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- PDB-6c0y: Lysinoalanine synthase, DurN, from duramycin biosynthesis bound t... -

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Basic information

Entry
Database: PDB / ID: 6c0y
TitleLysinoalanine synthase, DurN, from duramycin biosynthesis bound to duramycin
Components
  • CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
  • 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 / Duramycin / : / Lysinoalanine synthase / Cys-lys-gln-dal-cys-ala-phe-gly-pro-phe-dbb-phe-val-cys-bh2-gly-asn-dbb-lys
Function and homology information
Biological speciesStreptomyces cinnamoneus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 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
DepositionJan 3, 2018Deposition 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 1.3Aug 12, 2020Group: Derived calculations / Structure summary
Category: pdbx_molecule_features / struct_conn / struct_conn_type
Item: _struct_conn.conn_type_id / _struct_conn.id ..._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.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 1.4Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.5Nov 15, 2023Group: Data collection / Derived calculations / Category: chem_comp_atom / chem_comp_bond / struct_conn
Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 ..._chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag
Revision 2.0Jul 10, 2024Group: Polymer sequence / Category: entity_poly / Item: _entity_poly.pdbx_seq_one_letter_code_can
Revision 2.1Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Lysinoalanine synthase
B: Lysinoalanine synthase
C: Lysinoalanine synthase
D: Lysinoalanine synthase
E: Lysinoalanine synthase
F: Lysinoalanine synthase
G: Lysinoalanine synthase
H: Lysinoalanine synthase
O: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
I: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
J: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
K: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
L: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
M: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
N: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
P: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)124,29624
Polymers123,98316
Non-polymers3138
Water22,0321223
1
A: Lysinoalanine synthase
E: Lysinoalanine synthase
I: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
M: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0746
Polymers30,9964
Non-polymers782
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9590 Å2
ΔGint-63 kcal/mol
Surface area10460 Å2
MethodPISA
2
B: Lysinoalanine synthase
F: Lysinoalanine synthase
J: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
N: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0746
Polymers30,9964
Non-polymers782
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9580 Å2
ΔGint-65 kcal/mol
Surface area10810 Å2
MethodPISA
3
C: Lysinoalanine synthase
G: Lysinoalanine synthase
O: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
K: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0746
Polymers30,9964
Non-polymers782
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9730 Å2
ΔGint-65 kcal/mol
Surface area11080 Å2
MethodPISA
4
D: Lysinoalanine synthase
H: Lysinoalanine synthase
L: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
P: CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0746
Polymers30,9964
Non-polymers782
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9660 Å2
ΔGint-64 kcal/mol
Surface area10890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.881, 67.423, 69.122
Angle α, β, γ (deg.)71.51, 76.25, 72.92
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Lysinoalanine synthase


Mass: 13474.499 Da / Num. of mol.: 8
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
CYS-LYS-GLN-DAL-CYS-ALA-PHE-GLY-PRO-PHE-DBB-PHE-VAL-CYS-BH2-GLY-ASN-DBB-LYS


Type: Cyclic peptide / Class: Lantibiotic / Mass: 2023.358 Da / Num. of mol.: 8 / Source method: isolated from a natural source / Source: (natural) Streptomyces cinnamoneus (bacteria) / References: Duramycin, UniProt: A0A3F2YLX2*PLUS
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: K
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1223 / 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: 2.01 Å3/Da / Density % sol: 38.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 22.5% PEG 3350, 0.1 M MES pH 5.6

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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: Jul 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 1.658→64.72 Å / Num. obs: 109913 / % possible obs: 95.8 % / Redundancy: 4.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.072 / Rpim(I) all: 0.039 / Rrim(I) all: 0.082 / Net I/σ(I): 12
Reflection shellResolution: 1.658→1.687 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.726 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 5529 / CC1/2: 0.781 / Rpim(I) all: 0.387 / Rrim(I) all: 0.823 / % possible all: 95.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6C0H

6c0h


Resolution: 1.66→64.72 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.933 / SU B: 2.822 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24231 5255 4.8 %RANDOM
Rwork0.18437 ---
obs0.18719 104658 95.75 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.92 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å2-0.04 Å2-0.45 Å2
2---1.14 Å20.61 Å2
3---1.1 Å2
Refinement stepCycle: 1 / Resolution: 1.66→64.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7800 0 8 1223 9031
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0198058
X-RAY DIFFRACTIONr_bond_other_d0.0030.027853
X-RAY DIFFRACTIONr_angle_refined_deg2.1192.00210872
X-RAY DIFFRACTIONr_angle_other_deg1.315318213
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0435981
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.04724.65329
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.559151423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2911552
X-RAY DIFFRACTIONr_chiral_restr0.1380.21278
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0218625
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021467
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_it2.0271.924033
X-RAY DIFFRACTIONr_mcbond_other2.0261.9194032
X-RAY DIFFRACTIONr_mcangle_it2.852.8554975
X-RAY DIFFRACTIONr_mcangle_other2.852.8554976
X-RAY DIFFRACTIONr_scbond_it2.9462.2834025
X-RAY DIFFRACTIONr_scbond_other2.9462.2844025
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.4883.2965898
X-RAY DIFFRACTIONr_long_range_B_refined7.05626.35310295
X-RAY DIFFRACTIONr_long_range_B_other6.50225.1959815
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.658→1.701 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 398 -
Rwork0.25 7712 -
obs--95.27 %

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