SAXSdb — 1m15

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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	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

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 1M15	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 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）	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
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
1RL9 Crystal structure of Creatine-ADP arginine kinase ternary complex Deposited 2003-11-25	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）	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
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 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 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 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 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）	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 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）	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	1m15
Deposition date deposition_date	2002-06-17
Structure title title	Transition state structure of arginine kinase
Keywords keywords	ARGININE KINASE, CREATINE KINASE, PHOSPHAGEN KINASE, TRANSITION STATE ANALOG, ADENOSINE TRIPHOSPHATE, 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	20.65 Å
Radius of gyration Rg (electron density) rg_electron	19.95 Å
Forward intensity I(0) i0	29345100.00
Molecular weight molecular_weight	40810.0 kDa
Excluded volume excluded_volume	50736 Å³
Envelope volume envelope_volume	56905 Å³
Hydration-shell volume shell_volume	23287 Å³
Envelope diameter envelope_diameter	67.3 Å
Shell Rg shell_rg	27.16 Å
Envelope Rg envelope_rg	20.30 Å
Shape Rg shape_rg	19.93 Å
Total Rg total_rg	20.89 Å
Total atoms total_atoms	2865
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	69.2 Å
Rg (real space) rg_real	20.55 Å
Rg uncertainty (real space) rg_real_error	0.37 Å
I(0) (real space) i0_real	2.9350e+07
I(0) uncertainty (real space) i0_real_error	3.2230e+05
Rg (reciprocal space) rg_reciprocal	20.57 Å
I(0) (reciprocal space) i0_reciprocal	29350000.0000
Solution quality estimate total_estimate	0.8739
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	25.1 Å
Skewness Skewness skewness	0.243
Kurtosis Kurtosis kurtosis	-0.333
Angular range angular_range	— – 0.3850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9250000.0000
Real-space data points n_real_points	70
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.786; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	arginine kinase
Molecular weight formula_weight	40249.8 kDa
EC 编号 ec_number	2.7.3.3
Mutation mutation	E103Q, D112G, G116A
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	3459

MVDQATLDKLEAGFKKLQEASDCKSLLKKHLTKDVFDSIKNKKTGMGATLLDVIQSGVENLDSGVGIYAPDAESYRTFGPLFDPIIDDYHGGFKLTDKHPPKQWGDINTLVGLDPAGQFIISTRVRCGRSLQGYPFNPCLTAEQYKEMEEKVSSTLSSMEDELKGTYYPLTGMSKATQQQLIDDHFLFKEGDRFLQTANACRYWPTGRGIFHNDAKTFLVWVNEEDHLRIISMQKGGDLKTVYKRLVTAVDNIESKLPFSHDDRFGFLTFCPTNLGTTMRASVHIQLPKLAKDRKVLEDIASKFNLQVRGTRGEHTESEGGVYDISNKRRLGLTEYQAVREMQDGILEMIKMEKAAA

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

Entity 2 Entity 2 non-polymer

Description description	NITRATE ION
Molecular weight formula_weight	62.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

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

Entity 4 Entity 4 non-polymer

Description description	ARGININE
Molecular weight formula_weight	175.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 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 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	557

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1m15a1
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	d1m15a2
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	1m15A01
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	1m15A02
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 (4)

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Unit-cell length a length_a	65.393 Å
Unit-cell length b length_b	70.312 Å
Unit-cell length c length_c	80.319 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	1.200 Å
Low-resolution limit resolution_low	6.000 Å
R factor r_factor	0.1270
R_work r_work	0.1248
R_free r_free	0.1395

fit	/app/data/saxs_computation/m1/1m15/1m15.fit
pddf	/app/data/pr_computation/m1/1m15/1m15.pr.out
profile	/app/data/saxs_computation/m1/1m15/1m15.dat

Transition state structure of arginine kinase