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- PDB-8yx0: Crystal structure of Procambarus clarkii Arginine kinase -

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Basic information

Entry
Database: PDB / ID: 8yx0
TitleCrystal structure of Procambarus clarkii Arginine kinase
ComponentsArginine kinase Pro c 2.0101
KeywordsALLERGEN / arginine kinase
Function / homology
Function and homology information


arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / arginine binding / extracellular space / ATP binding
Similarity search - Function
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 active site / Phosphagen kinase active site signature. / 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
Similarity search - Domain/homology
Arginine kinase Pro c 2.0101
Similarity search - Component
Biological speciesProcambarus clarkii (red swamp crayfish)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.566 Å
AuthorsYang, Y. / Jin, T.C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31901811 China
CitationJournal: To Be Published
Title: Crystal structure of Procambarus clarkii Arginine kinase
Authors: Yang, Y. / Jin, T.C.
History
DepositionApr 1, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Arginine kinase Pro c 2.0101
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,0422
Polymers40,0191
Non-polymers231
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area110 Å2
ΔGint-7 kcal/mol
Surface area15040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.740, 59.900, 140.120
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 Pro c 2.0101 / AK


Mass: 40018.531 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Procambarus clarkii (red swamp crayfish) / References: UniProt: H6VGI2, arginine kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 298.15 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 0.1 M NaCl, 10% Glycerol, 25% PEG-4000, 0.1 M Cacodylate

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Data collection

DiffractionMean temperature: 190 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.56→45.53 Å / Num. obs: 52746 / % possible obs: 99.5 % / Redundancy: 5 % / CC1/2: 0.97 / Net I/σ(I): 1.38
Reflection shellResolution: 1.56→1.6 Å / Num. unique obs: 52481 / CC1/2: 0.682

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829)refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.566→45.528 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2166 2557 4.88 %
Rwork0.1831 --
obs0.1847 52441 99.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.566→45.528 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2756 0 1 191 2948
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0142831
X-RAY DIFFRACTIONf_angle_d1.3233814
X-RAY DIFFRACTIONf_dihedral_angle_d4.5572393
X-RAY DIFFRACTIONf_chiral_restr0.074416
X-RAY DIFFRACTIONf_plane_restr0.009495
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.566-1.59610.431190.36852657X-RAY DIFFRACTION97
1.57-1.60.18661370.15943006X-RAY DIFFRACTION99
1.5961-1.62870.30661280.30422745X-RAY DIFFRACTION99
1.6287-1.66410.31121580.26142700X-RAY DIFFRACTION99
1.6641-1.70290.29731340.22982738X-RAY DIFFRACTION99
1.7029-1.74540.25281410.21862741X-RAY DIFFRACTION99
1.7454-1.79260.20261370.21232724X-RAY DIFFRACTION99
1.7926-1.84540.25681360.22542735X-RAY DIFFRACTION99
1.8454-1.9050.27921340.20532783X-RAY DIFFRACTION99
1.905-1.9730.22781630.19492696X-RAY DIFFRACTION100
1.973-2.0520.24111630.18662742X-RAY DIFFRACTION100
2.052-2.14540.20741490.19022769X-RAY DIFFRACTION100
2.1454-2.25850.22531520.17982762X-RAY DIFFRACTION100
2.2585-2.40.21531420.18582803X-RAY DIFFRACTION100
2.4-2.58530.18531300.1862797X-RAY DIFFRACTION100
2.5853-2.84550.23541500.19652794X-RAY DIFFRACTION100
2.8455-3.25710.20821440.192824X-RAY DIFFRACTION100
3.2571-4.10320.21181400.16222868X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: 19.0822 Å / Origin y: -4.717 Å / Origin z: -17.1469 Å
111213212223313233
T0.1785 Å2-0.013 Å2-0.0141 Å2-0.2165 Å2-0.001 Å2--0.2117 Å2
L0.5788 °2-0.2756 °20.0117 °2-0.9732 °20.0281 °2--2.0324 °2
S0.0448 Å °0.0851 Å °0.0249 Å °-0.0611 Å °-0.0443 Å °0.0666 Å °-0.2377 Å °-0.1095 Å °-0.0132 Å °
Refinement TLS groupSelection details: all

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