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- PDB-6ky3: Structure of arginine kinase H284A mutant -

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Basic information

Entry
Database: PDB / ID: 6ky3
TitleStructure of arginine kinase H284A mutant
ComponentsArginine kinase
KeywordsTRANSFERASE / Arginine kinase
Function / homology
Function and homology information


arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / phosphorylation / 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 / : / PHOSPHATE ION / arginine kinase
Similarity search - Component
Biological speciesDaphnia magna (crustacean)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å
AuthorsRao, Z. / Park, J.H. / Kim, S.Y. / Kim, D.S.
CitationJournal: Mol.Cells / Year: 2020
Title: Insight into Structural Aspects of Histidine 284 of Daphnia magna Arginine Kinase.
Authors: Rao, Z. / Kim, S.Y. / Li, X. / Kim, D.S. / Kim, Y.J. / Park, J.H.
History
DepositionSep 16, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 16, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 31, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _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
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,0316
Polymers40,5881
Non-polymers4435
Water8,971498
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area180 Å2
ΔGint-6 kcal/mol
Surface area15840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.943, 57.840, 74.860
Angle α, β, γ (deg.)90.00, 100.46, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Arginine kinase /


Mass: 40587.918 Da / Num. of mol.: 1 / Mutation: H284A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Daphnia magna (crustacean) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A0A7CK57
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#4: Chemical ChemComp-ARG / ARGININE / Arginine


Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H15N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 498 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.07 Å3/Da / Density % sol: 40.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 1.8M phosphate buffer

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Jun 26, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.34→46.17 Å / Num. obs: 70591 / % possible obs: 96.6 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.038 / Net I/σ(I): 16.1
Reflection shellResolution: 1.34→1.41 Å / Rmerge(I) obs: 0.37 / Num. unique obs: 9870

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Processing

Software
NameVersionClassification
REFMAC5.8.0073refinement
XDSdata reduction
XDSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4BHL

4bhl


Resolution: 1.34→46.17 Å / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflection
Rfree0.21828 3543 -
Rwork0.17349 --
obs0.17572 67028 96.29 %
Refinement stepCycle: LAST / Resolution: 1.34→46.17 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2788 0 24 498 3310
LS refinement shellResolution: 1.341→1.376 Å
RfactorNum. reflection
Rfree0.365 240
Rwork0.287 -
obs-4626

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