SAXSdb — 10sr

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

Guanylate kinase

Burkholderia thailandensis E264

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 18–224 Chain B； UniProt 18–224	Not recorded	5GP GUANOSINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.6M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6. ButhA.01463.a.A1.PB00147 at 21.6 mg/mL. Cocrystallization with 2 mM GMP. plate Liu-S197 H3, Puck: PSL-1813, Cryo: 4.0M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6	Resolution 3.02 Å R-free 0.249
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 18–224 Chain D； UniProt 18–224	Not recorded	5GP GUANOSINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.6M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6. ButhA.01463.a.A1.PB00147 at 21.6 mg/mL. Cocrystallization with 2 mM GMP. plate Liu-S197 H3, Puck: PSL-1813, Cryo: 4.0M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6	Resolution 3.02 Å R-free 0.249
3	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain E； UniProt 18–224 Chain F； UniProt 18–224	Not recorded	5GP GUANOSINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.6M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6. ButhA.01463.a.A1.PB00147 at 21.6 mg/mL. Cocrystallization with 2 mM GMP. plate Liu-S197 H3, Puck: PSL-1813, Cryo: 4.0M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6	Resolution 3.02 Å R-free 0.249
4	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain G； UniProt 18–224 Chain H； UniProt 18–224	Not recorded	5GP GUANOSINE-5'-MONOPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.6M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6. ButhA.01463.a.A1.PB00147 at 21.6 mg/mL. Cocrystallization with 2 mM GMP. plate Liu-S197 H3, Puck: PSL-1813, Cryo: 4.0M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6	Resolution 3.02 Å R-free 0.249

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 10SR	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10SW Crystal structure of Guanylate Kinase from Burkholderia thailandensis in complex with GDP Deposited 2026-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 18–224（207 aa） Fragment：v18-224P Chain B 18–224（207 aa） Fragment：v18-224P	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.6M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6. ButhA.01463.a.A1.PB00147 at 21.6 mg/mL. Cocrystallization with 2 mM GDP. plate Liu-S197 H1, Puck: PSL-1813, Cryo: 4.0M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6	Resolution 2.96 Å R-free 0.259
10SW Crystal structure of Guanylate Kinase from Burkholderia thailandensis in complex with GDP Deposited 2026-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 18–224（207 aa） Fragment：v18-224P Chain D 18–224（207 aa） Fragment：v18-224P	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.6M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6. ButhA.01463.a.A1.PB00147 at 21.6 mg/mL. Cocrystallization with 2 mM GDP. plate Liu-S197 H1, Puck: PSL-1813, Cryo: 4.0M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6	Resolution 2.96 Å R-free 0.259
10SW Crystal structure of Guanylate Kinase from Burkholderia thailandensis in complex with GDP Deposited 2026-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 18–224（207 aa） Fragment：v18-224P Chain F 18–224（207 aa） Fragment：v18-224P	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.6M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6. ButhA.01463.a.A1.PB00147 at 21.6 mg/mL. Cocrystallization with 2 mM GDP. plate Liu-S197 H1, Puck: PSL-1813, Cryo: 4.0M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6	Resolution 2.96 Å R-free 0.259
10SW Crystal structure of Guanylate Kinase from Burkholderia thailandensis in complex with GDP Deposited 2026-02-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 18–224（207 aa） Fragment：v18-224P Chain H 18–224（207 aa） Fragment：v18-224P	Not recorded	GDP GUANOSINE-5'-DIPHOSPHATE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.6；291 K；1.6M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6. ButhA.01463.a.A1.PB00147 at 21.6 mg/mL. Cocrystallization with 2 mM GDP. plate Liu-S197 H1, Puck: PSL-1813, Cryo: 4.0M Sodium Formate, 0.1M Acetate/acidic acid, pH 4.6	Resolution 2.96 Å R-free 0.259

1 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KGUA_BURTA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–214； UniProt 18–224 Author chain B； PDBConstruct 8–214； UniProt 18–224 Author chain C； PDBConstruct 8–214； UniProt 18–224 Author chain D； PDBConstruct 8–214； UniProt 18–224 Author chain E； PDBConstruct 8–214； UniProt 18–224 Author chain F； PDBConstruct 8–214； UniProt 18–224 Author chain G； PDBConstruct 8–214； UniProt 18–224 Author chain H； PDBConstruct 8–214； UniProt 18–224

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	10sr
Deposition date deposition_date	2026-02-06
最后修订 last_revision	2026-02-18
Structure title title	Crystal structure of Guanylate Kinase from Burkholderia thailandensis in complex with GMP
Keywords keywords	SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, TRANSFERASE, Guanylate Kinase; 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	46.05 Å
Radius of gyration Rg (electron density) rg_electron	45.28 Å
Forward intensity I(0) i0	509900000.00
Molecular weight molecular_weight	183110.0 kDa
Excluded volume excluded_volume	227650 Å³
Envelope volume envelope_volume	351290 Å³
Hydration-shell volume shell_volume	63844 Å³
Envelope diameter envelope_diameter	141.0 Å
Shell Rg shell_rg	52.56 Å
Envelope Rg envelope_rg	42.60 Å
Shape Rg shape_rg	45.27 Å
Total Rg total_rg	45.65 Å
Total atoms total_atoms	12936
Residues n_residues	1630
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	139.2 Å
Rg (real space) rg_real	45.76 Å
Rg uncertainty (real space) rg_real_error	1.13 Å
I(0) (real space) i0_real	5.0990e+08
I(0) uncertainty (real space) i0_real_error	9.0230e+06
Rg (reciprocal space) rg_reciprocal	46.05 Å
I(0) (reciprocal space) i0_reciprocal	510100000.0000
Solution quality estimate total_estimate	0.8296
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	69.6 Å
Skewness Skewness skewness	-0.079
Kurtosis Kurtosis kurtosis	-0.823
Angular range angular_range	— – 0.1700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29370000.0000
Real-space data points n_real_points	35
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.927; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Guanylate kinase
Molecular weight formula_weight	24204.3 kDa
EC 编号 ec_number	2.7.4.8
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	12944

MHHHHHHVYPGNLFMVVAPSGAGKSTLVNALLSKDPEICLSISYTTRKPRSGEQDGQHYHFTTVEDFRARHASHEFLESAEVHGNYYGTSRVWIEEQMKSGHDVLLEIDWQGAQQVKKQFRNAVGIFILPPSLAALEERLKKRGQDEPNVITRRLLAAGSEIAHAAEAEYVVINETFEHALAELECIVAATRLRFTSQYARHAELFVELGIHLP

来源 Source

来源生物 organism	Burkholderia thailandensis E264
NCBI Class编号 ncbi_taxonomy_id	271848
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-MONOPHOSPHATE
Molecular weight formula_weight	363.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	8

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8. Citations (1)

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Unit-cell length a length_a	94.889 Å
Unit-cell length b length_b	63.259 Å
Unit-cell length c length_c	191.484 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	95.21 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	3.020 Å
Low-resolution limit resolution_low	47.670 Å
R factor r_factor	0.2061
R_work r_work	0.2039
R_free r_free	0.2493

fit	/app/data/saxs_computation/0s/10sr/10sr.fit
pddf	/app/data/pr_computation/0s/10sr/10sr.pr.out
profile	/app/data/saxs_computation/0s/10sr/10sr.dat

Crystal structure of Guanylate Kinase from Burkholderia thailandensis in complex with GMP

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

Guanylate 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