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- PDB-6c0h: Lysinoalanine synthase, DurN, from duramycin biosynthesis bound t... -

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Basic information

Entry
Database: PDB / ID: 6c0h
TitleLysinoalanine synthase, DurN, from duramycin biosynthesis bound to 1-Dha6Ala
Components
  • GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY
  • Lysinoalanine synthase
KeywordsBIOSYNTHETIC PROTEIN / Lysinoalanine synthase / Michael addition
Function / homologyProtein of unknown function DUF5950 / Protein of unknown function DUF5973 / DurN substrate-assisted peptide maturase / Lantibiotic duramycin B-like / : / Gln-dal-cys-ala-phe-gly-pro-phe-dbb-phe-val-cys-bh2-gly / Lysinoalanine synthase
Function and homology information
Biological speciesStreptomyces cinnamoneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsCogan, D.P. / Nair, S.K.
CitationJournal: Nat. Chem. Biol. / Year: 2018
Title: Substrate-assisted enzymatic formation of lysinoalanine in duramycin.
Authors: An, L. / Cogan, D.P. / Navo, C.D. / Jimenez-Oses, G. / Nair, S.K. / van der Donk, W.A.
History
DepositionDec 31, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Oct 3, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 2.0Jul 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Polymer sequence
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity_poly / struct_conn / struct_conn_type
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity_poly.pdbx_seq_one_letter_code_can / _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 / _struct_conn_type.id
Revision 2.1Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Lysinoalanine synthase
B: Lysinoalanine synthase
C: GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3405
Polymers29,2623
Non-polymers782
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8200 Å2
ΔGint-61 kcal/mol
Surface area11080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)39.990, 39.990, 303.353
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein Lysinoalanine synthase


Mass: 13474.499 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cinnamoneus (bacteria) / Gene: durN / Plasmid: pET28a-MBP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A3F2YLX1*PLUS
#2: Protein/peptide GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY


Mass: 2312.687 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptomyces cinnamoneus (bacteria) / Gene: durA / Plasmid: pET28a-MBP / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A0A3F2YLX0*PLUS
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: H2O
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: 2.07 Å3/Da / Density % sol: 40.65 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 25% PEG 3350, 0.2 M magnesium chloride, 0.1 M bis-tris pH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Apr 23, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.9→151.676 Å / Num. obs: 447453 / % possible obs: 100 % / Redundancy: 21.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.078 / Rpim(I) all: 0.017 / Rrim(I) all: 0.08 / Net I/σ(I): 25.5
Reflection shellResolution: 1.9→1.932 Å / Redundancy: 14.6 % / Rmerge(I) obs: 1.022 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 14211 / CC1/2: 0.844 / Rpim(I) all: 0.274 / Rrim(I) all: 1.059 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
autoSHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.9→75.84 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.933 / SU B: 3.722 / SU ML: 0.108 / Cross valid method: THROUGHOUT / ESU R: 0.151 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2509 1029 5 %RANDOM
Rwork0.19045 ---
obs0.19351 19755 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.358 Å2
Baniso -1Baniso -2Baniso -3
1-0.9 Å2-0 Å2-0 Å2
2--0.9 Å2-0 Å2
3----1.81 Å2
Refinement stepCycle: 1 / Resolution: 1.9→75.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1827 0 2 143 1972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0191866
X-RAY DIFFRACTIONr_bond_other_d0.0020.021811
X-RAY DIFFRACTIONr_angle_refined_deg1.8511.9972527
X-RAY DIFFRACTIONr_angle_other_deg2.0073.0014200
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3515231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.9462576
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.29215331
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.7271512
X-RAY DIFFRACTIONr_chiral_restr0.1150.2302
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0212008
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02328
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_it2.9593.258941
X-RAY DIFFRACTIONr_mcbond_other2.963.257940
X-RAY DIFFRACTIONr_mcangle_it3.7634.8551165
X-RAY DIFFRACTIONr_mcangle_other3.7614.8561166
X-RAY DIFFRACTIONr_scbond_it4.5483.789925
X-RAY DIFFRACTIONr_scbond_other4.5463.789926
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6795.4791363
X-RAY DIFFRACTIONr_long_range_B_refined8.05141.4732194
X-RAY DIFFRACTIONr_long_range_B_other7.99741.0282160
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.328 78 -
Rwork0.272 1388 -
obs--100 %

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