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- PDB-1w3m: Crystal structure of tsushimycin -

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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
Revision 1.5Apr 9, 2025Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_entry_details.has_protein_modification / _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_alt_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.ptnr1_symmetry / _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.ptnr2_symmetry / _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_alt_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.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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

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Components

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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

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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


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


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


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

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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
Has protein modificationY

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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: 2.41 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

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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

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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

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