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- PDB-5o9j: Crystal structure of transcription factor IIB Mja mini-intein -

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Basic information

Entry
Database: PDB / ID: 5o9j
TitleCrystal structure of transcription factor IIB Mja mini-intein
ComponentsTranscription initiation factor IIB,Transcription initiation factor IIB
KeywordsHYDROLASE / Transcription factor IIB / mini-intein / HINT fold
Function / homology
Function and homology information


transcription preinitiation complex assembly / intron homing / intein-mediated protein splicing / transcription preinitiation complex / TBP-class protein binding / DNA-templated transcription initiation / endonuclease activity / Hydrolases; Acting on ester bonds / DNA-binding transcription factor activity / zinc ion binding
Similarity search - Function
Transcription initiation factor TFIIB, archaea / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal ...Transcription initiation factor TFIIB, archaea / Endonuclease - Pi-scei; Chain A, domain 1 / Hedgehog/Intein (Hint) domain / Intein splicing domain / Intein / Intein DOD homing endonuclease / Intein DOD-type homing endonuclease domain profile. / Intein C-terminal splicing region / Intein C-terminal splicing motif profile. / Hint domain C-terminal / Hint (Hedgehog/Intein) domain C-terminal region / Intein N-terminal splicing region / Intein N-terminal splicing motif profile. / Transcription factor TFIIB, cyclin-like domain / Transcription factor TFIIB, conserved site / Transcription factor TFIIB repeat / Transcription factor TFIIB repeat signature. / Homing endonuclease / Hint domain N-terminal / Hint (Hedgehog/Intein) domain N-terminal region / Hint domain superfamily / Zinc finger TFIIB-type profile. / Transcription factor TFIIB / Zinc finger, TFIIB-type / TFIIB zinc-binding / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / Beta Complex / Mainly Beta
Similarity search - Domain/homology
1,4-DIETHYLENE DIOXIDE / AMMONIUM ION / Transcription initiation factor IIB
Similarity search - Component
Biological speciesMethanocaldococcus jannaschii (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMikula, K.M. / Iwai, H. / Zhou, D. / Wlodawer, A.
Funding support Finland, United States, 3items
OrganizationGrant numberCountry
Academy of Finland1131413 Finland
Academy of Finland137995 Finland
National Institutes of Health/National Cancer Institute (NIH/NCI)HHSN261200800001E United States
CitationJournal: J. Mol. Biol. / Year: 2017
Title: Structural Basis for the Persistence of Homing Endonucleases in Transcription Factor IIB Inteins.
Authors: Iwai, H. / Mikula, K.M. / Oeemig, J.S. / Zhou, D. / Li, M. / Wlodawer, A.
History
DepositionJun 19, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 1, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 6, 2017Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.2Mar 30, 2022Group: Author supporting evidence / Database references / Category: database_2 / pdbx_audit_support
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_audit_support.funding_organization
Revision 1.3Jan 17, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Transcription initiation factor IIB,Transcription initiation factor IIB
B: Transcription initiation factor IIB,Transcription initiation factor IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,93833
Polymers41,7442
Non-polymers2,19431
Water3,495194
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A: Transcription initiation factor IIB,Transcription initiation factor IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,60914
Polymers20,8721
Non-polymers73713
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription initiation factor IIB,Transcription initiation factor IIB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,32919
Polymers20,8721
Non-polymers1,45718
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)42.360, 50.798, 60.118
Angle α, β, γ (deg.)77.42, 75.83, 76.93
Int Tables number1
Space group name H-MP1

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Transcription initiation factor IIB,Transcription initiation factor IIB / TFIIB


Mass: 20872.121 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus jannaschii (archaea)
Strain: ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440
Gene: tfb, MJ0782 / Production host: Escherichia coli (E. coli)
References: UniProt: Q58192, Hydrolases; Acting on ester bonds

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Non-polymers , 5 types, 225 molecules

#2: Chemical
ChemComp-DIO / 1,4-DIETHYLENE DIOXIDE


Mass: 88.105 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C4H8O2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: H4N
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 194 / 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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: MES, dioxane, ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 1, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2→28.7 Å / Num. obs: 30100 / % possible obs: 95.9 % / Redundancy: 2.4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.6
Reflection shellHighest resolution: 2.07 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.724 / Mean I/σ(I) obs: 1.6 / % possible all: 92.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XDSdata scaling
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CW8

2cw8


Resolution: 2→28.7 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 33.92
RfactorNum. reflection% reflection
Rfree0.2612 945 3.14 %
Rwork0.2137 --
obs0.2153 30100 95.9 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→28.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2920 0 142 194 3256
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0073085
X-RAY DIFFRACTIONf_angle_d1.0134124
X-RAY DIFFRACTIONf_dihedral_angle_d13.7791191
X-RAY DIFFRACTIONf_chiral_restr0.039463
X-RAY DIFFRACTIONf_plane_restr0.005514
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.10550.40591100.34193961X-RAY DIFFRACTION91
2.1055-2.23730.34281330.3024139X-RAY DIFFRACTION95
2.2373-2.410.32671230.25944149X-RAY DIFFRACTION95
2.41-2.65240.29561470.24624173X-RAY DIFFRACTION96
2.6524-3.03580.26251420.21734218X-RAY DIFFRACTION97
3.0358-3.82340.27191290.18934258X-RAY DIFFRACTION98
3.8234-28.71290.21521610.17914228X-RAY DIFFRACTION98

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