[English] 日本語
Yorodumi
- PDB-9fho: Crystal structure of the arginine kinase Der p 20_like (putative ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 9fho
TitleCrystal structure of the arginine kinase Der p 20_like (putative isoform)
Componentsarginine kinase
KeywordsALLERGEN / House dust mite allergen / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 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 kinase To be published.
Authors: Schooltink, L. / Todorovic, N. / Hofer, G. / Sagmeister, T. / 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

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: arginine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,5002
Polymers40,4041
Non-polymers961
Water5,513306
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area200 Å2
ΔGint-16 kcal/mol
Surface area15380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)48.561, 61.894, 61.769
Angle α, β, γ (deg.)90.000, 96.442, 90.000
Int Tables number4
Space group name H-MP1211

-
Components

#1: Protein arginine kinase


Mass: 40403.988 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Dermatophagoides pteronyssinus (European house dust mite)
Gene: LOC113799794 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0A6P6YM67, arginine kinase
#2: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 306 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.12 %
Crystal growTemperature: 293 K / Method: microbatch
Details: 0.05 M Calcium chloride dihydrate, 0.1 M BIS-TRIS pH 6.5, 30% v/v Polyethylene glycol monomethyl ether 550

-
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: 1.8→48.25 Å / Num. obs: 33156 / % possible obs: 97.9 % / Redundancy: 3.2 % / CC1/2: 0.988 / Rmerge(I) obs: 0.086 / Rpim(I) all: 0.081 / Rrim(I) all: 0.119 / Net I/σ(I): 6.4
Reflection shell

Diffraction-ID: 1 / Redundancy: 3.3 %

Resolution (Å)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
9-48.250.0852820.9550.0830.119
1.8-1.840.42719670.8570.3930.582

-
Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→48.25 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.951 / SU B: 8.294 / SU ML: 0.125 / Cross valid method: FREE R-VALUE / ESU R: 0.137 / ESU R Free: 0.13
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2252 1594 4.81 %
Rwork0.1847 31545 -
all0.187 --
obs-33139 97.923 %
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: 37.66 Å2
Baniso -1Baniso -2Baniso -3
1--1.851 Å20 Å2-1.743 Å2
2--3.346 Å2-0 Å2
3----1.073 Å2
Refinement stepCycle: LAST / Resolution: 1.8→48.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2779 0 5 306 3090
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0122852
X-RAY DIFFRACTIONr_bond_other_d0.0010.0162721
X-RAY DIFFRACTIONr_angle_refined_deg1.4511.663843
X-RAY DIFFRACTIONr_angle_other_deg0.481.5856281
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6455350
X-RAY DIFFRACTIONr_dihedral_angle_2_deg15.805517
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.1610526
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.59410139
X-RAY DIFFRACTIONr_chiral_restr0.0680.2415
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.023352
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02656
X-RAY DIFFRACTIONr_nbd_refined0.2240.2603
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.22541
X-RAY DIFFRACTIONr_nbtor_refined0.1760.21409
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0770.21487
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2380.2215
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.2490.22
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3810.211
X-RAY DIFFRACTIONr_nbd_other0.2110.225
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3370.213
X-RAY DIFFRACTIONr_mcbond_it1.932.3591400
X-RAY DIFFRACTIONr_mcbond_other1.9292.3591400
X-RAY DIFFRACTIONr_mcangle_it2.914.2251750
X-RAY DIFFRACTIONr_mcangle_other2.9114.2271751
X-RAY DIFFRACTIONr_scbond_it2.7052.6841452
X-RAY DIFFRACTIONr_scbond_other2.7032.6771449
X-RAY DIFFRACTIONr_scangle_it4.1864.7752093
X-RAY DIFFRACTIONr_scangle_other4.1854.762088
X-RAY DIFFRACTIONr_lrange_it7.60926.0763308
X-RAY DIFFRACTIONr_lrange_other7.57324.8283247
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.8470.3771380.3762334X-RAY DIFFRACTION99.7981
1.847-1.8970.3531100.3092292X-RAY DIFFRACTION99.8753
1.897-1.9520.2641200.2572254X-RAY DIFFRACTION99.6641
1.952-2.0120.34910.2232185X-RAY DIFFRACTION99.6497
2.012-2.0780.313910.2242108X-RAY DIFFRACTION99.4123
2.078-2.1510.2111120.2112027X-RAY DIFFRACTION99.5347
2.151-2.2320.272970.1991974X-RAY DIFFRACTION99.6631
2.232-2.3230.2521050.191899X-RAY DIFFRACTION99.2571
2.323-2.4260.23880.191803X-RAY DIFFRACTION98.9017
2.426-2.5440.268770.1871720X-RAY DIFFRACTION97.8758
2.544-2.6810.264880.1891613X-RAY DIFFRACTION97.4227
2.681-2.8430.228810.1831503X-RAY DIFFRACTION96.2333
2.843-3.0390.284630.1941441X-RAY DIFFRACTION95.8572
3.039-3.2810.199580.2031299X-RAY DIFFRACTION93.9751
3.281-3.5930.22690.1931163X-RAY DIFFRACTION92.009
3.593-4.0140.237550.1511087X-RAY DIFFRACTION94.1467
4.014-4.6290.129550.119958X-RAY DIFFRACTION94.145
4.629-5.6570.169470.143831X-RAY DIFFRACTION95.6427
5.657-7.9460.215360.164665X-RAY DIFFRACTION97.6323
7.946-48.250.15130.185389X-RAY DIFFRACTION96.1722
Refinement TLS params.Method: refined / Origin x: 8.375 Å / Origin y: 4.7021 Å / Origin z: 13.3336 Å
111213212223313233
T0.0305 Å20.0013 Å20.0156 Å2-0.1238 Å20.0274 Å2--0.0362 Å2
L1.4134 °2-0.014 °2-0.2428 °2-2.5253 °2-1.0056 °2--1.1865 °2
S-0.0431 Å °0.1475 Å °-0.0058 Å °-0.2642 Å °-0.163 Å °-0.1736 Å °0.0978 Å °0.1344 Å °0.2062 Å °
Refinement TLS groupSelection: ALL

+
About Yorodumi

-
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

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

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

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
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

Read more