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- PDB-5txe: AtxE2 Isopeptidase - S527A Variant with Astexin3-dC4 Bound -

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Basic information

Entry
Database: PDB / ID: 5txe
TitleAtxE2 Isopeptidase - S527A Variant with Astexin3-dC4 Bound
Components
  • Astexin3-dC4
  • AtxE2
KeywordsHYDROLASE / Isopeptidase / Lasso peptide / Natural Product
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / defense response to bacterium / serine-type endopeptidase activity / proteolysis / extracellular region / cytoplasm
Similarity search - Function
: / Peptidase S9, prolyl oligopeptidase, catalytic domain / Prolyl oligopeptidase family / Six-bladed beta-propeller, TolB-like / Alpha/Beta hydrolase fold
Similarity search - Domain/homology
Lasso peptide isopeptidase AtxE2 / Astexin-3
Similarity search - Component
Biological speciesAsticcacaulis excentricus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsChekan, J.R. / Nair, S.K.
CitationJournal: J. Am. Chem. Soc. / Year: 2016
Title: Structure of the Lasso Peptide Isopeptidase Identifies a Topology for Processing Threaded Substrates.
Authors: Chekan, J.R. / Koos, J.D. / Zong, C. / Maksimov, M.O. / Link, A.J. / Nair, S.K.
History
DepositionNov 16, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 21, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 4, 2017Group: Database references
Revision 1.2Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AtxE2
C: Astexin3-dC4
B: AtxE2
D: Astexin3-dC4


Theoretical massNumber of molelcules
Total (without water)162,4534
Polymers162,4534
Non-polymers00
Water16,394910
1
A: AtxE2
C: Astexin3-dC4


Theoretical massNumber of molelcules
Total (without water)81,2272
Polymers81,2272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2000 Å2
ΔGint-17 kcal/mol
Surface area27290 Å2
MethodPISA
2
B: AtxE2
D: Astexin3-dC4


Theoretical massNumber of molelcules
Total (without water)81,2272
Polymers81,2272
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2070 Å2
ΔGint-17 kcal/mol
Surface area27410 Å2
MethodPISA
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7200 Å2
ΔGint-52 kcal/mol
Surface area51570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)151.253, 202.854, 110.399
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: ALA / Beg label comp-ID: ALA / End auth comp-ID: HOH / End label comp-ID: HOH / Refine code: _ / Auth seq-ID: 35 - 1016 / Label seq-ID: 35

Dom-IDAuth asym-IDLabel asym-ID
1AA - E
2BC - G

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Components

#1: Protein AtxE2


Mass: 78683.836 Da / Num. of mol.: 2 / Mutation: S527A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asticcacaulis excentricus (strain ATCC 15261 / DSM 4724 / VKM B-1370 / CB 48) (bacteria)
Strain: ATCC 15261 / DSM 4724 / VKM B-1370 / CB 48 / Gene: Astex_2444 / Production host: Escherichia coli (E. coli) / References: UniProt: E8RUP5
#2: Protein/peptide Astexin3-dC4


Mass: 2542.755 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Asticcacaulis excentricus (strain ATCC 15261 / DSM 4724 / VKM B-1370 / CB 48) (bacteria)
Strain: ATCC 15261 / DSM 4724 / VKM B-1370 / CB 48 / Gene: Astex_2447 / Production host: Escherichia coli (E. coli) / References: UniProt: E8RUP8
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 910 / 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: 2.61 Å3/Da / Density % sol: 52.81 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / Details: 18% PEG3350, 0.3 M ammonium citrate dibasic

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.97853 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 17, 2016
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 2.2→29.817 Å / Num. obs: 86021 / % possible obs: 99.9 % / Redundancy: 8.4 % / Rmerge(I) obs: 0.107 / Net I/σ(I): 16.2
Reflection shellResolution: 2.2→2.207 Å / Redundancy: 8.4 % / Rmerge(I) obs: 0.737 / Mean I/σ(I) obs: 2.8 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→29.817 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.946 / SU B: 4.647 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.196 / ESU R Free: 0.166 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19759 4255 4.9 %RANDOM
Rwork0.15445 ---
obs0.15655 81764 99.84 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.766 Å2
Baniso -1Baniso -2Baniso -3
1-1.03 Å2-0 Å20 Å2
2---0.9 Å2-0 Å2
3----0.13 Å2
Refinement stepCycle: LAST / Resolution: 2.2→29.817 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10555 0 0 910 11465
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.01910868
X-RAY DIFFRACTIONr_bond_other_d0.0060.0210188
X-RAY DIFFRACTIONr_angle_refined_deg1.7481.95414838
X-RAY DIFFRACTIONr_angle_other_deg1.191323343
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.83451349
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.90522.605522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.201151703
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.76415124
X-RAY DIFFRACTIONr_chiral_restr0.1070.21621
X-RAY DIFFRACTIONr_gen_planes_refined0.010.02112458
X-RAY DIFFRACTIONr_gen_planes_other0.0050.022608
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.9863.1565372
X-RAY DIFFRACTIONr_mcbond_other2.9853.1555371
X-RAY DIFFRACTIONr_mcangle_it4.2874.7196714
X-RAY DIFFRACTIONr_mcangle_other4.2874.726715
X-RAY DIFFRACTIONr_scbond_it4.1393.6745495
X-RAY DIFFRACTIONr_scbond_other4.1393.6745496
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.3455.3088120
X-RAY DIFFRACTIONr_long_range_B_refined8.27426.34112942
X-RAY DIFFRACTIONr_long_range_B_other8.21926.02912520
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 40295 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.25 331 -
Rwork0.21 5980 -
obs--99.7 %

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