PDB-4rf7: Crystal structure of double-domain arginine kinase from Anthopleu...

ID or keywords:

Entry

Database: PDB / ID: 4rf7

Title

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

Components

Arginine kinase

Keywords

TRANSFERASE / double domain / tandem domain / phosphagen 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 /

MOLECULAR REPLACEMENT / Resolution: 2.1 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

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PDBx/mmCIF format	4rf7.cif.gz	578.4 KB	Display	PDBx/mmCIF format
PDB format	pdb4rf7.ent.gz	475 KB	Display	PDB format
PDBx/mmJSON format	4rf7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	4rf7_validation.pdf.gz	469.9 KB	Display	wwPDB validaton report
Full document	4rf7_full_validation.pdf.gz	482.1 KB	Display
Data in XML	4rf7_validation.xml.gz	59.8 KB	Display
Data in CIF	4rf7_validation.cif.gz	88.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/rf/4rf7 ftp://data.pdbj.org/pub/pdb/validation_reports/rf/4rf7	HTTPS FTP

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Related structure data

Related structure data	4rf6SC 4rf8C 4rf9C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4rf9-1 4rf8-2 4rf8-1 4rf6-2 4rf9-2 1j3h-d 5c0v-d 5xgs-d 5ig2-d 3gq2-2 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#30 - Jun 2002 Glutamine Synthetase similarity (1) #133 - Jan 2011 Nitric Oxide Synthase similarity (1)

Deposited unit

A: Arginine kinase

B: Arginine kinase

hetero molecules

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

1

A: Arginine kinase

hetero molecules

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

2

B: Arginine kinase

hetero molecules

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

Unit cell

Length a, b, c (Å)	78.500, 59.271, 162.256
Angle α, β, γ (deg.)	90.00, 91.31, 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-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₂H₃O₂
#3: Chemical	ChemComp-ARG / ARGININE Type: L-peptide linking / Mass: 175.209 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₆H₁₅N₄O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1072 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.35 Å³/Da / Density % sol: 47.56 %
Crystal grow	Method: vapor diffusion, hanging drop / pH: 7.8 Details: 20mM Tris, 50mM NaCl, 10mM, L-arginine, 200mM Potassium Acetate, 20% PEG3350, pH 7.8, VAPOR DIFFUSION, HANGING DROP

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54178 Å
Detector	Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Apr 12, 2013
Radiation	Monochromator: Be filter / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54178 Å / Relative weight: 1
Reflection	Resolution: 2.1→47.9 Å / Num. all: 87800 / Num. obs: 87800 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shell	Resolution: 2.1→2.14 Å / % possible all: 100

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Processing

Software

Name	Version	Classification
CrystalClear		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: 2.1→47.855 Å / SU ML: 0.21 / σ(F): 1.34 / Phase error: 23.79 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2175	4399	5.01 %	random
R_work	0.1801	-	-	-
obs	0.1821	87762	99.83 %	-
all	-	87800	-	-

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.1→47.855 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10991	0	104	1072	12167

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	11327
X-RAY DIFFRACTION	f_angle_d	0.802	15257
X-RAY DIFFRACTION	f_dihedral_angle_d	12.566	4294
X-RAY DIFFRACTION	f_chiral_restr	0.051	1649
X-RAY DIFFRACTION	f_plane_restr	0.004	1994

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 (%)
2.1-2.1214	0.2984	144	0.2647	2686	X-RAY DIFFRACTION	96
2.1214-2.1464	0.3125	144	0.2501	2709	X-RAY DIFFRACTION	100
2.1464-2.1725	0.3089	150	0.2521	2763	X-RAY DIFFRACTION	100
2.1725-2.2	0.3178	134	0.2495	2777	X-RAY DIFFRACTION	100
2.2-2.229	0.2807	130	0.2418	2786	X-RAY DIFFRACTION	100
2.229-2.2595	0.2909	134	0.2358	2778	X-RAY DIFFRACTION	100
2.2595-2.2918	0.2774	140	0.2235	2792	X-RAY DIFFRACTION	100
2.2918-2.326	0.2771	150	0.2144	2700	X-RAY DIFFRACTION	100
2.326-2.3624	0.2677	174	0.2141	2782	X-RAY DIFFRACTION	100
2.3624-2.4011	0.2484	143	0.2205	2761	X-RAY DIFFRACTION	100
2.4011-2.4425	0.2644	151	0.2159	2736	X-RAY DIFFRACTION	100
2.4425-2.4869	0.3194	142	0.2125	2759	X-RAY DIFFRACTION	100
2.4869-2.5347	0.2466	150	0.2094	2794	X-RAY DIFFRACTION	100
2.5347-2.5865	0.2745	148	0.2049	2780	X-RAY DIFFRACTION	100
2.5865-2.6427	0.2462	145	0.2001	2733	X-RAY DIFFRACTION	100
2.6427-2.7042	0.2346	160	0.1938	2791	X-RAY DIFFRACTION	100
2.7042-2.7718	0.2864	135	0.2039	2742	X-RAY DIFFRACTION	100
2.7718-2.8467	0.2681	139	0.1977	2805	X-RAY DIFFRACTION	100
2.8467-2.9305	0.2756	156	0.208	2774	X-RAY DIFFRACTION	100
2.9305-3.025	0.2454	156	0.2051	2760	X-RAY DIFFRACTION	100
3.025-3.1331	0.2283	126	0.1829	2837	X-RAY DIFFRACTION	100
3.1331-3.2586	0.2375	153	0.1813	2750	X-RAY DIFFRACTION	100
3.2586-3.4068	0.1985	124	0.1649	2816	X-RAY DIFFRACTION	100
3.4068-3.5864	0.1903	166	0.1622	2756	X-RAY DIFFRACTION	100
3.5864-3.811	0.1894	140	0.1547	2806	X-RAY DIFFRACTION	100
3.811-4.1051	0.1683	155	0.1478	2802	X-RAY DIFFRACTION	100
4.1051-4.5179	0.1669	135	0.1378	2824	X-RAY DIFFRACTION	100
4.5179-5.171	0.1829	159	0.1502	2803	X-RAY DIFFRACTION	100
5.171-6.5123	0.2172	157	0.1821	2850	X-RAY DIFFRACTION	100
6.5123-47.8672	0.1627	159	0.1674	2911	X-RAY DIFFRACTION	100

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	0.6741	-0.2316	0.2163	0.4279	-0.0297	1.446	0.0477	-0.0662	0.0197	-0.0438	0.0126	0.0502	0.1012	0.0213	0.0454	0.1537	-0.0039	0.0403	0.1388	0.0188	0.1678	19.2299	9.7813	-10.7485
2	0.2798	-0.1845	0.2437	0.356	-0.39	0.8768	0.0775	0.1717	0.0068	-0.0685	0.045	-0.1234	0.5146	0.6012	0.046	0.2934	0.1172	0.0346	0.3805	0.0251	0.3055	33.9131	0.859	8.5399
3	0.7613	-0.0146	-0.1811	0.2264	0.6731	2.0382	0.0687	0.1031	0.1148	-0.0528	-0.0596	-0.1027	-0.2222	0.0378	-0.0642	0.1801	-0.0018	0.039	0.2127	0.0761	0.2313	27.4711	23.9389	32.7736
4	0.4646	-0.5027	-0.0503	0.2331	0.4175	1.1064	-0.0154	-0.0139	0.2935	-0.1529	-0.0348	-0.3886	-0.1577	-0.2439	-0.1516	0.2205	0.0385	-0.0146	0.1482	0.0176	0.4243	25.2954	36.9161	42.0247
5	0.5682	-0.317	0.0534	0.9741	-0.221	1.1429	-0.0216	0.0602	-0.0025	-0.0602	-0.0283	0.0103	0.1922	-0.08	-0.0005	0.1812	0.0026	-0.0007	0.1905	-0.0185	0.2252	2.0713	28.9692	122.1575
6	0.3681	0.0848	-0.1761	0.3678	-0.3292	1.4467	0.3942	-0.0236	0.4935	0.2693	0.0574	0.2828	-1.197	-0.9411	0.0998	0.4367	0.2211	-0.0833	-0.1312	-0.0189	0.178	3.0484	48.8249	94.4066
7	0.3669	-0.1631	-0.6864	0.4311	0.2782	1.1692	-0.1177	-0.1292	0.0094	0.2107	0.0353	-0.1228	-0.0311	0.1454	-0.0107	0.3082	0.0446	-0.1222	0.2751	-0.0072	0.2755	24.3368	29.8027	75.3497
8	0.1461	0.0703	0.794	0.6078	1.2581	7.3839	0.1996	-0.0226	0.0475	0.0007	0.3232	0.0498	-0.5225	0.5158	-0.5913	0.4407	-0.1035	-0.0235	0.3049	-0.205	0.5705	14.5085	27.4207	59.0712

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 1:290 )	A	1 - 290
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 291:368 )	A	291 - 368
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 369:578 )	A	369 - 578
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 579:714 )	A	579 - 714
5	X-RAY DIFFRACTION	5	( CHAIN B AND RESID 1:290 )	B	1 - 290
6	X-RAY DIFFRACTION	6	( CHAIN B AND RESID 291:405 )	B	291 - 405
7	X-RAY DIFFRACTION	7	( CHAIN B AND RESID 406:713 )	B	406 - 713
8	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 801:807 ) OR ( CHAIN B AND RESID 1001:1007 )	A	801 - 807
9	X-RAY DIFFRACTION	8	( CHAIN A AND RESID 801:807 ) OR ( CHAIN B AND RESID 1001:1007 )	B	1001 - 1007

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