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- PDB-6qp0: Crystal structure of Chaetomium thermophilum Kti12 in complex wit... -

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Basic information

Entry
Database: PDB / ID: 6qp0
TitleCrystal structure of Chaetomium thermophilum Kti12 in complex with ADP-AlF3
ComponentsPutative chromatin binding protein
KeywordsRNA BINDING PROTEIN / Elongator / tRNA / tRNA modification / mcm5 / cm5 / ncm5. Elongator regulatory protein / Elongator regulation. #Elongator
Function / homologyProtein KTI12/L-seryl-tRNA(Sec) kinase / Chromatin associated protein KTI12 / P-loop containing nucleoside triphosphate hydrolase / ATP binding / ADENOSINE-5'-DIPHOSPHATE / ALUMINUM FLUORIDE / Putative chromatin binding protein
Function and homology information
Biological speciesChaetomium thermophilum (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.409 Å
AuthorsKrutyholowa, R. / Glatt, S.
Funding support Poland, 1items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2015/19/B/NZ1/00343 Poland
CitationJournal: Nucleic Acids Res. / Year: 2019
Title: Kti12, a PSTK-like tRNA dependent ATPase essential for tRNA modification by Elongator.
Authors: Krutyholowa, R. / Hammermeister, A. / Zabel, R. / Abdel-Fattah, W. / Reinhardt-Tews, A. / Helm, M. / Stark, M.J.R. / Breunig, K.D. / Schaffrath, R. / Glatt, S.
History
DepositionFeb 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2019Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2019Group: Data collection / Refinement description / Category: pdbx_refine_tls / pdbx_refine_tls_group
Item: _pdbx_refine_tls.pdbx_refine_id / _pdbx_refine_tls_group.pdbx_refine_id
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.3May 22, 2019Group: Data collection / Database references
Category: citation / database_PDB_rev ...citation / database_PDB_rev / database_PDB_rev_record / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative chromatin binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,8045
Polymers30,0741
Non-polymers7314
Water82946
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, monomer, light scattering, monomer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1250 Å2
ΔGint-13 kcal/mol
Surface area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.020, 71.020, 88.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Putative chromatin binding protein / G0SHI1


Mass: 30073.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Chaetomium thermophilum (fungus) / Gene: CTHT_0070100 / Production host: Escherichia coli (E. coli) / References: UniProt: G0SHI1

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Non-polymers , 5 types, 50 molecules

#2: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-AF3 / ALUMINUM FLUORIDE / Aluminium fluoride


Mass: 83.977 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: AlF3 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID / MES (buffer)


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


Mass: 18.015 Da / Num. of mol.: 46 / 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: 2.14 Å3/Da / Density % sol: 42.63 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, sitting drop
Details: 3 mM ADP, 6 mM AlCl3 and 60 mM NaF; Protein concentration = 45 mg/ml; 3 days; Mother liquor contained 100 mM MMT buffer (DL-malic acid, MES monohydrate, TRIS at pH 5.5) and 25% w/v PEG1500.

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.982 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 6, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.982 Å / Relative weight: 1
ReflectionResolution: 2.4→50 Å / Num. obs: 10334 / % possible obs: 99.5 % / Redundancy: 7.9 % / Rsym value: 0.15 / Net I/σ(I): 12.3
Reflection shellResolution: 2.4→2.48 Å / Redundancy: 4.8 % / Mean I/σ(I) obs: 1.98 / Num. unique obs: 723 / % possible all: 95

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
SHELXSphasing
RESOLVEphasing
RefinementResolution: 2.409→35.51 Å / SU ML: 0.37 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 30.06
RfactorNum. reflection% reflection
Rfree0.2747 514 4.99 %
Rwork0.2386 --
obs0.2404 10300 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.409→35.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1526 0 44 46 1616
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0021600
X-RAY DIFFRACTIONf_angle_d0.6192169
X-RAY DIFFRACTIONf_dihedral_angle_d15.699962
X-RAY DIFFRACTIONf_chiral_restr0.038230
X-RAY DIFFRACTIONf_plane_restr0.003273
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4094-2.65180.34861240.32632368X-RAY DIFFRACTION98
2.6518-3.03540.36481280.2962413X-RAY DIFFRACTION99
3.0354-3.82350.24751270.22632446X-RAY DIFFRACTION100
3.8235-35.51380.23711350.20262559X-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)
11.0177-1.07010.7363.7126-1.24152.2997-0.0534-0.6266-0.10910.12170.30480.504-0.0568-0.8079-0.18810.4769-0.08970.01770.5871-0.01430.1971-3.481234.885843.5481
22.4930.4632-0.01861.0999-0.60921.5763-0.0247-0.8069-0.01110.09150.0720.20220.329-0.9696-0.64410.5097-0.40970.06891.1332-0.00950.3295-16.331735.85443.6164
31.47660.18250.55420.62010.41284.07420.0956-0.11810.1454-0.0938-0.03860.00090.0253-0.0753-0.08760.4238-0.04860.03560.4821-0.00350.1838-1.529239.245835.0942
44.1977-1.0963-0.85340.28880.25629.4573-0.0913-0.5276-0.9905-0.0028-0.0985-0.24531.443-0.78010.28221.0815-0.0902-0.16870.6420.19380.4395-0.50917.484447.0043
51.71760.42840.69741.69122.0935.94530.164-0.0668-0.29880.4524-0.0344-0.19380.97410.4257-0.16660.54810.0439-0.00740.48430.07240.25293.250829.749342.8473
61.6870.999-0.61133.8564-1.27335.44570.0946-0.4491-0.4473-0.0219-0.15710.18131.451-1.039-0.00810.8195-0.2228-0.05070.87310.06310.2515-7.803333.110853.9797
71.98222.507-2.64963.8901-4.90636.95220.1015-0.75330.15140.86650.48860.7303-1.052-1.276-0.55450.5069-0.03190.07231.3436-0.08980.2971-14.790242.073751.3289
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 2 through 13 )
2X-RAY DIFFRACTION2chain 'A' and (resid 14 through 30 )
3X-RAY DIFFRACTION3chain 'A' and (resid 31 through 160 )
4X-RAY DIFFRACTION4chain 'A' and (resid 161 through 173 )
5X-RAY DIFFRACTION5chain 'A' and (resid 174 through 226 )
6X-RAY DIFFRACTION6chain 'A' and (resid 227 through 235 )
7X-RAY DIFFRACTION7chain 'A' and (resid 236 through 252 )

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