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- PDB-5jrl: Crystal Structure of the Sphingopyxin I Lasso Peptide Isopeptidas... -

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Basic information

Entry
Database: PDB / ID: 5jrl
TitleCrystal Structure of the Sphingopyxin I Lasso Peptide Isopeptidase SpI-IsoP (Native)
ComponentsDipeptidyl aminopeptidases/acylaminoacyl-peptidases-like protein
KeywordsHYDROLASE / Lasso peptide isopeptidase / serine protease / beta-propeller / alpha/beta-hydrolase / catalytic triad / oxyanion hole
Function / homologyPeptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / aminopeptidase activity / serine-type peptidase activity / Alpha/Beta hydrolase fold / proteolysis / Dipeptidyl aminopeptidases/acylaminoacyl-peptidases-like protein
Function and homology information
Biological speciesSphingopyxis alaskensis RB2256 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.2 Å
AuthorsFage, C.D. / Hegemann, J.D. / 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 6, 2016Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: 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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Dipeptidyl aminopeptidases/acylaminoacyl-peptidases-like protein
B: Dipeptidyl aminopeptidases/acylaminoacyl-peptidases-like protein
C: Dipeptidyl aminopeptidases/acylaminoacyl-peptidases-like protein
D: Dipeptidyl aminopeptidases/acylaminoacyl-peptidases-like protein


Theoretical massNumber of molelcules
Total (without water)331,5584
Polymers331,5584
Non-polymers00
Water00
1
A: Dipeptidyl aminopeptidases/acylaminoacyl-peptidases-like protein
C: Dipeptidyl aminopeptidases/acylaminoacyl-peptidases-like protein


Theoretical massNumber of molelcules
Total (without water)165,7792
Polymers165,7792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Dipeptidyl aminopeptidases/acylaminoacyl-peptidases-like protein

D: Dipeptidyl aminopeptidases/acylaminoacyl-peptidases-like protein


Theoretical massNumber of molelcules
Total (without water)165,7792
Polymers165,7792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_648-x+1,y-1/2,-z+31
3
D: Dipeptidyl aminopeptidases/acylaminoacyl-peptidases-like protein

B: Dipeptidyl aminopeptidases/acylaminoacyl-peptidases-like protein


Theoretical massNumber of molelcules
Total (without water)165,7792
Polymers165,7792
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_658-x+1,y+1/2,-z+31
Unit cell
Length a, b, c (Å)108.466, 136.586, 110.777
Angle α, β, γ (deg.)90.000, 97.620, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Dipeptidyl aminopeptidases/acylaminoacyl-peptidases-like protein / SpI-IsoP


Mass: 82889.383 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sphingopyxis alaskensis RB2256 (bacteria)
Gene: Sala_2532 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q1GQ33
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: 2.45 Å3/Da / Density % sol: 49.86 % / Description: Plate-like
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / Details: 0.2 M sodium acetate, 20%(w/v) PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 7, 2015
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 3.2→48.394 Å / Num. obs: 52747 / % possible obs: 99.7 % / Redundancy: 3.5 % / Biso Wilson estimate: 81.83 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.098 / Net I/σ(I): 10.1
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
3.2-3.33.60.654199.9
13.19-48.3943.40.032197.6

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation5.14 Å48.39 Å
Translation5.14 Å48.39 Å

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Processing

Software
NameVersionClassification
Aimless0.5.17data scaling
PHASER2.5.7phasing
PHENIX1.10-2152refinement
PDB_EXTRACT3.2data extraction
XDSOct 15, 2015data reduction
Coot0.8-pre (revision 4727)model building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5JRK

5jrk


Resolution: 3.2→48.394 Å / SU ML: 0.5 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.04
RfactorNum. reflection% reflectionSelection details
Rfree0.2658 2557 4.85 %RANDOM SELECTION
Rwork0.2212 ---
obs0.2234 52720 99.72 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 155.2 Å2 / Biso mean: 79.1881 Å2 / Biso min: 24.18 Å2
Refinement stepCycle: final / Resolution: 3.2→48.394 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms20892 0 0 0 20892
Num. residues----2674
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00221351
X-RAY DIFFRACTIONf_angle_d0.51928994
X-RAY DIFFRACTIONf_chiral_restr0.0423172
X-RAY DIFFRACTIONf_plane_restr0.0043812
X-RAY DIFFRACTIONf_dihedral_angle_d9.52912819
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 18

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
3.2-3.26150.43461450.336227772922100
3.2615-3.32810.34921570.310427302887100
3.3281-3.40050.35221430.309227702913100
3.4005-3.47950.34251540.288727682922100
3.4795-3.56650.31831220.285228102932100
3.5665-3.66290.36221260.271728002926100
3.6629-3.77070.31391230.26827862909100
3.7707-3.89230.32271320.251528002932100
3.8923-4.03140.30271400.226327742914100
4.0314-4.19270.26111750.215127422917100
4.1927-4.38340.25671530.210627762929100
4.3834-4.61430.29921150.202428132928100
4.6143-4.90320.271210.192828112932100
4.9032-5.28130.23181750.189627552930100
5.2813-5.8120.2241680.202927822950100
5.812-6.65120.2261290.198128072936100
6.6512-8.37270.20281220.1942834295699
8.3727-48.40.211570.18292828298599

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