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- PDB-8btx: Structure of human Archease -

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Basic information

Entry
Database: PDB / ID: 8btx
TitleStructure of human Archease
ComponentsProtein archease
KeywordsLIGASE / archease / human / tRNA splicing
Function / homologyArchease / Archease domain / Archease domain superfamily / Archease protein family (MTH1598/TM1083) / tRNA-splicing ligase complex / tRNA splicing, via endonucleolytic cleavage and ligation / metal ion binding / Protein archease
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.84 Å
AuthorsKopp, J. / Gerber, J.L. / Peschek, J.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Research Foundation (DFG)442512666 Germany
CitationJournal: Nat Commun / Year: 2024
Title: Structural and mechanistic insights into activation of the human RNA ligase RTCB by Archease.
Authors: Gerber, J.L. / Morales Guzman, S.I. / Worf, L. / Hubbe, P. / Kopp, J. / Peschek, J.
History
DepositionNov 30, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 13, 2023Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2024Group: 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_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein archease


Theoretical massNumber of molelcules
Total (without water)21,1091
Polymers21,1091
Non-polymers00
Water77543
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration, monomeric
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8500 Å2
Unit cell
Length a, b, c (Å)79.981, 79.981, 65.164
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number93
Space group name H-MP4222
Space group name HallP4c2
Symmetry operation#1: x,y,z
#2: -y,x,z+1/2
#3: y,-x,z+1/2
#4: x,-y,-z
#5: -x,y,-z
#6: -x,-y,z
#7: y,x,-z+1/2
#8: -y,-x,-z+1/2

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Components

#1: Protein Protein archease


Mass: 21108.562 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ZBTB8OS / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: A8K0B5
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.47 Å3/Da / Density % sol: 50.17 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop
Details: protein: 1966 uM in 25 mM HEPES pH 7.5, 100mM NaCl, 5 % glycerol, 1mM TCEP reservoir: 0.2 M ammonium chloride, 20% w/v PEG 3350 drop composition: 200 nl reservoir + 200 nl protein

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9737 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Sep 3, 2021 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9737 Å / Relative weight: 1
ReflectionResolution: 1.84→79.98 Å / Num. obs: 18949 / % possible obs: 100 % / Redundancy: 27.5 % / Biso Wilson estimate: 49.91 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.068 / Rpim(I) all: 0.013 / Net I/σ(I): 23.7
Reflection shellResolution: 1.84→1.88 Å / Redundancy: 25.1 % / Num. unique obs: 1137 / CC1/2: 0.471 / Rpim(I) all: 0.743 / % possible all: 100

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Processing

Software
NameVersionClassification
XDS20210205data reduction
Aimless1.12.10data scaling
PHASER2.8.3phasing
PHENIX1.19.2_4158refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5YZ1

5yz1


Resolution: 1.84→39.99 Å / SU ML: 0.2102 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.4189
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2212 942 4.98 %
Rwork0.1937 17983 -
obs0.195 18925 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 58.33 Å2
Refinement stepCycle: LAST / Resolution: 1.84→39.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1300 0 0 43 1343
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00661351
X-RAY DIFFRACTIONf_angle_d0.84071839
X-RAY DIFFRACTIONf_chiral_restr0.0528198
X-RAY DIFFRACTIONf_plane_restr0.0077240
X-RAY DIFFRACTIONf_dihedral_angle_d13.1023498
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.84-1.940.32751440.30832491X-RAY DIFFRACTION99.96
1.94-2.060.36831250.28262522X-RAY DIFFRACTION100
2.06-2.220.26371330.24182539X-RAY DIFFRACTION100
2.22-2.440.2691310.2292524X-RAY DIFFRACTION100
2.44-2.790.30541400.25062564X-RAY DIFFRACTION99.96
2.79-3.520.24891370.21752586X-RAY DIFFRACTION100
3.52-39.990.17431320.15882757X-RAY DIFFRACTION99.9
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)
10.235004010003-0.2040477619270.5829271541661.19007245067-1.0978748371.79378456665-0.1658504652870.574882998285-0.0198342347247-0.417642162050.251232517599-0.0330529885331-1.197843199310.2410787398630.00725050899740.8368741661630.1518511128370.004645292452230.6747868947760.009595857174490.78434170047611.205493282728.457746621929.7069904739
22.63044459577-1.32485187832-0.2758604698213.21185015734-0.3488900830182.010196236740.202684849070.0802943047768-0.1195038305770.0997214916176-0.1223873092670.239890749814-0.162254084467-0.0234448351009-0.0701872929730.468675401473-0.01298819237560.04913421797680.449809785661-0.105170592720.47469048019823.776825393312.294455682937.5015676915
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 22 through 35 )22 - 351 - 14
22chain 'A' and (resid 36 through 179 )36 - 17915 - 158

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