PDB-4rf8: Crystal structure of double-domain arginine kinase from Anthopleu...

ID or keywords:

Entry

Database: PDB / ID: 4rf8

Title

Crystal structure of double-domain arginine kinase from Anthopleura japonicas in complex with ADP

Components

Arginine kinase

Keywords

TRANSFERASE / double domain / tandem domain / phsphagen kinase

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

Anthopleura japonica (sea anemone)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.17 Å

Authors

Wang, Z. / Qiao, Z. / Ye, S. / Zhang, R.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2015
Title: Structure of a double-domain phosphagen kinase reveals an asymmetric arrangement of the tandem domains.
Authors: Wang, Z. / Qiao, Z. / Ye, S. / Zhang, R.

History

Deposition	Sep 25, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 8, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 22, 2015	Group: Database references
Revision 1.2	Sep 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4rf8.cif.gz	568.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4rf8.ent.gz	466.7 KB	Display	PDB format
PDBx/mmJSON format	4rf8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Summary document	4rf8_validation.pdf.gz	1 MB	Display	wwPDB validaton report
Full document	4rf8_full_validation.pdf.gz	1.1 MB	Display
Data in XML	4rf8_validation.xml.gz	55 KB	Display
Data in CIF	4rf8_validation.cif.gz	76.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rf/4rf8 ftp://data.pdbj.org/pub/pdb/validation_reports/rf/4rf8	HTTPS FTP

-
Related structure data

Related structure data	4rf6SC 4rf7C 4rf9C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4rf9-1 4rf7-1 4rf6-2 4rf7-2 4rf9-2 5nh3-d 5kov-3 5oqu-d 6gmd-d 2q36-1 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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

hetero molecules

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

1

A: Arginine kinase

hetero molecules

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

2

B: Arginine kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	79.481, 59.274, 163.706
Angle α, β, γ (deg.)	90.00, 90.75, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Arginine kinase / AK Mass: 80442.328 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Anthopleura japonica (sea anemone) / Production host: Escherichia coli (E. coli) / References: UniProt: O15992, arginine kinase
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-NO3 / NITRATE ION Mass: 62.005 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: NO₃
#4: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 548 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.4 Å³/Da / Density % sol: 48.68 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 20mM HEPES, 50mM NaCl, 10mM L-arginine, 10mM Sodium Nitrate, 10mM ADP, 0.2M Potassium Acetate, 20% PEG3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 289K

-
Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: May 5, 2013
Radiation	Monochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97915 Å / Relative weight: 1
Reflection	Resolution: 2.17→47.514 Å / Num. all: 79856 / Num. obs: 79696 / % possible obs: 99.8 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell	Resolution: 2.17→2.19 Å / % possible all: 100

-
Processing

Software

Name	Version	Classification
Blu-Ice		data collection
PHENIX	(phenix.phaser)	model building
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4RF6

4rf6

Resolution: 2.17→47.514 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 24.34 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.239	3994	5.01 %
R_work	0.1923	-	-
obs	0.1948	79663	98.36 %
all	-	80992	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.17→47.514 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10896	0	164	548	11608

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.003	11297
X-RAY DIFFRACTION	f_angle_d	0.833	15228
X-RAY DIFFRACTION	f_dihedral_angle_d	13.259	4277
X-RAY DIFFRACTION	f_chiral_restr	0.051	1638
X-RAY DIFFRACTION	f_plane_restr	0.004	1981

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 (%)
2.17-2.1974	0.3098	92	0.253	1623	X-RAY DIFFRACTION	61
2.1974-2.2242	0.2736	126	0.2442	2555	X-RAY DIFFRACTION	100
2.2242-2.2524	0.3125	109	0.229	2665	X-RAY DIFFRACTION	100
2.2524-2.282	0.279	139	0.2222	2633	X-RAY DIFFRACTION	100
2.282-2.3133	0.2644	154	0.2193	2595	X-RAY DIFFRACTION	100
2.3133-2.3463	0.2548	136	0.2152	2680	X-RAY DIFFRACTION	100
2.3463-2.3814	0.2743	129	0.2025	2628	X-RAY DIFFRACTION	100
2.3814-2.4186	0.2496	130	0.2071	2678	X-RAY DIFFRACTION	100
2.4186-2.4582	0.2352	144	0.2089	2585	X-RAY DIFFRACTION	100
2.4582-2.5006	0.2504	151	0.2012	2623	X-RAY DIFFRACTION	100
2.5006-2.5461	0.2791	167	0.2059	2622	X-RAY DIFFRACTION	100
2.5461-2.5951	0.2266	114	0.2083	2657	X-RAY DIFFRACTION	100
2.5951-2.648	0.3438	122	0.2336	2639	X-RAY DIFFRACTION	100
2.648-2.7056	0.3111	163	0.236	2609	X-RAY DIFFRACTION	100
2.7056-2.7685	0.2544	123	0.2183	2656	X-RAY DIFFRACTION	100
2.7685-2.8377	0.2482	141	0.195	2667	X-RAY DIFFRACTION	100
2.8377-2.9145	0.2551	149	0.1838	2621	X-RAY DIFFRACTION	100
2.9145-3.0002	0.2404	137	0.1852	2645	X-RAY DIFFRACTION	100
3.0002-3.097	0.2219	121	0.1721	2676	X-RAY DIFFRACTION	100
3.097-3.2077	0.2049	149	0.1719	2617	X-RAY DIFFRACTION	100
3.2077-3.3361	0.2001	137	0.172	2661	X-RAY DIFFRACTION	100
3.3361-3.4879	0.2104	158	0.1607	2658	X-RAY DIFFRACTION	100
3.4879-3.6717	0.1889	145	0.1671	2649	X-RAY DIFFRACTION	100
3.6717-3.9017	0.2488	133	0.1645	2636	X-RAY DIFFRACTION	100
3.9017-4.2027	0.2163	148	0.171	2672	X-RAY DIFFRACTION	100
4.2027-4.6254	0.2623	137	0.1708	2669	X-RAY DIFFRACTION	100
4.6254-5.2939	0.2314	149	0.2007	2692	X-RAY DIFFRACTION	100
5.2939-6.6668	0.253	155	0.2302	2693	X-RAY DIFFRACTION	100
6.6668-47.5256	0.2271	136	0.2069	2665	X-RAY DIFFRACTION	95

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	0.9834	-0.3171	0.448	0.652	-0.2328	2.8589	0.0764	0.0461	0.1349	-0.0254	-0.0179	-0.0438	-0.0516	0.0064	-0.0699	0.2437	0.0262	0.0271	0.2363	0.0166	0.2614	19.8886	10.3262	-10.0132
2	0.7213	-0.0387	-0.2111	0.5903	0.6572	2.9612	0.1519	-0.0698	0.0711	-0.1993	-0.0812	-0.0831	-0.5099	0.2392	-0.0755	0.318	-0.0509	0.0197	0.2556	0.0349	0.2875	29.6849	18.7031	27.6145
3	0.7432	-0.0787	-0.1158	2.2313	1.0714	1.123	0.1975	-0.1207	0.2596	-0.4497	0.0268	-0.3122	-1.2038	0.331	-0.1255	0.7504	-0.2616	0.1056	0.3867	-0.0705	0.3392	25.4772	36.7656	44.3929
4	0.7092	-0.378	-0.0004	1.1006	-0.1815	2.4455	-0.0788	-0.0193	-0.022	0.0601	0.0536	-0.0057	0.1645	0.1214	0.0244	0.1979	0.0072	0.0311	0.236	0.0273	0.2886	3.6027	29.0617	123.5542
5	0.6083	0.049	-0.52	0.3093	0.1982	1.6922	-0.0364	-0.0296	0.0091	0.0992	0.0939	-0.037	0.0263	0.0442	-0.0727	0.2188	0.0066	-0.0568	0.2003	-0.0014	0.2864	15.9708	34.7846	83.8206
6	3.0704	0.0478	0.5009	1.4318	0.0154	0.5018	0.0454	0.2802	0.5292	0.0145	-0.1224	-0.4739	-0.4292	0.2887	0.0478	0.2864	-0.0639	-0.0591	0.4461	0.0463	0.4951	39.4779	32.6604	66.0347

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 3:290 )	A	3 - 290
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 291:578 )	A	291 - 578
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 579:713 )	A	579 - 713
4	X-RAY DIFFRACTION	4	( CHAIN B AND RESID 2:290 )	B	2 - 290
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 291:642 )	B	291 - 642
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 643:713 )	B	643 - 713

-
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