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- PDB-7ews: Crystal structure of arginine kinase (AK3) from the ciliate Param... -

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Basic information

Entry
Database: PDB / ID: 7ews
TitleCrystal structure of arginine kinase (AK3) from the ciliate Paramecium tetraurelia
Componentsarginine kinase
KeywordsTRANSFERASE / arginine kinase / phosphagen kinase
Function / homology
Function and homology information


phosphocreatine biosynthetic process / creatine kinase activity / kinase activity / extracellular space / ATP binding
Similarity search - Function
Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. ...Transferase Creatine Kinase; Chain A, domain 1 / ATP:guanido phosphotransferase, N-terminal domain / ATP:guanido phosphotransferase, N-terminal / ATP:guanido phosphotransferase, N-terminal domain superfamily / ATP:guanido phosphotransferase, N-terminal domain / Phosphagen kinase N-terminal domain profile. / ATP:guanido phosphotransferase / ATP:guanido phosphotransferase, catalytic domain / ATP:guanido phosphotransferase, C-terminal catalytic domain / Phosphagen kinase C-terminal domain profile. / Glutamine synthetase/guanido kinase, catalytic domain / Creatine Kinase; Chain A, domain 2 / Glutamine synthetase/guanido kinase, catalytic domain / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chromosome undetermined scaffold_155, whole genome shotgun sequence
Similarity search - Component
Biological speciesParamecium tetraurelia (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOtsuka, Y. / Yokota, J. / Yano, D. / Uda, K. / Suzuki, T. / Sugiyama, S.
Funding support Japan, 3items
OrganizationGrant numberCountry
Japan Science and TechnologyJPMJTM19DC Japan
Japan Society for the Promotion of Science (JSPS)19K06588 Japan
Other private09-003-005 Japan
CitationJournal: To Be Published
Title: Crystal structure of arginine kinase (AK3) from the ciliate Paramecium tetraurelia
Authors: Otsuka, Y. / Yokota, J. / Yano, D. / Uda, K. / Suzuki, T. / Sugiyama, S.
History
DepositionMay 26, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jun 1, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: arginine kinase
B: arginine kinase


Theoretical massNumber of molelcules
Total (without water)91,0472
Polymers91,0472
Non-polymers00
Water9,296516
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1890 Å2
ΔGint-4 kcal/mol
Surface area32700 Å2
Unit cell
Length a, b, c (Å)70.109, 77.727, 162.197
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein arginine kinase


Mass: 45523.379 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Paramecium tetraurelia (eukaryote) / Production host: Escherichia coli (E. coli) / References: UniProt: A0C7I4
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 516 / 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: 2.59 Å3/Da / Density % sol: 52.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: 0.1M Hepes-NaOH, pH 7.0, 20% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Feb 3, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→44.42 Å / Num. obs: 58371 / % possible obs: 99.7 % / Redundancy: 11.8 % / Rrim(I) all: 0.33 / Net I/σ(I): 9
Reflection shellResolution: 2.03→2.17 Å / Num. unique obs: 20108 / CC1/2: 0.74

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSdata reduction
Aimlessdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7EGZ

7egz
PDB Unreleased entry


Resolution: 2→44.42 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.895 / SU B: 4.816 / SU ML: 0.13 / Cross valid method: THROUGHOUT / ESU R: 0.188 / ESU R Free: 0.165 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.23685 3039 5 %RANDOM
Rwork0.19667 ---
obs0.19874 57655 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.958 Å2
Baniso -1Baniso -2Baniso -3
1-2.71 Å20 Å2-0 Å2
2---1.55 Å20 Å2
3----1.16 Å2
Refinement stepCycle: 1 / Resolution: 2→44.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6012 0 0 516 6528
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0136338
X-RAY DIFFRACTIONr_bond_other_d0.0010.0175887
X-RAY DIFFRACTIONr_angle_refined_deg1.5081.648578
X-RAY DIFFRACTIONr_angle_other_deg1.381.58513729
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1615799
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.3923.314344
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.586151176
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.391537
X-RAY DIFFRACTIONr_chiral_restr0.0780.2819
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027216
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021303
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_it1.1920.9273136
X-RAY DIFFRACTIONr_mcbond_other1.1880.9263135
X-RAY DIFFRACTIONr_mcangle_it1.9571.3793955
X-RAY DIFFRACTIONr_mcangle_other1.9571.383956
X-RAY DIFFRACTIONr_scbond_it1.681.1293202
X-RAY DIFFRACTIONr_scbond_other1.681.1293202
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6711.6174623
X-RAY DIFFRACTIONr_long_range_B_refined4.12611.4897344
X-RAY DIFFRACTIONr_long_range_B_other3.97311.3017228
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.297 229 -
Rwork0.265 4211 -
obs--99.98 %

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