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- PDB-8cpo: Crystal structure of the PolB16_OarG intein variant S1A, N183A, C... -

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Basic information

Entry
Database: PDB / ID: 8cpo
TitleCrystal structure of the PolB16_OarG intein variant S1A, N183A, C111A, C165A
ComponentsPolB16 Intein Cys-less
KeywordsSPLICING / split intein / ligation / protein engineering
Biological speciesmetagenome (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsKattelmann, S. / Pasch, T. / Mootz, H.D. / Kuemmel, 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 Cys-less


Theoretical massNumber of molelcules
Total (without water)23,4331
Polymers23,4331
Non-polymers00
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area9050 Å2
Unit cell
Length a, b, c (Å)68.899, 68.899, 79.093
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 Cys-less


Mass: 23433.471 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: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.31 Å3/Da / Density % sol: 46.81 %
Crystal growTemperature: 298 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: 14.1 / Wavelength: 0.976252 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Mar 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976252 Å / Relative weight: 1
ReflectionResolution: 2.6→50 Å / Num. obs: 7009 / % possible obs: 99.6 % / Redundancy: 19.2 % / CC1/2: 1 / Rrim(I) all: 0.047 / Net I/σ(I): 37.59
Reflection shellResolution: 2.6→2.75 Å / Num. unique obs: 1109 / CC1/2: 0.96 / Rrim(I) all: 0.975

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.6→47.634 Å / SU ML: 0.52 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 39.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2827 351 5.02 %
Rwork0.242 --
obs0.2441 6998 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.6→47.634 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1254 0 0 17 1271
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111273
X-RAY DIFFRACTIONf_angle_d1.6241712
X-RAY DIFFRACTIONf_dihedral_angle_d5.561772
X-RAY DIFFRACTIONf_chiral_restr0.101198
X-RAY DIFFRACTIONf_plane_restr0.01211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.97330.42691140.32982154X-RAY DIFFRACTION99
2.9733-3.74580.32411160.30132197X-RAY DIFFRACTION100
3.7458-47.6340.25541210.21472296X-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)
14.07451.82383.2554.97916.03847.4174-0.3166-0.60180.00231.5566-0.00140.07141.0030.48490.40291.08060.15860.17490.95450.06380.782327.58911.53139.628
26.2248-4.13181.85763.309-0.72131.01171.2522-2.95760.45252.4795-0.68660.82471.4426-0.3586-0.2752.2532-0.04380.7421.60520.02461.396718.813-0.39946.645
34.1868-0.48730.88198.00823.82317.1003-0.1906-0.4684-0.06911.431-0.32981.25111.0331-0.64340.53640.79230.02220.21930.5468-0.0740.770421.248.30733.042
45.56850.2887-0.24544.2963.76375.57960.12990.98960.4746-0.868-0.1726-0.3627-0.51520.1319-0.13370.96110.1258-0.04210.75660.14160.912324.75912.21217.616
51.7347-0.34550.74477.25090.90669.2701-0.1661-0.3487-0.22020.3799-0.22691.08380.5819-0.38460.32790.5331-0.00760.10260.5795-0.02440.797621.5818.32526.929
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 10:45 )A10 - 45
2X-RAY DIFFRACTION2( CHAIN A AND RESID 46:55 )A46 - 55
3X-RAY DIFFRACTION3( CHAIN A AND RESID 56:96 )A56 - 96
4X-RAY DIFFRACTION4( CHAIN A AND RESID 97:151 )A97 - 151
5X-RAY DIFFRACTION5( CHAIN A AND RESID 152:182 )A152 - 182

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