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- PDB-6jx3: Lasso peptide synthetase B1 complexed with the leader peptide -

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Basic information

Entry
Database: PDB / ID: 6jx3
TitleLasso peptide synthetase B1 complexed with the leader peptide
Components
  • TfuA-Leader
  • TfuB1
KeywordsPEPTIDE BINDING PROTEIN / lasso peptide / RRE
Function / homologyCoenzyme PQQ synthesis protein D / Coenzyme PQQ synthesis protein D superfamily / Coenzyme PQQ synthesis protein D (PqqD) / metal ion binding / TfuA-Leader / Coenzyme PQQ synthesis protein D (PqqD)
Function and homology information
Biological speciesThermobifida fusca (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsSumida, T. / Tagami, S.
Funding support Japan, 1items
OrganizationGrant numberCountry
Other private Japan
CitationJournal: Acs Chem.Biol. / Year: 2019
Title: Structural Basis of Leader Peptide Recognition in Lasso Peptide Biosynthesis Pathway.
Authors: Sumida, T. / Dubiley, S. / Wilcox, B. / Severinov, K. / Tagami, S.
History
DepositionApr 22, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 26, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 27, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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_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.pdbx_dist_value / _struct_conn.pdbx_ptnr1_label_alt_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_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_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
B: TfuB1
A: TfuA-Leader
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7689
Polymers13,3102
Non-polymers4587
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: isothermal titration calorimetry
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2270 Å2
ΔGint-151 kcal/mol
Surface area6510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.960, 90.300, 58.380
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11B-106-

ZN

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Components

#1: Protein TfuB1 / Uncharacterized protein


Mass: 10849.984 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermobifida fusca (bacteria) / Strain: YX / Production host: Escherichia coli (E. coli) / References: UniProt: Q47QT5
#2: Protein/peptide TfuA-Leader


Mass: 2459.876 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Thermobifida fusca (bacteria) / References: UniProt: A0A5H1ZR43*PLUS
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 293 K / Method: vapor diffusion
Details: 15% (v/v) Ethanol, 100 mM MES/ Sodium hydroxide pH 6.0, 200 mM Zinc acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Jul 16, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→45.15 Å / Num. obs: 27376 / % possible obs: 99.5 % / Redundancy: 3.5 % / Biso Wilson estimate: 21 Å2 / Rsym value: 0.059 / Net I/σ(I): 12.9
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2009 / Rsym value: 0.447 / % possible all: 99.4

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 1.7→45.15 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.15 / Phase error: 20.38
RfactorNum. reflection% reflection
Rfree0.2067 1370 5 %
Rwork0.1823 --
obs0.1836 27373 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 78.31 Å2 / Biso mean: 25.879 Å2 / Biso min: 11.05 Å2
Refinement stepCycle: final / Resolution: 1.7→45.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms806 0 7 126 939
Biso mean--25.57 36.11 -
Num. residues----103
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006848
X-RAY DIFFRACTIONf_angle_d0.8981158
X-RAY DIFFRACTIONf_chiral_restr0.052135
X-RAY DIFFRACTIONf_plane_restr0.005151
X-RAY DIFFRACTIONf_dihedral_angle_d7.27678
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7001-1.76080.35291380.30082610274899
1.7608-1.83130.25951320.220926082740100
1.8313-1.91470.24261380.20182585272399
1.9147-2.01560.23151370.182925842721100
2.0156-2.14190.21360.177326312767100
2.1419-2.30730.22571380.17352605274399
2.3073-2.53950.2041400.18392592273299
2.5395-2.90690.23371380.18262587272599
2.9069-3.66210.19791340.16862602273699
3.6621-45.16590.17071390.17462599273899

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