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- PDB-8yv4: The crystal structure of G.acetivorans RNA kinase Ark1 -

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Basic information

Entry
Database: PDB / ID: 8yv4
TitleThe crystal structure of G.acetivorans RNA kinase Ark1
ComponentsPutative serine/threonine protein kinase
KeywordsTRANSFERASE / Kinase
Function / homologyprotein serine/threonine kinase activity / Protein kinase-like domain superfamily / Putative serine/threonine protein kinase
Function and homology information
Biological speciesGeoglobus acetivorans (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.87 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 27, 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

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)42,0013
Polymers41,9092
Non-polymers921
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-18 kcal/mol
Surface area16150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.870, 63.297, 70.220
Angle α, β, γ (deg.)90.00, 109.46, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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


Mass: 20954.289 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.: 1 / Source method: obtained synthetically / Formula: C3H8O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 2.68 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 0.1M tri-Sodium citrate pH5.5 20%(w/v) PEG 3000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.987 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: 0.987 Å / Relative weight: 1
ReflectionResolution: 1.87→50.79 Å / Num. obs: 35482 / % possible obs: 96.2 % / Redundancy: 5.7 % / CC1/2: 0.992 / Net I/σ(I): 11.7
Reflection shellResolution: 1.87→1.97 Å / Num. unique obs: 35482 / CC1/2: 0.539

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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: 1.87→26.86 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 25.18 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2204 1752 4.94 %
Rwork0.1914 --
obs0.1929 35482 95.38 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.87→26.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2835 0 0 77 2912
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0092904
X-RAY DIFFRACTIONf_angle_d1.023908
X-RAY DIFFRACTIONf_dihedral_angle_d16.3481117
X-RAY DIFFRACTIONf_chiral_restr0.066423
X-RAY DIFFRACTIONf_plane_restr0.019504
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.87-1.920.4123650.32991726X-RAY DIFFRACTION63
1.92-1.970.3638990.26592259X-RAY DIFFRACTION83
1.97-2.040.29171330.22322585X-RAY DIFFRACTION96
2.04-2.110.22881510.2142676X-RAY DIFFRACTION100
2.11-2.190.19761220.19522732X-RAY DIFFRACTION100
2.19-2.290.23041340.20012692X-RAY DIFFRACTION100
2.29-2.410.27091550.21292695X-RAY DIFFRACTION100
2.41-2.560.24591480.21352696X-RAY DIFFRACTION100
2.56-2.760.26931440.21282735X-RAY DIFFRACTION100
2.76-3.040.23081420.22112710X-RAY DIFFRACTION100
3.04-3.480.23731710.19912703X-RAY DIFFRACTION100
3.48-4.380.1751350.16252749X-RAY DIFFRACTION100
4.38-26.860.1891530.16252772X-RAY DIFFRACTION99
Refinement TLS params.Method: refined / Origin x: 0.4417 Å / Origin y: 6.8477 Å / Origin z: 25.3529 Å
111213212223313233
T0.2352 Å20.0634 Å2-0.0212 Å2-0.2398 Å2-0.0231 Å2--0.2514 Å2
L2.5108 °20.3479 °2-0.0448 °2-1.3815 °2-0.0004 °2--2.5698 °2
S-0.0361 Å °0.2331 Å °0.0352 Å °-0.0903 Å °0.0482 Å °0.0957 Å °-0.2069 Å °-0.5224 Å °-0.0143 Å °
Refinement TLS groupSelection details: all

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