SAXSdb — 1rl9

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Arginine kinase

Limulus polyphemus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–357	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 IOM (DIAMINOMETHYL-METHYL-AMINO)-ACETIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；PEG 6000, magnesium chloride, ATP, Creatine, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.45 Å R-free 0.237

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1RL9	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BG0 TRANSITION STATE STRUCTURE OF ARGININE KINASE Deposited 1998-06-03	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–357（356 aa）	Not recorded	NO3 NITRATE ION × 2 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 DAR D-ARGININE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 7.5；PROTEIN WAS CRYSTALLIZED FROM 18% PEG 6000, 53 MM MGCL2, 2MM MGADP-, 25 MM KNO3, 10 MM ARGININE 0.5 MM DTT, 2.5 MM SODIUM AZIDE, 25 MM HEPES, PH 7.5, WITH 20 MG/ML OF PROTEIN CONCENTRATION.	Resolution 1.86 Å R-free 0.224
1M15 Transition state structure of arginine kinase Deposited 2002-06-17	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–357（357 aa）	Mutation：E103Q, D112G, G116A	NO3 NITRATE ION × 2 MG MAGNESIUM ION × 1 ARG ARGININE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；pH 8	Resolution 1.20 Å R-free 0.140
1P50 Transition state structure of an Arginine Kinase mutant Deposited 2003-04-24	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–357（356 aa）	Mutation：E103Q, G116A, D112G, E225Q	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 NO3 NITRATE ION × 1 ARG ARGININE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；PEG 6000, Hepes, magnesium chloride, ADP, nitrate, arginine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.80 Å R-free 0.246
1P52 Structure of Arginine kinase E314D mutant Deposited 2003-04-24	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–357（357 aa）	Mutation：E314D	NO3 NITRATE ION × 2 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 DAR D-ARGININE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；peg 6000, hEPES, MgCl2, ADP, NO3, ARGININE, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 1.90 Å R-free 0.235
1SD0 Structure of arginine kinase C271A mutant Deposited 2004-02-12	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–357（357 aa）	Mutation：C271A	NO3 NITRATE ION × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 ARG ARGININE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；PEG 6000, magnesium chloride, HEPES, L-arginine, ADP, sodium nitrate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 278K	Resolution 2.30 Å R-free 0.236
3M10 Substrate-free form of Arginine Kinase Deposited 2010-03-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–357（357 aa）	Mutation：E103Q, D112G, G116A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20 mg/mL protein, 26% PEG5000 MME, 0.1M MES, 0.1M (NH4)2SO4. Small crystals were used for macroseeding identical conditions, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.73 Å R-free 0.242
3M10 Substrate-free form of Arginine Kinase Deposited 2010-03-03	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–357（357 aa）	Mutation：E103Q, D112G, G116A	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；20 mg/mL protein, 26% PEG5000 MME, 0.1M MES, 0.1M (NH4)2SO4. Small crystals were used for macroseeding identical conditions, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 1.73 Å R-free 0.242
4GVY Crystal structure of arginine kinase in complex with L-citrulline and MgADP Deposited 2012-08-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–357（357 aa）	Mutation：E103N, D112G, G116A	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 CIR CITRULLINE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Protein at 30 mg/ml, 26% PEG 6000, 0.05M HEPES, 0.1M Magnesium chloride, 0.02M Potassium ADP, 0.25M Sodium nitrate, 0.025M Sodium azide, 0.005M DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.09 Å R-free 0.211
4GVZ Crystal structure of arginine kinase in complex with D-arginine, MgADP, and nitrate. Deposited 2012-08-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–357（357 aa）	Mutation：E103Q, D112G, G116A	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 NO3 NITRATE ION × 1 DAR D-ARGININE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Protein at 30 mg/ml, 26% PEG 6000, 0.05M HEPES, 0.1M Magnesium chloride, 0.02M Potassium ADP, 0.25M Sodium nitrate, 0.025M Sodium azide, 0.005M DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.96 Å R-free 0.229
4GW0 Crystal structure of arginine kinase in complex with imino-L-ornithine, MgADP, and nitrate. Deposited 2012-08-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–357（357 aa）	Mutation：E103N, D112G, G116A	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ILO N5-IMINOETHYL-L-ORNITHINE × 1 NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Protein at 30 mg/ml, 26% PEG 6000, 0.05M HEPES, 0.1M Magnesium chloride, 0.02M Potassium ADP, 0.25M Sodium nitrate, 0.025M Sodium azide, 0.005M DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.45 Å R-free 0.210
4GW2 Crystal structure of arginine kinase in complex with L-ornithine, MgADP, and nitrate. Deposited 2012-08-31	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–357（357 aa）	Mutation：E103N, D112G, G116A	ADP ADENOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 1 ORN L-ornithine × 1 NO3 NITRATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；Protein at 30 mg/ml, 26% PEG 6000, 0.05M HEPES, 0.1M Magnesium chloride, 0.02M Potassium ADP, 0.25M Sodium nitrate, 0.025M Sodium azide, 0.005M DTT, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 398.0K	Resolution 2.16 Å R-free 0.229
5J99 Ambient temperature transition state structure of arginine kinase - crystal 8/Form I Deposited 2016-04-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–357（357 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 ARG ARGININE × 1 NO3 NITRATE ION × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25 mM HEPES, pH 7.5 18% PEG 6000	Resolution 1.70 Å R-free 0.183
5J9A Ambient temperature transition state structure of arginine kinase - crystal 11/Form II Deposited 2016-04-08	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–357（357 aa）	Not recorded	NO3 NITRATE ION × 1 MG MAGNESIUM ION × 1 ARG ARGININE × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；25 mM HEPES, pH 7.5 18% PEG 6000	Resolution 2.00 Å R-free 0.179

12 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KARG_LIMPO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–357； UniProt 1–357

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1rl9
Deposition date deposition_date	2003-11-25
Structure title title	Crystal structure of Creatine-ADP arginine kinase ternary complex
Keywords keywords	arginine kinase, TRANSFERASE; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	20.72 Å
Radius of gyration Rg (electron density) rg_electron	19.98 Å
Forward intensity I(0) i0	28900100.00
Molecular weight molecular_weight	40626.0 kDa
Excluded volume excluded_volume	50597 Å³
Envelope volume envelope_volume	57339 Å³
Hydration-shell volume shell_volume	23449 Å³
Envelope diameter envelope_diameter	67.8 Å
Shell Rg shell_rg	27.25 Å
Envelope Rg envelope_rg	20.28 Å
Shape Rg shape_rg	19.96 Å
Total Rg total_rg	20.93 Å
Total atoms total_atoms	2853
Residues n_residues	356
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	66.8 Å
Rg (real space) rg_real	20.62 Å
Rg uncertainty (real space) rg_real_error	0.36 Å
I(0) (real space) i0_real	2.8900e+07
I(0) uncertainty (real space) i0_real_error	3.5610e+05
Rg (reciprocal space) rg_reciprocal	20.64 Å
I(0) (reciprocal space) i0_reciprocal	28900000.0000
Solution quality estimate total_estimate	0.8101
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.2 Å
Skewness Skewness skewness	0.230
Kurtosis Kurtosis kurtosis	-0.335
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9477000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.844; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Arginine kinase
Molecular weight formula_weight	40308.8 kDa
EC 编号 ec_number	2.7.3.3
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3284

MVDQATLDKLEAGFKKLQEASDCKSLLKKHLTKDVFDSIKNKKTGMGATLLDVIQSGVENLDSGVGIYAPDAESYRTFGPLFDPIIDDYHGGFKLTDKHPPKEWGDINTLVDLDPAGQFIISTRVRCGRSLQGYPFNPCLTAEQYKEMEEKVSSTLSSMEDELKGTYYPLTGMSKATQQQLIDDHFLFKEGDRFLQTANACRYWPTGRGIFHNDAKTFLVWVNEEDHLRIISMQKGGDLKTVYKRLVTAVDNIESKLPFSHDDRFGFLTFCPTNLGTTMRASVHIQLPKLAKDRKVLEDIASKFNLQVRGTRGEHTESEGGVYDISNKRRLGLTEYQAVREMQDGILEMIKMEKAAA

来源 Source

来源生物 organism	Limulus polyphemus
通用名 common_name	Atlantic horseshoe crab
NCBI Class编号 ncbi_taxonomy_id	6850
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	(DIAMINOMETHYL-METHYL-AMINO)-ACETIC ACID
Molecular weight formula_weight	133.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	431

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1rl9a1
Class class	a — All alpha proteins
Fold Fold fold	a.83 — Guanido kinase N-terminal domain
Superfamily Superfamily superfamily	a.83.1 — Guanido kinase N-terminal domain
Family Family family	a.83.1.1 — Guanido kinase N-terminal domain

Domain ID domain_id	d1rl9a2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.128 — Glutamine synthetase/guanido kinase
Superfamily Superfamily superfamily	d.128.1 — Glutamine synthetase/guanido kinase
Family Family family	d.128.1.2 — Guanido kinase catalytic domain

CATH v4.4 (2 domains)

Domain ID domain_id	1rl9A01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	135 — Transferase Creatine Kinase; Chain A, domain 1
Homologous superfamily homologous superfamily	10 — ATP:guanido phosphotransferase, N-terminal domain

Domain ID domain_id	1rl9A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	590 — Creatine Kinase; Chain A, domain 2
Homologous superfamily homologous superfamily	10 — Glutamine synthetase/guanido kinase, catalytic domain

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8. Citations (1)

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Unit-cell length a length_a	64.100 Å
Unit-cell length b length_b	65.300 Å
Unit-cell length c length_c	85.800 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.450 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.1950
R_work r_work	0.1940
R_free r_free	0.2370

fit	/app/data/saxs_computation/rl/1rl9/1rl9.fit
pddf	/app/data/pr_computation/rl/1rl9/1rl9.pr.out
profile	/app/data/saxs_computation/rl/1rl9/1rl9.dat

Crystal structure of Creatine-ADP arginine kinase ternary complex

1. Protein Identity and Related Structures Protein Identity & Related Structures

Arginine kinase

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction