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- PDB-8cpn: Crystal structure of the PolB16_OarG intein variant S1A, N183A -

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Basic information

Entry
Database: PDB / ID: 8cpn
TitleCrystal structure of the PolB16_OarG intein variant S1A, N183A
ComponentsPolB16 intein
KeywordsSPLICING / split intein / ligation / protein engineering
Function / homologyIODIDE ION
Function and homology information
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.85 Å
AuthorsKattelmann, S. / Pasch, T. / Mootz, H.D. / Kummel, D.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)MO1073/7-1 Germany
CitationJournal: Chem Sci / Year: 2023
Title: Structural and biochemical analysis of a novel atypically split intein reveals a conserved histidine specific to cysteine-less inteins.
Authors: Pasch, T. / Schroder, A. / Kattelmann, S. / Eisenstein, M. / Pietrokovski, S. / Kummel, D. / Mootz, H.D.
History
DepositionMar 3, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 17, 2023Provider: repository / Type: Initial release
Revision 1.1May 31, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PolB16 intein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,27415
Polymers23,4981
Non-polymers1,77714
Water82946
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1780 Å2
ΔGint-2 kcal/mol
Surface area9210 Å2
Unit cell
Length a, b, c (Å)69.425, 69.425, 79.162
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein PolB16 intein


Mass: 23497.600 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) metagenome (others) / Production host: Escherichia coli (E. coli)
#2: Chemical
ChemComp-IOD / IODIDE ION


Mass: 126.904 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: I
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.34 Å3/Da / Density % sol: 47.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M Phosphate/citrate pH 4.2 38% EtOH 5% PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 1.5498 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jan 24, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5498 Å / Relative weight: 1
ReflectionResolution: 1.85→50 Å / Num. obs: 36175 / % possible obs: 98.9 % / Redundancy: 9.3 % / CC1/2: 0.999 / Rrim(I) all: 0.054 / Net I/σ(I): 19.31
Reflection shellResolution: 1.85→1.96 Å / Num. unique obs: 5587 / CC1/2: 0.721

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.85→33.06 Å / SU ML: 0.29 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2474 1785 4.94 %
Rwork0.2109 --
obs0.2128 36161 98.92 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.85→33.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1273 0 14 46 1333
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161300
X-RAY DIFFRACTIONf_angle_d1.3441750
X-RAY DIFFRACTIONf_dihedral_angle_d4.0911097
X-RAY DIFFRACTIONf_chiral_restr0.087201
X-RAY DIFFRACTIONf_plane_restr0.007217
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.85-1.89840.4381250.40732368X-RAY DIFFRACTION89
1.8984-1.95430.37041370.33472672X-RAY DIFFRACTION99
1.9543-2.01740.30361360.26732657X-RAY DIFFRACTION100
2.0174-2.08950.321370.2352683X-RAY DIFFRACTION100
2.0895-2.17310.27661360.22392633X-RAY DIFFRACTION99
2.1731-2.2720.25261390.21942675X-RAY DIFFRACTION100
2.272-2.39170.2451420.22322692X-RAY DIFFRACTION100
2.3917-2.54150.26941320.23442636X-RAY DIFFRACTION100
2.5415-2.73770.23071430.23622667X-RAY DIFFRACTION100
2.7377-3.0130.24111410.23562690X-RAY DIFFRACTION100
3.013-3.44860.24531360.21582664X-RAY DIFFRACTION100
3.4486-4.34330.25371430.18242670X-RAY DIFFRACTION100
4.3433-33.060.21671380.18962669X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.8634-0.41020.31195.4154.18783.55990.2328-0.2086-0.0540.6204-0.53420.00230.5017-0.02320.41030.512-0.07060.08020.4427-0.040.385426.1212.72737.593
21.86890.9850.90165.53115.41317.8030.0382-0.1832-0.14721.5507-0.0482-0.39191.37110.00580.0150.7721-0.06230.01240.48980.00960.386429.26710.88441.766
37.8562-6.22643.54815.7195-1.7753.0081.0449-1.3138-0.75572.0652-0.50891.62291.3634-0.41261.04151.6568-0.28860.45630.8835-0.08720.653417.726-1.38945.966
41.41220.60950.56025.74492.33024.82320.1187-0.34030.10361.1014-0.47520.5610.7957-0.68830.24670.4664-0.09420.13020.3929-0.12970.439921.5068.31332.947
54.83191.8837-1.4999.2745-1.22678.23730.3620.25990.6443-0.1536-0.16780.328-0.52610.34070.13640.33650.03450.03220.4219-0.01290.369429.79812.99917.434
67.76451.07362.00044.70083.99779.22160.18570.0635-0.7669-0.4495-0.57390.55590.4826-1.03070.4410.52160.0377-0.02830.5957-0.13270.617318.9178.63918.948
72.8182.61362.39058.61764.97373.3875-0.16280.14840.5094-1.2271-0.2679-0.0619-0.888-0.09270.44840.48390.00610.00180.4246-0.07730.567125.17820.39420.933
81.61741.4691-0.02466.16240.55379.00340.1181-0.2418-0.22150.6998-0.34490.36481.65070.07280.3430.6169-0.0050.07330.373-0.05090.503223.527-0.91228.03
94.2353-0.9298-2.26693.15050.79897.05130.08760.15030.18490.4226-0.42580.95750.0219-1.45520.27560.3384-0.02490.10580.516-0.1850.595117.58412.71929.212
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 10:27 )A10 - 27
2X-RAY DIFFRACTION2( CHAIN A AND RESID 28:46 )A28 - 46
3X-RAY DIFFRACTION3( CHAIN A AND RESID 47:55 )A47 - 55
4X-RAY DIFFRACTION4( CHAIN A AND RESID 56:88 )A56 - 88
5X-RAY DIFFRACTION5( CHAIN A AND RESID 98:112 )A98 - 112
6X-RAY DIFFRACTION6( CHAIN A AND RESID 131:151 )A131 - 151
7X-RAY DIFFRACTION7( CHAIN A AND RESID 152:161 )A152 - 161
8X-RAY DIFFRACTION8( CHAIN A AND RESID 162:180 )A162 - 180
9X-RAY DIFFRACTION9( CHAIN A AND RESID 181:185 )A181 - 185

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