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- PDB-5o9i: Crystal structure of transcription factor IIB Mvu mini-intein -

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Basic information

Entry
Database: PDB / ID: 5o9i
TitleCrystal structure of transcription factor IIB Mvu mini-intein
ComponentsTranscription initiation factor IIB,Transcription initiation factor IIB
KeywordsTRANSCRIPTION / Transcription factor IIB / Mini-intein / HINT fold
Function / homology
Function and homology information


transcription preinitiation complex assembly / intein-mediated protein splicing / TBP-class protein binding / endonuclease activity / 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. / 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
Transcription initiation factor IIB
Similarity search - Component
Biological speciesMethanocaldococcus vulcanius (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMikula, K.M. / Iwai, H. / Li, M. / 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 1.3Jun 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: Transcription initiation factor IIB,Transcription initiation factor IIB
B: Transcription initiation factor IIB,Transcription initiation factor IIB


Theoretical massNumber of molelcules
Total (without water)44,1292
Polymers44,1292
Non-polymers00
Water28816
1
A: Transcription initiation factor IIB,Transcription initiation factor IIB


Theoretical massNumber of molelcules
Total (without water)22,0641
Polymers22,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Transcription initiation factor IIB,Transcription initiation factor IIB


Theoretical massNumber of molelcules
Total (without water)22,0641
Polymers22,0641
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)108.183, 67.245, 51.226
Angle α, β, γ (deg.)90.00, 102.43, 90.00
Int Tables number5
Space group name H-MC121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1010A5 - 194
2010B5 - 194

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Components

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


Mass: 22064.412 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Methanocaldococcus vulcanius (archaea) / Strain: ATCC 700851 / DSM 12094 / M7 / Gene: tfb, Metvu_0030 / Production host: Escherichia coli (E. coli) / References: UniProt: C9REA0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 16 / 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: 2.06 Å3/Da / Density % sol: 40.34 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: calcium chloride, PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-3 / Wavelength: 0.9677 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 14, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9677 Å / Relative weight: 1
ReflectionResolution: 2.5→56.7 Å / Num. obs: 12418 / % possible obs: 99.5 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.083 / Net I/σ(I): 13.3
Reflection shellResolution: 2.5→2.67 Å / Redundancy: 7.8 % / Rmerge(I) obs: 1.011 / Mean I/σ(I) obs: 1.9 / % possible all: 96.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
XDSdata reduction
XDSdata scaling
PHENIXphasing
MR-Rosettaphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→56.7 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.921 / SU B: 36.297 / SU ML: 0.363 / Cross valid method: THROUGHOUT / ESU R: 1.09 / ESU R Free: 0.344 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27847 580 4.7 %RANDOM
Rwork0.22162 ---
obs0.22444 11837 99.49 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 81.158 Å2
Baniso -1Baniso -2Baniso -3
1--1.82 Å2-0 Å2-0.47 Å2
2--2.03 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 2.5→56.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2757 0 0 16 2773
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0192801
X-RAY DIFFRACTIONr_bond_other_d0.0020.022765
X-RAY DIFFRACTIONr_angle_refined_deg1.9571.9733773
X-RAY DIFFRACTIONr_angle_other_deg1.10136422
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.6135343
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35225.242124
X-RAY DIFFRACTIONr_dihedral_angle_3_deg22.08915536
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2841512
X-RAY DIFFRACTIONr_chiral_restr0.1240.2439
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0213030
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02526
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_it2.9224.4471384
X-RAY DIFFRACTIONr_mcbond_other2.9224.4471383
X-RAY DIFFRACTIONr_mcangle_it4.756.6631723
X-RAY DIFFRACTIONr_mcangle_other4.7496.6631724
X-RAY DIFFRACTIONr_scbond_it2.9964.8351416
X-RAY DIFFRACTIONr_scbond_other2.9934.8351414
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.0337.0812050
X-RAY DIFFRACTIONr_long_range_B_refined8.83552.9533028
X-RAY DIFFRACTIONr_long_range_B_other8.81952.9333027
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9930 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.505→2.57 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.362 35 -
Rwork0.338 837 -
obs--93.76 %
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)
15.7377-1.4067-0.61081.0086-0.85771.59610.34621.9584-0.30690.3465-0.6008-0.0521-0.6814-0.00070.25460.3140.0594-0.04270.7440.01860.234828.31921.58553.632
25.8988-0.41540.41890.37410.40280.58750.15720.3163-0.04930.0296-0.0988-0.0190.0353-0.0422-0.05840.16240.00810.02670.1165-0.01840.323614.53527.51421.657
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 194
2X-RAY DIFFRACTION2B4 - 194

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