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- PDB-6m7y: Dehydratase, NisB, bound to a non-eliminable substrate analog -

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Basic information

Entry
Database: PDB / ID: 6m7y
TitleDehydratase, NisB, bound to a non-eliminable substrate analog
Components
  • Lantibiotic
  • Nisin biosynthesis protein NisB
KeywordsBIOSYNTHETIC PROTEIN / RiPP / nisin / tRNA-dependent / dehydratase
Function / homology
Function and homology information


killing of cells of another organism / defense response to bacterium / signaling receptor binding / extracellular region / plasma membrane
Similarity search - Function
Lantibiotic, Type A, Bacillales-type / Gallidermin / Lantibiotic dehydratase, N-terminal / Lantibiotic dehydratase, N terminus / Thiopeptide-type bacteriocin biosynthesis domain / Lantibiotic biosynthesis dehydratase C-term
Similarity search - Domain/homology
Nisin biosynthesis protein NisB / Lantibiotic nisin-Z / Lantibiotic
Similarity search - Component
Biological speciesLactococcus lactis subsp. lactis (lactic acid bacteria)
Lactococcus lactis (lactic acid bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.794 Å
AuthorsCogan, D.P. / Nair, S.K.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2019
Title: Characterization of glutamyl-tRNA-dependent dehydratases using nonreactive substrate mimics.
Authors: Bothwell, I.R. / Cogan, D.P. / Kim, T. / Reinhardt, C.J. / van der Donk, W.A. / Nair, S.K.
History
DepositionAug 21, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 14, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Sep 4, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 11, 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 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_peptide_omega / pdbx_validate_rmsd_angle / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id
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: Nisin biosynthesis protein NisB
B: Nisin biosynthesis protein NisB
C: Lantibiotic
D: Lantibiotic


Theoretical massNumber of molelcules
Total (without water)244,5764
Polymers244,5764
Non-polymers00
Water4,450247
1
A: Nisin biosynthesis protein NisB
C: Lantibiotic


Theoretical massNumber of molelcules
Total (without water)122,2882
Polymers122,2882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-9 kcal/mol
Surface area46120 Å2
MethodPISA
2
B: Nisin biosynthesis protein NisB
D: Lantibiotic


Theoretical massNumber of molelcules
Total (without water)122,2882
Polymers122,2882
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1490 Å2
ΔGint-10 kcal/mol
Surface area45240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.644, 107.143, 135.438
Angle α, β, γ (deg.)90.00, 109.57, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Nisin biosynthesis protein NisB


Mass: 118647.109 Da / Num. of mol.: 2 / Mutation: V169C
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. lactis (lactic acid bacteria)
Gene: nisB / Plasmid: pET28b-NisB-V169C / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P20103
#2: Protein/peptide Lantibiotic


Mass: 3641.135 Da / Num. of mol.: 2 / Mutation: S12C, S26(J9A), C30A, C34A / Source method: obtained synthetically / Source: (synth.) Lactococcus lactis (lactic acid bacteria) / References: UniProt: Q7BB86, UniProt: P29559*PLUS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 247 / 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: 2.8 Å3/Da / Density % sol: 56.14 %
Crystal growTemperature: 282 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 18.3% PEG 6000, 0.1 M bicine pH 8.0, 1 mM dithiothreitol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 2.79→127.61 Å / Num. obs: 62069 / % possible obs: 93.1 % / Redundancy: 6.9 % / CC1/2: 0.998 / Rmerge(I) obs: 0.09 / Net I/σ(I): 21.5
Reflection shellResolution: 2.79→2.89 Å / Rmerge(I) obs: 0.836 / Num. unique obs: 4205 / CC1/2: 0.867

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Processing

Software
NameVersionClassification
PHENIX(1.10.1_2155: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WD9

4wd9


Resolution: 2.794→29.393 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 28.79
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 3031 4.88 %RANDOM
Rwork0.1849 ---
obs0.189 62048 93.08 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.794→29.393 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms16077 0 0 247 16324
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0116481
X-RAY DIFFRACTIONf_angle_d1.18522219
X-RAY DIFFRACTIONf_dihedral_angle_d17.3259991
X-RAY DIFFRACTIONf_chiral_restr0.0592442
X-RAY DIFFRACTIONf_plane_restr0.0062830
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7936-2.83720.3788930.23531603X-RAY DIFFRACTION56
2.8372-2.88370.32211050.22321961X-RAY DIFFRACTION69
2.8837-2.93340.3532990.22842112X-RAY DIFFRACTION73
2.9334-2.98670.34971200.23592282X-RAY DIFFRACTION80
2.9867-3.04410.33361130.25072439X-RAY DIFFRACTION85
3.0441-3.10610.34721550.23892563X-RAY DIFFRACTION89
3.1061-3.17360.34591300.22862769X-RAY DIFFRACTION96
3.1736-3.24730.31071500.22282841X-RAY DIFFRACTION99
3.2473-3.32840.34691370.21932914X-RAY DIFFRACTION100
3.3284-3.41830.32581320.2092824X-RAY DIFFRACTION100
3.4183-3.51870.2851590.20282861X-RAY DIFFRACTION100
3.5187-3.63210.32851530.18882870X-RAY DIFFRACTION100
3.6321-3.76170.30091630.18662892X-RAY DIFFRACTION100
3.7617-3.91190.26511460.18282846X-RAY DIFFRACTION100
3.9119-4.08950.27311120.17262941X-RAY DIFFRACTION100
4.0895-4.30450.25591450.15572886X-RAY DIFFRACTION100
4.3045-4.57330.22351630.14422853X-RAY DIFFRACTION100
4.5733-4.92490.20821400.13692907X-RAY DIFFRACTION100
4.9249-5.41770.21971560.15722897X-RAY DIFFRACTION100
5.4177-6.19520.23531550.18722886X-RAY DIFFRACTION100
6.1952-7.78130.2731440.19732922X-RAY DIFFRACTION100
7.7813-29.39430.19231610.1672948X-RAY DIFFRACTION99

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