIS (bacteria) / References: NOR: NOR00763, Tsushimycin

-
Non-polymers , 5 types, 255 molecules ABCDEFGHIJKL

#2: Chemical
ChemComp-LNG / Delta-3isotetradecenoic acid


Type: Lipopeptide / Class: Antibiotic / Mass: 226.355 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C14H26O2
Details: TSUSHIMYCIN IS A CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) ASP1 N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE RING. RESIDUE 2 AND 11 FORM A PEPTIDE BOND. A TETRADECENOIC FATTY ...Details: TSUSHIMYCIN IS A CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) ASP1 N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE RING. RESIDUE 2 AND 11 FORM A PEPTIDE BOND. A TETRADECENOIC FATTY ACID IS LINKED TO THE RESIDUE 1
References: Tsushimycin
#3: Chemical...
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 25 / Source method: obtained synthetically / Formula: Ca
#4: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EOH / ETHANOL / Ethanol


Mass: 46.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

-
Details

Compound detailsTSUSHIMYCIN IS A CYCLIC DODEDECAMER LIPOPETIDE. HERE, TSUSHIMYCIN IS REPRESENTED BY GROUPING ...TSUSHIMYCIN IS A CYCLIC DODEDECAMER LIPOPETIDE. HERE, TSUSHIMYCIN IS REPRESENTED BY GROUPING TOGETHER THE SEQUENCE (SEQRES) AND ONE LIGAND (HET) LNG. GROUP: 1 NAME: TSUSHIMYCIN CHAIN: A, B, C, D, E, F, G, H, I, J, K, L COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 11 COMPONENT_2: FATTY ACID RESIDUE 0 DESCRIPTION: TSUSHIMYCIN IS A CYCLIC LIPOPEPTIDE. THE SCAFFOLD IS MADE OF TWO PARTS: (1) ASP1 N-TERM EXOCYCLIC PART (2) A DECAPEPTIDE RING. RESIDUE 2 AND 11 FORM A PEPTIDE BOND. A TETRADECENOIC FATTY ACID IS LINKED TO THE RESIDUE 1

-
Experimental details

-
Experiment

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

-
Sample preparation

CrystalDensity Matthews: 2.41 Å3/Da / Density % sol: 40 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 4
Details: 0.1 M NAAC/HAC PH=4.0 0.12 M HAC 38% ETOH 0.80 M CACL2 0.40 M 1,6-HEXANEDIOL

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: CCD / Date: Dec 12, 2003 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 1→26.02 Å / Num. obs: 355145 / % possible obs: 96.2 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.49
Reflection shellResolution: 1→1.1 Å / Redundancy: 3.62 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 3.35 / % possible all: 92.1

-
Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
XDSdata scaling
SHELXDphasing
RefinementMethod to determine structure: DIRECT METHODS / Resolution: 1→99 Å / Num. parameters: 11896 / Num. restraintsaints: 14162 / Cross valid method: FREE R-VALUE / σ(F): 0
Stereochemistry target values: ENGH AND HUBER GENERATED USING CCDC
RfactorNum. reflection% reflectionSelection details
Rfree0.1711 3848 5 %THIN SHELLS
all0.1385 75901 --
obs0.1374 -96.2 %-
Refine analyzeNum. disordered residues: 26 / Occupancy sum hydrogen: 829 / Occupancy sum non hydrogen: 1259.82
Refinement stepCycle: LAST / Resolution: 1→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms924 0 161 191 1276
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.015
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist
X-RAY DIFFRACTIONs_from_restr_planes0.428
X-RAY DIFFRACTIONs_zero_chiral_vol0.09
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.117
X-RAY DIFFRACTIONs_anti_bump_dis_restr
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.049
X-RAY DIFFRACTIONs_approx_iso_adps0.089

+
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