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- PDB-5jqf: Crystal structure of the lasso peptide Sphingopyxin I (SpI) -

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Basic information

Entry
Database: PDB / ID: 5jqf
TitleCrystal structure of the lasso peptide Sphingopyxin I (SpI)
ComponentsSphingopyxin I
KeywordsUNKNOWN FUNCTION / Lasso peptide / isopeptide bond / macrolactam ring
Function / homologySphingopyxin I
Function and homology information
Biological speciesSphingopyxis alaskensis RB2256 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO PHASING / Resolution: 0.85 Å
AuthorsFage, C.D. / Hegemann, J.D. / Harms, K. / Bange, G. / Marahiel, M.A.
Funding support Germany, 2items
OrganizationGrant numberCountry
German Research Foundation Germany
LOEWE-Zentrum fuer Synthetische Mikrobiologie Germany
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2016
Title: Structure and Mechanism of the Sphingopyxin I Lasso Peptide Isopeptidase.
Authors: Fage, C.D. / Hegemann, J.D. / Nebel, A.J. / Steinbach, R.M. / Zhu, S. / Linne, U. / Harms, K. / Bange, G. / Marahiel, M.A.
History
DepositionMay 4, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Apr 18, 2018Group: Data collection / Database references / Category: citation
Item: _citation.journal_abbrev / _citation.journal_volume ..._citation.journal_abbrev / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
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 2.0Jun 16, 2021Group: Advisory / Atomic model / Derived calculations
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_close_contact / struct_conn

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Sphingopyxin I
B: Sphingopyxin I


Theoretical massNumber of molelcules
Total (without water)4,4032
Polymers4,4032
Non-polymers00
Water63135
1
A: Sphingopyxin I


Theoretical massNumber of molelcules
Total (without water)2,2011
Polymers2,2011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Sphingopyxin I


Theoretical massNumber of molelcules
Total (without water)2,2011
Polymers2,2011
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)39.240, 39.240, 31.410
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A1 - 21
2010B1 - 21

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Components

#1: Protein/peptide Sphingopyxin I


Mass: 2201.326 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: An isopeptide bond exists between the N-terminus of Gly1 and side chain of Asp9
Source: (gene. exp.) Sphingopyxis alaskensis RB2256 (bacteria)
Plasmid: pET41a / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A1D5B387*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 35 / 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: 1.59 Å3/Da / Density % sol: 22.43 % / Description: Needle-like
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M K2SO4, 20%(w/v) PEG 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.82656 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Apr 15, 2016
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.82656 Å / Relative weight: 1
ReflectionResolution: 0.85→50 Å / Num. obs: 24225 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 5 % / Biso Wilson estimate: 8.602 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.067 / Net I/σ(I): 12.01
Reflection shell
Resolution (Å)Highest resolution (Å)Rmerge(I) obsMean I/σ(I) obsDiffraction-ID% possible all
0.85-0.90.6892.2199.6
0.9-0.960.3884.05199.9
0.96-1.040.1947.821100
1.04-1.140.11212.08199.9
1.14-1.270.08415.671100
1.27-1.470.07617.311100
1.47-1.80.06221.54199.5
1.8-2.540.05225.35199.5
2.540.05227.04198.5

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
Coot0.8-pre (revision 4727)model building
XDSOct 15, 2015data reduction
XSCALEOct 15, 2015data scaling
Sir2014Sir2014phasing
RefinementMethod to determine structure: AB INITIO PHASING / Resolution: 0.85→33.98 Å / Cor.coef. Fo:Fc: 0.979 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.358 / SU ML: 0.01 / SU R Cruickshank DPI: 0.0154 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.015 / ESU R Free: 0.017
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.153 1212 5 %RANDOM
Rwork0.1292 ---
obs0.1304 23012 99.8 %-
Solvent computationIon probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1.7 Å
Displacement parametersBiso max: 25.23 Å2 / Biso mean: 6.914 Å2 / Biso min: 3.57 Å2
Baniso -1Baniso -2Baniso -3
1-0.13 Å20.07 Å20 Å2
2--0.13 Å2-0 Å2
3----0.42 Å2
Refinement stepCycle: final / Resolution: 0.85→33.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms310 0 0 41 351
Biso mean---12.89 -
Num. residues----42
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.019346
X-RAY DIFFRACTIONr_bond_other_d0.010.02297
X-RAY DIFFRACTIONr_angle_refined_deg1.8132.012469
X-RAY DIFFRACTIONr_angle_other_deg1.7923695
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.74546
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.33925.88217
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.8871543
X-RAY DIFFRACTIONr_chiral_restr0.1060.243
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021418
X-RAY DIFFRACTIONr_gen_planes_other0.0080.0274
X-RAY DIFFRACTIONr_mcbond_it0.6080.551178
X-RAY DIFFRACTIONr_mcbond_other0.5920.541175
X-RAY DIFFRACTIONr_mcangle_it0.7920.833220
X-RAY DIFFRACTIONr_rigid_bond_restr2.7413643
X-RAY DIFFRACTIONr_sphericity_free17.62854
X-RAY DIFFRACTIONr_sphericity_bonded4.1975667
Refine LS restraints NCS

Ens-ID: 1 / Number: 1806 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.21 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 0.85→0.896 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.388 176 -
Rwork0.325 3345 -
all-3521 -
obs--99.83 %

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