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- PDB-9fig: Crystal structure of the arginine kinase Sar s 20 -

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Basic information

Entry
Database: PDB / ID: 9fig
TitleCrystal structure of the arginine kinase Sar s 20
Componentsarginine kinase
KeywordsALLERGEN / Itch mite / IgE binding / Arginine kinase / cross-reactivity
Function / homology
Function and homology information


arginine kinase / arginine kinase activity / phosphocreatine biosynthetic process / creatine kinase activity / 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
Biological speciesSarcoptes scabiei (arthropod)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsSchooltink, L. / Sagmeister, T. / Todorovic, N. / Hofer, G. / Keller, W.
Funding support Austria, 2items
OrganizationGrant numberCountry
Austrian Science FundF4604 Austria
Austrian Science FundDoc130 Austria
Citation
Journal: To Be Published
Title: Crystal structure of arginine kinases To be published.
Authors: Schooltink, L. / Todorovic, N. / Sagmeister, T. / Hofer, G. / Keller, W.
#1: Journal: PLoS Negl Trop Dis / Year: 2017
Title: Identification of antigenic Sarcoptes scabiei proteins for use in a diagnostic test and of non-antigenic proteins that may be immunomodulatory.
Authors: Morgan, M.S. / Rider, S.D. / Arlian, L.G.
History
DepositionMay 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: arginine kinase


Theoretical massNumber of molelcules
Total (without water)40,6541
Polymers40,6541
Non-polymers00
Water11,800655
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area15700 Å2
Unit cell
Length a, b, c (Å)48.476, 80.904, 100.504
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein arginine kinase


Mass: 40653.660 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Sarcoptes scabiei (arthropod) / Gene: SSS_5952 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A834RHR6, arginine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 655 / Source method: isolated from a natural source / Formula: H2O
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: 2.42 Å3/Da / Density % sol: 49.26 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.2 M Ammonium sulfate, 0.1 M BIS-TRIS pH 5.5, 25% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, DESY / Beamline: P11 / Wavelength: 0.978564 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Dec 5, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978564 Å / Relative weight: 1
ReflectionResolution: 1.4→48.48 Å / Num. obs: 77680 / % possible obs: 99 % / Redundancy: 6.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.066 / Rpim(I) all: 0.042 / Rrim(I) all: 0.079 / Net I/σ(I): 13.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.67-48.485.90.0345710.9980.0210.04
1.4-1.426.81.24437830.5720.7631.462

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.4→43.662 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.962 / SU B: 2.167 / SU ML: 0.042 / Cross valid method: FREE R-VALUE / ESU R: 0.058 / ESU R Free: 0.061
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1939 3925 5.057 %
Rwork0.1639 73689 -
all0.165 --
obs-77614 98.776 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 18.46 Å2
Baniso -1Baniso -2Baniso -3
1--0.424 Å2-0 Å2-0 Å2
2--0.832 Å20 Å2
3----0.408 Å2
Refinement stepCycle: LAST / Resolution: 1.4→43.662 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2797 0 0 655 3452
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0123018
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162894
X-RAY DIFFRACTIONr_angle_refined_deg1.8051.6644080
X-RAY DIFFRACTIONr_angle_other_deg0.571.596701
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3025381
X-RAY DIFFRACTIONr_dihedral_angle_2_deg8.007517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.59810576
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.76510144
X-RAY DIFFRACTIONr_chiral_restr0.0910.2434
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.023591
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02689
X-RAY DIFFRACTIONr_nbd_refined0.230.2691
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.22694
X-RAY DIFFRACTIONr_nbtor_refined0.1860.21483
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.080.21574
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.3040.2509
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1780.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2320.213
X-RAY DIFFRACTIONr_nbd_other0.210.261
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2940.2100
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.140.21
X-RAY DIFFRACTIONr_mcbond_it1.4891.2471482
X-RAY DIFFRACTIONr_mcbond_other1.4891.2471482
X-RAY DIFFRACTIONr_mcangle_it2.2642.2291877
X-RAY DIFFRACTIONr_mcangle_other2.2642.2291878
X-RAY DIFFRACTIONr_scbond_it2.8711.6141536
X-RAY DIFFRACTIONr_scbond_other2.871.6141537
X-RAY DIFFRACTIONr_scangle_it4.4422.782203
X-RAY DIFFRACTIONr_scangle_other4.4412.782204
X-RAY DIFFRACTIONr_lrange_it9.21228.9753953
X-RAY DIFFRACTIONr_lrange_other8.34817.6773579
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.4-1.4360.3213010.30553270.30557610.9450.94997.69140.285
1.436-1.4760.2662820.25651860.25755780.9610.96298.0280.233
1.476-1.5180.2552890.22250600.22354540.9610.96998.07480.196
1.518-1.5650.2162470.20149460.20252800.9710.97498.35230.177
1.565-1.6160.2062520.18548090.18651420.9740.97898.42470.164
1.616-1.6730.2132350.17346350.17549380.9720.9898.62290.154
1.673-1.7360.2062360.16945290.17148230.9720.98298.79740.15
1.736-1.8070.22160.16643370.16746040.9740.98298.89230.15
1.807-1.8870.1952180.16441910.16644500.9750.98399.07870.149
1.887-1.9790.192310.16139660.16342410.9790.98598.96250.149
1.979-2.0860.1912230.16738100.16840640.9790.98599.23720.157
2.086-2.2120.1761840.15536320.15638400.9830.98799.3750.149
2.212-2.3640.1691800.14733970.14836060.9830.98799.19580.142
2.364-2.5530.1731820.14432120.14534140.980.98799.41420.141
2.553-2.7960.21460.15529540.15731080.9750.98499.74260.154
2.796-3.1240.1791470.15126740.15228390.9790.98699.3660.154
3.124-3.6040.1731210.14223840.14325290.9840.98899.0510.15
3.604-4.4070.175970.14220650.14321650.9830.98899.86140.155
4.407-6.2010.224880.16816140.17117140.9790.98799.29990.186
6.201-43.6620.195500.1999600.19810230.9740.97298.72920.211
Refinement TLS params.Method: refined / Origin x: -3.6765 Å / Origin y: 1.8038 Å / Origin z: -5.2039 Å
111213212223313233
T0.019 Å20.0007 Å2-0.0064 Å2-0.0081 Å20.0017 Å2--0.0287 Å2
L0.5081 °2-0.0219 °2-0.1043 °2-0.0978 °2-0.0128 °2--1.4001 °2
S0.0111 Å °-0.0207 Å °-0.1124 Å °0.0211 Å °-0.004 Å °-0.009 Å °0.1124 Å °0.074 Å °-0.0071 Å °
Refinement TLS groupSelection: ALL

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