SAXSdb — 9iit

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

L-fucokinase/L-fucose-1-P guanylyltransferase

Bacteroides fragilis

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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 1–949 Chain B； UniProt 1–949	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 6 FMT FORMIC ACID × 4 MLA MALONIC ACID × 2 GOL GLYCEROL × 8 GDP GUANOSINE-5'-DIPHOSPHATE × 2 ACT ACETATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；8% Tascimate, 20% PEG 3350, 15mM GTP, 15mM MgCl2	Resolution 2.30 Å R-free 0.232

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 9IIT	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5YYS Cryo-EM structure of L-fucokinase, GDP-fucose pyrophosphorylase (FKP)in Bacteroides fragilis Deposited 2017-12-11	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–949（949 aa） Chain B 1–949（949 aa） Chain C 1–949（949 aa） Chain D 1–949（949 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
9IIP Fucokinase part of FKP with beta-L-fucose 1-phosphate Deposited 2024-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 531–949（419 aa） Fragment：fucokinase part	Not recorded	ED6 6-deoxy-1-O-phosphono-beta-L-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；295 K；PEG 3350, Trypton, HEPES, beta-L-fucose 1-phosphate, MnCl2	Resolution 2.45 Å R-free 0.217
9IIS GDP-fucose pyrophosphorylase part of FKP with a SUMO tag Deposited 2024-06-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–496（496 aa）	Not recorded	EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；295 K；PEG 3350, ammonium acetate, HEPES	Resolution 2.36 Å R-free 0.254

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q58T34_BACFG
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 21–969； UniProt 1–949 Author chain B； PDBConstruct 21–969； UniProt 1–949

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	9iit
Deposition date deposition_date	2024-06-21
Structure title title	Full length structure of FKP in complex with GTP and GDP
Keywords keywords	fucose, ATP, GTP, kinase, pyrophosphorylase, 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	39.60 Å
Radius of gyration Rg (electron density) rg_electron	38.82 Å
Forward intensity I(0) i0	676396000.00
Molecular weight molecular_weight	214250.0 kDa
Excluded volume excluded_volume	268620 Å³
Envelope volume envelope_volume	342700 Å³
Hydration-shell volume shell_volume	70887 Å³
Envelope diameter envelope_diameter	124.9 Å
Shell Rg shell_rg	46.72 Å
Envelope Rg envelope_rg	38.27 Å
Shape Rg shape_rg	38.81 Å
Total Rg total_rg	39.25 Å
Total atoms total_atoms	15083
Residues n_residues	1900
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	122.8 Å
Rg (real space) rg_real	39.27 Å
Rg uncertainty (real space) rg_real_error	0.78 Å
I(0) (real space) i0_real	6.7640e+08
I(0) uncertainty (real space) i0_real_error	1.1160e+07
Rg (reciprocal space) rg_reciprocal	39.48 Å
I(0) (reciprocal space) i0_reciprocal	676500000.0000
Solution quality estimate total_estimate	0.8939
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	52.2 Å
Skewness Skewness skewness	0.078
Kurtosis Kurtosis kurtosis	-0.500
Angular range angular_range	— – 0.2000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	93170000.0000
Real-space data points n_real_points	41
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.904; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.974; Smooth: 0.929

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (8)

Entity 1 Entity 1 polymer

Description description	L-fucokinase/L-fucose-1-P guanylyltransferase
Molecular weight formula_weight	107954.2 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	15926

MGSSHHHHHHSSGLVPRGSHMQKLLSLPSNLVQSFHELERVNRTDWFCTSDPVGKKLGSGGGTSWLLEECYNEYSDGATFGEWLEKEKRILLHAGGQSRRLPGYAPSGKILTPVPVFRWERGQHLGQNLLSLQLPLYEKIMSLAPDKLHTLIASGDVYIRSEKPLQSIPEADVVCYGLWVDPSLATHHGVFASDRKHPEQLDFMLQKPSLAELESLSKTHLFLMDIGIWLLSDRAVEILMKRSHKESSEELKYYDLYSDFGLALGTHPRIEDEEVNTLSVAILPLPGGEFYHYGTSKELISSTLSVQNKVYDQRRIMHRKVKPNPAMFVQNAVVRIPLCAENADLWIENSHIGPKWKIASRHIITGVPENDWSLAVPAGVCVDVVPMGDKGFVARPYGLDDVFKGDLRDSKTTLTGIPFGEWMSKRGLSYTDLKGRTDDLQAVSVFPMVNSVEELGLVLRWMLSEPELEEGKNIWLRSEHFSADEISAGANLKRLYAQREEFRKGNWKALAVNHEKSVFYQLDLADAAEDFVRLGLDMPELLPEDALQMSRIHNRMLRARILKLDGKDYRPEEQAAFDLLRDGLLDGISNRKSTPKLDVYSDQIVWGRSPVRIDMAGGWTDTPPYSLYSGGNVVNLAIELNGQPPLQVYVKPCKDFHIVLRSIDMGAMEIVSTFDELQDYKKIGSPFSIPKAALSLAGFAPAFSAVSYASLEEQLKDFGAGIEVTLLAAIPAGSGLGTSSILASTVLGAINDFCGLAWDKNEICQRTLVLEQLLTTGGGWQDQYGGVLQGVKLLQTEAGFAQSPLVRWLPDHLFTHPEYKDCHLLYYTGITRTAKGILAEIVSSMFLNSSLHLNLLSEMKAHALDMNEAIQRGSFVEFGRLVGKTWEQNKALDSGTNPPAVEAIIDLIKDYTLGYKLPGAGGGGYLYMVAKDPQAAVRIRKILTENAPNPRARFVEMTLSDKGFQVSRS

来源 Source

来源生物 organism	Bacteroides fragilis
NCBI Class编号 ncbi_taxonomy_id	817
宿主生物 host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 3 Entity 3 non-polymer

Description description	FORMIC ACID
Molecular weight formula_weight	46.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MALONIC ACID
Molecular weight formula_weight	104.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 6 Entity 6 non-polymer

Description description	GUANOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	443.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	843

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8. Citations (1)

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Unit-cell length a length_a	211.821 Å
Unit-cell length b length_b	96.061 Å
Unit-cell length c length_c	127.369 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	97.09 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	monoclinic

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	29.150 Å
R factor r_factor	0.2005
R_work r_work	0.1999
R_free r_free	0.2315

fit	/app/data/saxs_computation/ii/9iit/9iit.fit
pddf	/app/data/pr_computation/ii/9iit/9iit.pr.out
profile	/app/data/saxs_computation/ii/9iit/9iit.dat

Full length structure of FKP in complex with GTP and GDP

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

L-fucokinase/L-fucose-1-P guanylyltransferase

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