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- PDB-9fhn: Crystal structure of the arginine kinase Der p 20.0101 -

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Basic information

Entry
Database: PDB / ID: 9fhn
TitleCrystal structure of the arginine kinase Der p 20.0101
Componentsarginine kinase
KeywordsALLERGEN / House dust 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 speciesDermatophagoides pteronyssinus (European house dust mite)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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 the arginine kinase To be published.
Authors: Schooltink, L. / Todorovic, N. / Sagmeister, T. / Hofer, G. / Keller, W.
#1: Journal: Allergy Asthma Immunol Res / Year: 2021
Title: Expression in Escherichia coli and Purification of Folded rDer p 20, the Arginine Kinase From Dermatophagoides pteronyssinus: A Possible Biomarker for Allergic Asthma
Authors: Sarzsinszky, E. / Lupinek, C. / Vrtala, S. / Huang, H.J. / Hofer, G. / Keller, W. / Chen, K.W. / Panaitescu, C.B. / Resch-Marat, Y. / Zieglmayer, P. / Zieglmayer, R. / Lemell, P. / Horak, F. ...Authors: Sarzsinszky, E. / Lupinek, C. / Vrtala, S. / Huang, H.J. / Hofer, G. / Keller, W. / Chen, K.W. / Panaitescu, C.B. / Resch-Marat, Y. / Zieglmayer, P. / Zieglmayer, R. / Lemell, P. / Horak, F. / Duchene, M. / Valenta, R.
History
DepositionMay 28, 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
B: arginine kinase


Theoretical massNumber of molelcules
Total (without water)81,0752
Polymers81,0752
Non-polymers00
Water3,585199
1
A: arginine kinase


Theoretical massNumber of molelcules
Total (without water)40,5371
Polymers40,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: arginine kinase


Theoretical massNumber of molelcules
Total (without water)40,5371
Polymers40,5371
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.280, 99.020, 77.883
Angle α, β, γ (deg.)90.000, 108.056, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21A

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: MET / End label comp-ID: MET / Auth asym-ID: A / Label asym-ID: A / Auth seq-ID: 1 - 356 / Label seq-ID: 1 - 356

Dom-ID
1
2

NCS ensembles : (Details: Local NCS retraints between domains: 1 2)

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Components

#1: Protein arginine kinase


Mass: 40537.371 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dermatophagoides pteronyssinus (European house dust mite)
Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: B2ZSY4, arginine kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.18 Å3/Da / Density % sol: 43.66 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.2 M Lithium sulfate monohydrate, 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: LIQUID ANODE / Type: Excillum MetalJet D2+ 70 kV / Wavelength: 1.34138 Å
DetectorType: Bruker PHOTON III / Detector: PIXEL / Date: May 19, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.34138 Å / Relative weight: 1
ReflectionResolution: 1.9→59.3 Å / Num. obs: 49720 / % possible obs: 90.8 % / Redundancy: 2.9 % / CC1/2: 0.978 / Rmerge(I) obs: 0.144 / Net I/σ(I): 4.3
Reflection shellResolution: 1.9→1.94 Å / Rmerge(I) obs: 0.5 / Num. unique obs: 3229 / CC1/2: 0.708

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→59.3 Å / Cor.coef. Fo:Fc: 0.823 / Cor.coef. Fo:Fc free: 0.783 / SU B: 14.28 / SU ML: 0.21 / Cross valid method: FREE R-VALUE / ESU R: 0.361 / ESU R Free: 0.259
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.3098 2044 5.1 %
Rwork0.2697 38031 -
all0.272 --
obs-40075 73.106 %
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: 7.484 Å2
Baniso -1Baniso -2Baniso -3
1-0.213 Å2-0 Å2-0.444 Å2
2--1.494 Å2-0 Å2
3----1.169 Å2
Refinement stepCycle: LAST / Resolution: 1.9→59.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5580 0 0 199 5779
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0125695
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165498
X-RAY DIFFRACTIONr_angle_refined_deg1.2321.6647659
X-RAY DIFFRACTIONr_angle_other_deg0.4251.58612689
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6795694
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.974534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45101071
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.14610272
X-RAY DIFFRACTIONr_chiral_restr0.0580.2825
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026634
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021302
X-RAY DIFFRACTIONr_nbd_refined0.220.21285
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2070.25019
X-RAY DIFFRACTIONr_nbtor_refined0.1760.22814
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.22934
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2430.2260
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.1510.25
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2210.29
X-RAY DIFFRACTIONr_nbd_other0.2440.248
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.350.214
X-RAY DIFFRACTIONr_mcbond_it0.4090.2682785
X-RAY DIFFRACTIONr_mcbond_other0.4090.2682785
X-RAY DIFFRACTIONr_mcangle_it0.5860.4783476
X-RAY DIFFRACTIONr_mcangle_other0.5860.4793477
X-RAY DIFFRACTIONr_scbond_it0.3940.3042910
X-RAY DIFFRACTIONr_scbond_other0.3940.3042911
X-RAY DIFFRACTIONr_scangle_it0.5920.5414183
X-RAY DIFFRACTIONr_scangle_other0.5920.5414184
X-RAY DIFFRACTIONr_lrange_it1.0872.596519
X-RAY DIFFRACTIONr_lrange_other1.0592.5726487
X-RAY DIFFRACTIONr_ncsr_local_group_10.0880.0511651
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.088450.05009
12AX-RAY DIFFRACTIONLocal ncs0.088450.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.9490.35710.341400X-RAY DIFFRACTION36.2405
1.949-2.0030.379730.3541842X-RAY DIFFRACTION48.6411
2.003-2.0610.3481080.3152154X-RAY DIFFRACTION59.9047
2.061-2.1240.3251300.3082359X-RAY DIFFRACTION66.8188
2.124-2.1940.3491150.2992547X-RAY DIFFRACTION73.1721
2.194-2.270.3421210.292515X-RAY DIFFRACTION76.4945
2.27-2.3560.3521690.2952446X-RAY DIFFRACTION77.4127
2.356-2.4520.3331100.2872427X-RAY DIFFRACTION78.8133
2.452-2.5610.321440.2762518X-RAY DIFFRACTION84.6423
2.561-2.6860.331610.2712460X-RAY DIFFRACTION87.3667
2.686-2.8310.384950.2882346X-RAY DIFFRACTION86.5603
2.831-3.0020.311170.2632119X-RAY DIFFRACTION83.6513
3.002-3.2090.3381430.2622011X-RAY DIFFRACTION85.9537
3.209-3.4650.316930.2611893X-RAY DIFFRACTION84.6547
3.465-3.7940.279970.2261647X-RAY DIFFRACTION80.5543
3.794-4.240.215860.1991309X-RAY DIFFRACTION71.2462
4.24-4.8920.217740.1841525X-RAY DIFFRACTION91.476
4.892-5.9810.215600.2371106X-RAY DIFFRACTION78.4657
5.981-8.4160.211490.197893X-RAY DIFFRACTION82.9225
8.416-59.30.233280.206514X-RAY DIFFRACTION82.6219
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.60910.0114-0.00361.09580.06740.0079-0.0195-0.1097-0.0150.09280.0196-0.04950.00580.0005-0.00010.0090.0054-0.00190.02080.00090.0109-3.8463-0.294334.6861
20.5555-0.12-0.01041.07830.10850.24030.0159-0.08830.00340.0839-0.0185-0.0637-0.00370.00750.00260.0142-0.0070.00280.01590.0010.0163-16.02383.141171.9344
Refinement TLS groupSelection: ALL

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