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- PDB-5oqz: Crystal structure of the lasso peptide rubrivinodin -

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Basic information

Entry
Database: PDB / ID: 5oqz
TitleCrystal structure of the lasso peptide rubrivinodin
ComponentsRubrivinodin
KeywordsUNKNOWN FUNCTION / Lasso peptide / ribosomally synthesized and post-translationally modified peptide / RiPP
Function / homologyUncharacterized protein
Function and homology information
Biological speciesRubrivivax gelatinosus IL144 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.806 Å
AuthorsFage, C.D. / Hegemann, J.D. / Marahiel, M.A.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation Germany
SYNMIKRO (Hessen) Germany
CitationJournal: Analyst / Year: 2018
Title: General rules of fragmentation evidencing lasso structures in CID and ETD.
Authors: Jeanne Dit Fouque, K. / Lavanant, H. / Zirah, S. / Hegemann, J.D. / Fage, C.D. / Marahiel, M.A. / Rebuffat, S. / Afonso, C.
History
DepositionAug 14, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 7, 2018Provider: repository / Type: Initial release
Revision 1.1Feb 14, 2018Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _citation.journal_id_ISSN ..._citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Mar 7, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.3May 8, 2019Group: Advisory / Data collection / Derived calculations
Category: database_PDB_remark / pdbx_unobs_or_zero_occ_atoms ...database_PDB_remark / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn / struct_conn_type
Item: _database_PDB_remark.text
Revision 1.4Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.5May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rubrivinodin


Theoretical massNumber of molelcules
Total (without water)1,9131
Polymers1,9131
Non-polymers00
Water21612
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area1610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)15.034, 27.243, 15.174
Angle α, β, γ (deg.)90.000, 116.760, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein/peptide Rubrivinodin


Mass: 1913.073 Da / Num. of mol.: 1 / Fragment: UNP residues 21-38
Source method: isolated from a genetically manipulated source
Details: Isopeptide bond between Gly1N and Glu9CD
Source: (gene. exp.) Rubrivivax gelatinosus IL144 (bacteria)
Gene: RGE_06990 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: I0HM07
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 12 / 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: 1.45 Å3/Da / Density % sol: 15.19 % / Description: Prismatic
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 4.6
Details: 0.7 M sodium acetate pH 4.6, 30%(v/v) glycerol, 4.6%(w/v) PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.799905 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 3, 2013
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.799905 Å / Relative weight: 1
ReflectionResolution: 0.8→50 Å / Num. obs: 9545 / % possible obs: 81.8 % / Redundancy: 3 % / CC1/2: 1 / Net I/σ(I): 35.85

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XPREPv. 2014/2data scaling
PDB_EXTRACT3.22data extraction
XDSVERSION March 30, 2013data reduction
SHELXDEphasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.806→13.622 Å / Cor.coef. Fo:Fc: 0.99 / Cor.coef. Fo:Fc free: 0.988 / SU B: 0.192 / SU ML: 0.006 / SU R Cruickshank DPI: 0.0104 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.01 / ESU R Free: 0.01
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.0913 470 4.9 %RANDOM
Rwork0.0844 ---
obs0.0848 9038 83.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.7 Å
Displacement parametersBiso max: 16.09 Å2 / Biso mean: 3.933 Å2 / Biso min: 1.74 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å20 Å2-0.08 Å2
2--0.05 Å20 Å2
3---0.06 Å2
Refinement stepCycle: final / Resolution: 0.806→13.622 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms134 0 0 16 150
Biso mean---8.51 -
Num. residues----18
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.02144
X-RAY DIFFRACTIONr_bond_other_d0.0020.02128
X-RAY DIFFRACTIONr_angle_refined_deg2.1472.021198
X-RAY DIFFRACTIONr_angle_other_deg1.1053303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.534519
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.758256
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.3621518
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.941151
X-RAY DIFFRACTIONr_chiral_restr0.0960.221
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.023162
X-RAY DIFFRACTIONr_gen_planes_other0.0020.0223
X-RAY DIFFRACTIONr_rigid_bond_restr1.5163272
X-RAY DIFFRACTIONr_sphericity_free11.26958
X-RAY DIFFRACTIONr_sphericity_bonded3.9845274
LS refinement shellResolution: 0.806→0.827 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.141 12 -
Rwork0.121 175 -
all-187 -
obs--22.53 %

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