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- PDB-5txc: AtxE2 Isopeptidase - APO -

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Basic information

Entry
Database: PDB / ID: 5txc
TitleAtxE2 Isopeptidase - APO
ComponentsAtxE2
KeywordsHYDROLASE / Lasso Peptide / Isopeptidase
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases) / serine-type endopeptidase activity / proteolysis / 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
Similarity search - Component
Biological speciesAsticcacaulis excentricus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.401 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 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: AtxE2
B: AtxE2


Theoretical massNumber of molelcules
Total (without water)157,4002
Polymers157,4002
Non-polymers00
Water10,178565
1
A: AtxE2


Theoretical massNumber of molelcules
Total (without water)78,7001
Polymers78,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: AtxE2


Theoretical massNumber of molelcules
Total (without water)78,7001
Polymers78,7001
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3100 Å2
ΔGint-17 kcal/mol
Surface area51950 Å2
MethodPISA
Unit cell
Length a, b, c (Å)150.492, 201.742, 109.131
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number21
Space group name H-MC222
Components on special symmetry positions
IDModelComponents
11A-927-

HOH

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Components

#1: Protein AtxE2


Mass: 78699.836 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_2444 / Production host: Escherichia coli (E. coli)
References: UniProt: E8RUP5, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 2.63 Å3/Da / Density % sol: 53.25 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 21% PEG3350, 0.4 M sodium chloride, 0.1 M Bis-Tris, pH 5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 23, 2014
RadiationMonochromator: diamond(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 64978 / % possible obs: 98.6 % / Redundancy: 4.6 % / Rsym value: 0.138 / Net I/σ(I): 16
Reflection shellResolution: 2.4→2.44 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.749 / Mean I/σ(I) obs: 4.3 / % possible all: 83.8

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.401→49.716 Å / SU ML: 0.33 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.55
RfactorNum. reflection% reflection
Rfree0.2364 3164 5.07 %
Rwork0.1943 --
obs0.1965 62464 96.1 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.401→49.716 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10316 0 0 565 10881
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00810576
X-RAY DIFFRACTIONf_angle_d1.07614426
X-RAY DIFFRACTIONf_dihedral_angle_d12.626376
X-RAY DIFFRACTIONf_chiral_restr0.0631578
X-RAY DIFFRACTIONf_plane_restr0.0071906
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4014-2.43730.3694760.29671681X-RAY DIFFRACTION63
2.4373-2.47540.30281120.27662111X-RAY DIFFRACTION79
2.4754-2.5160.29951250.25682266X-RAY DIFFRACTION86
2.516-2.55930.33751290.2512430X-RAY DIFFRACTION92
2.5593-2.60590.28041530.2482562X-RAY DIFFRACTION97
2.6059-2.6560.32551430.24152630X-RAY DIFFRACTION99
2.656-2.71020.29471390.24062628X-RAY DIFFRACTION100
2.7102-2.76910.28291340.23472664X-RAY DIFFRACTION100
2.7691-2.83350.29921250.23412678X-RAY DIFFRACTION100
2.8335-2.90440.27711590.2372639X-RAY DIFFRACTION100
2.9044-2.98290.2821280.23492680X-RAY DIFFRACTION100
2.9829-3.07070.28471470.232682X-RAY DIFFRACTION100
3.0707-3.16980.26241160.22792662X-RAY DIFFRACTION100
3.1698-3.2830.26121370.2212676X-RAY DIFFRACTION100
3.283-3.41450.24311450.21392702X-RAY DIFFRACTION100
3.4145-3.56980.23331440.19722657X-RAY DIFFRACTION100
3.5698-3.7580.24681550.19392687X-RAY DIFFRACTION100
3.758-3.99330.22021630.18232647X-RAY DIFFRACTION100
3.9933-4.30150.21161440.16272707X-RAY DIFFRACTION100
4.3015-4.73410.1851590.14332699X-RAY DIFFRACTION100
4.7341-5.41840.18461420.14642704X-RAY DIFFRACTION100
5.4184-6.82380.20451510.16922713X-RAY DIFFRACTION99
6.8238-49.72630.18021380.15172795X-RAY DIFFRACTION97

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