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- PDB-8yv5: The crystal structure of G. acetivorans RNA kinase Ark1 in comple... -

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Basic information

Entry
Database: PDB / ID: 8yv5
TitleThe crystal structure of G. acetivorans RNA kinase Ark1 in complex with ATP
ComponentsPutative serine/threonine protein kinase
KeywordsTRANSFERASE / Kinase
Function / homologyprotein serine/threonine kinase activity / Protein kinase-like domain superfamily / ADENOSINE-5'-TRIPHOSPHATE / Putative serine/threonine protein kinase
Function and homology information
Biological speciesGeoglobus acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsCao, C.L. / Gan, J.H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC) China
CitationJournal: To Be Published
Title: The crystal structure of G.acetivorans RNA kinase Ark1
Authors: Cao, C.L. / Gan, J.H.
History
DepositionMar 28, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Apr 2, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Putative serine/threonine protein kinase
A: Putative serine/threonine protein kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,4017
Polymers42,1672
Non-polymers1,2345
Water3,153175
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4050 Å2
ΔGint-25 kcal/mol
Surface area15860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.920, 146.920, 146.920
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213

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Components

#1: Protein Putative serine/threonine protein kinase / Archaeal RNA kinase


Mass: 21083.469 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Geoglobus acetivorans (archaea) / Gene: GACE_0057 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0A7GDU7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 3.13 Å3/Da / Density % sol: 60.75 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 0.1M Sodium acetate trihydrate pH4.6 2.0M Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: Y
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Sep 24, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.98→73.46 Å / Num. obs: 36696 / % possible obs: 100 % / Redundancy: 35 % / CC1/2: 0.999 / Net I/σ(I): 19.7
Reflection shellResolution: 1.98→2.03 Å / Num. unique obs: 36696 / CC1/2: 0.82
Serial crystallography sample deliveryMethod: injection

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Processing

Software
NameVersionClassification
PHENIX(1.19.1_4122: ???)refinement
REFMAC5.8.0123refinement
HKL-30007.21data reduction
HKL-30007.21data scaling
PHASER2.7.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→51.94 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 24.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2163 1800 4.91 %
Rwork0.1782 --
obs0.1801 36696 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.98→51.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2841 0 75 175 3091
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122973
X-RAY DIFFRACTIONf_angle_d1.2664013
X-RAY DIFFRACTIONf_dihedral_angle_d16.7831122
X-RAY DIFFRACTIONf_chiral_restr0.077431
X-RAY DIFFRACTIONf_plane_restr0.025507
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.030.26141280.22592655X-RAY DIFFRACTION100
2.03-2.090.22451260.20422674X-RAY DIFFRACTION100
2.09-2.160.2821400.19122686X-RAY DIFFRACTION100
2.16-2.240.25341100.18192692X-RAY DIFFRACTION100
2.24-2.330.22321500.18182639X-RAY DIFFRACTION100
2.33-2.430.23421480.19092660X-RAY DIFFRACTION100
2.44-2.560.22261430.18612656X-RAY DIFFRACTION100
2.56-2.720.23931440.20222661X-RAY DIFFRACTION100
2.72-2.930.24021240.20922718X-RAY DIFFRACTION100
2.93-3.230.2241480.19752647X-RAY DIFFRACTION100
3.23-3.690.21211450.18522710X-RAY DIFFRACTION100
3.7-4.660.18931460.1452715X-RAY DIFFRACTION100
4.66-51.940.20041480.16332783X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 16.9122 Å / Origin y: -38.888 Å / Origin z: 14.9176 Å
111213212223313233
T0.3065 Å20.0938 Å2-0.0238 Å2-0.3722 Å20.0109 Å2--0.2315 Å2
L1.2931 °2-1.0053 °20.264 °2-2.3207 °2-0.1544 °2--0.2633 °2
S-0.2777 Å °-0.3139 Å °0.0833 Å °0.5365 Å °0.2618 Å °-0.0134 Å °-0.0714 Å °0.0248 Å °0.0334 Å °
Refinement TLS groupSelection details: all

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