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

ID or keywords:

Entry

Database: PDB / ID: 9fhn

Title

Crystal structure of the arginine kinase Der p 20.0101

Components

arginine kinase

Keywords

ALLERGEN / 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

Biological species

Dermatophagoides pteronyssinus (European house dust mite)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 1.9 Å

Authors

Schooltink, L. / Sagmeister, T. / Todorovic, N. / Hofer, G. / Keller, W.

Funding support

Austria, 2items

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.

History

Deposition	May 28, 2024	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Jun 11, 2025	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	9fhn.cif.gz	688.3 KB	Display	PDBx/mmCIF format
PDB format	pdb9fhn.ent.gz	426.9 KB	Display	PDB format
PDBx/mmJSON format	9fhn.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/fh/9fhn ftp://data.pdbj.org/pub/pdb/validation_reports/fh/9fhn	HTTPS FTP

-
Related structure data

Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#30 - Jun 2002 Glutamine Synthetase similarity (1)

Deposited unit

A: arginine kinase

B: arginine kinase

81.1 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: arginine kinase

defined by author
40.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: arginine kinase

defined by author
40.5 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

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 number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	A

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)

#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 modification	N

-
Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

Crystal	Density Matthews: 2.18 Å³/Da / Density % sol: 43.66 %
Crystal grow	Temperature: 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

-
Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: LIQUID ANODE / Type: Excillum MetalJet D2+ 70 kV / Wavelength: 1.34138 Å
Detector	Type: Bruker PHOTON III / Detector: PIXEL / Date: May 19, 2022
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.34138 Å / Relative weight: 1
Reflection	Resolution: 1.9→59.3 Å / Num. obs: 49720 / % possible obs: 90.8 % / Redundancy: 2.9 % / CC_1/2: 0.978 / R_merge(I) obs: 0.144 / Net I/σ(I): 4.3
Reflection shell	Resolution: 1.9→1.94 Å / R_merge(I) obs: 0.5 / Num. unique obs: 3229 / CC_1/2: 0.708

-
Processing

Software

Name	Version	Classification
REFMAC	5.8.0419	refinement
DIALS		data reduction
Aimless		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.9→59.3 Å / Cor.coef. F_o:F_c: 0.823 / Cor.coef. F_o:F_c 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

	R_factor	Num. reflection	% reflection
R_free	0.3098	2044	5.1 %
R_work	0.2697	38031	-
all	0.272	-	-
obs	-	40075	73.106 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 7.484 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.213 Å²	-0 Å²	-0.444 Å²
2-	-	1.494 Å²	-0 Å²
3-	-	-	-1.169 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→59.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5580	0	0	199	5779

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.012	5695
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.016	5498
X-RAY DIFFRACTION	r_angle_refined_deg	1.232	1.664	7659
X-RAY DIFFRACTION	r_angle_other_deg	0.425	1.586	12689
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.679	5	694
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	6.974	5	34
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.45	10	1071
X-RAY DIFFRACTION	r_dihedral_angle_6_deg	15.146	10	272
X-RAY DIFFRACTION	r_chiral_restr	0.058	0.2	825
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	6634
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1302
X-RAY DIFFRACTION	r_nbd_refined	0.22	0.2	1285
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.207	0.2	5019
X-RAY DIFFRACTION	r_nbtor_refined	0.176	0.2	2814
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.077	0.2	2934
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.243	0.2	260
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.151	0.2	5
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.221	0.2	9
X-RAY DIFFRACTION	r_nbd_other	0.244	0.2	48
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.35	0.2	14
X-RAY DIFFRACTION	r_mcbond_it	0.409	0.268	2785
X-RAY DIFFRACTION	r_mcbond_other	0.409	0.268	2785
X-RAY DIFFRACTION	r_mcangle_it	0.586	0.478	3476
X-RAY DIFFRACTION	r_mcangle_other	0.586	0.479	3477
X-RAY DIFFRACTION	r_scbond_it	0.394	0.304	2910
X-RAY DIFFRACTION	r_scbond_other	0.394	0.304	2911
X-RAY DIFFRACTION	r_scangle_it	0.592	0.541	4183
X-RAY DIFFRACTION	r_scangle_other	0.592	0.541	4184
X-RAY DIFFRACTION	r_lrange_it	1.087	2.59	6519
X-RAY DIFFRACTION	r_lrange_other	1.059	2.572	6487
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.088	0.05	11651

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08845	0.05009
1	2	A	X-RAY DIFFRACTION	Local ncs	0.08845	0.05009

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.9-1.949	0.35	71	0.34	1400	X-RAY DIFFRACTION	36.2405
1.949-2.003	0.379	73	0.354	1842	X-RAY DIFFRACTION	48.6411
2.003-2.061	0.348	108	0.315	2154	X-RAY DIFFRACTION	59.9047
2.061-2.124	0.325	130	0.308	2359	X-RAY DIFFRACTION	66.8188
2.124-2.194	0.349	115	0.299	2547	X-RAY DIFFRACTION	73.1721
2.194-2.27	0.342	121	0.29	2515	X-RAY DIFFRACTION	76.4945
2.27-2.356	0.352	169	0.295	2446	X-RAY DIFFRACTION	77.4127
2.356-2.452	0.333	110	0.287	2427	X-RAY DIFFRACTION	78.8133
2.452-2.561	0.32	144	0.276	2518	X-RAY DIFFRACTION	84.6423
2.561-2.686	0.33	161	0.271	2460	X-RAY DIFFRACTION	87.3667
2.686-2.831	0.384	95	0.288	2346	X-RAY DIFFRACTION	86.5603
2.831-3.002	0.31	117	0.263	2119	X-RAY DIFFRACTION	83.6513
3.002-3.209	0.338	143	0.262	2011	X-RAY DIFFRACTION	85.9537
3.209-3.465	0.316	93	0.261	1893	X-RAY DIFFRACTION	84.6547
3.465-3.794	0.279	97	0.226	1647	X-RAY DIFFRACTION	80.5543
3.794-4.24	0.215	86	0.199	1309	X-RAY DIFFRACTION	71.2462
4.24-4.892	0.217	74	0.184	1525	X-RAY DIFFRACTION	91.476
4.892-5.981	0.215	60	0.237	1106	X-RAY DIFFRACTION	78.4657
5.981-8.416	0.211	49	0.197	893	X-RAY DIFFRACTION	82.9225
8.416-59.3	0.233	28	0.206	514	X-RAY DIFFRACTION	82.6219

Refinement TLS params.

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

ID	L11 (°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)
1	0.6091	0.0114	-0.0036	1.0958	0.0674	0.0079	-0.0195	-0.1097	-0.015	0.0928	0.0196	-0.0495	0.0058	0.0005	-0.0001	0.009	0.0054	-0.0019	0.0208	0.0009	0.0109	-3.8463	-0.2943	34.6861
2	0.5555	-0.12	-0.0104	1.0783	0.1085	0.2403	0.0159	-0.0883	0.0034	0.0839	-0.0185	-0.0637	-0.0037	0.0075	0.0026	0.0142	-0.007	0.0028	0.0159	0.001	0.0163	-16.0238	3.1411	71.9344

Refinement TLS group

Selection: ALL

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi