SAXSdb — 11yz

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

GTP cyclohydrolase 1

Mycobacterium tuberculosis H37Rv

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 × 10 PDB declaration: decameric（10） Consistent with protein copy count	Chain A； UniProt 1–202 Chain B； UniProt 1–202 Chain C； UniProt 1–202 Chain D； UniProt 1–202 Chain E； UniProt 1–202 Chain F； UniProt 1–202 Chain G； UniProt 1–202 Chain H； UniProt 1–202 Chain I； UniProt 1–202 Chain J； UniProt 1–202	Not recorded	ZN ZINC ION × 10	ELECTRON MICROSCOPY cryo-EM buffer：pH 7；25 mM HEPES pH 7.0, 500 mM NaCl, 5% Glycerol, 2 mM DTT, 0.025% Azide cryo-EM vitrification conditions：Cryogen ETHANE	Resolution 2.77 Å

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 11YZ	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
9P8Z Crystal Structure of GTP cyclohydrolase 1 (FolE) from Mycobacterium tuberculosis Deposited 2025-06-23	Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain A 1–202（202 aa） Chain B 1–202（202 aa） Chain C 1–202（202 aa） Chain D 1–202（202 aa） Chain E 1–202（202 aa） Chain F 1–202（202 aa） Chain G 1–202（202 aa） Chain H 1–202（202 aa） Chain I 1–202（202 aa） Chain J 1–202（202 aa）	Not recorded	ZN ZINC ION × 10 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；JCSG+ B8: 0.2M Magnesium Chloride hexahydrate, 0.1M Tris pH 7.0, 10% PEG 8K. MytuD.00091.a.A1.PW39335 at 8.3 mg/mL. plate 19669 well B8 drop1, Puck: PSL-1009, Cryo: 80% crystallant + 20% PEG 200	Resolution 2.74 Å R-free 0.259
9P8Z Crystal Structure of GTP cyclohydrolase 1 (FolE) from Mycobacterium tuberculosis Deposited 2025-06-23	Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 10 PDB declaration: decameric	Chain K 1–202（202 aa） Chain L 1–202（202 aa） Chain M 1–202（202 aa） Chain N 1–202（202 aa） Chain O 1–202（202 aa） Chain P 1–202（202 aa） Chain Q 1–202（202 aa） Chain R 1–202（202 aa） Chain S 1–202（202 aa） Chain T 1–202（202 aa）	Not recorded	ZN ZINC ION × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；JCSG+ B8: 0.2M Magnesium Chloride hexahydrate, 0.1M Tris pH 7.0, 10% PEG 8K. MytuD.00091.a.A1.PW39335 at 8.3 mg/mL. plate 19669 well B8 drop1, Puck: PSL-1009, Cryo: 80% crystallant + 20% PEG 200	Resolution 2.74 Å R-free 0.259

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GCH1_MYCTU
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 22–223； UniProt 1–202 Author chain B； PDBConstruct 22–223； UniProt 1–202 Author chain C； PDBConstruct 22–223； UniProt 1–202 Author chain D； PDBConstruct 22–223； UniProt 1–202 Author chain E； PDBConstruct 22–223； UniProt 1–202 Author chain F； PDBConstruct 22–223； UniProt 1–202 Author chain G； PDBConstruct 22–223； UniProt 1–202 Author chain H； PDBConstruct 22–223； UniProt 1–202 Author chain I； PDBConstruct 22–223； UniProt 1–202 Author chain J； PDBConstruct 22–223； UniProt 1–202

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	11yz
Deposition date deposition_date	2026-03-19
Structure title title	Cryo EM Structure of GTP cyclohydrolase 1 (FolE) from Mycobacterium tuberculosis
Keywords keywords	;SSGCID, STRUCTURAL GENOMICS, SEATTLE STRUCTURAL GENOMICS CENTER FOR INFECTIOUS DISEASE, GTP CYCLOHYDROLASE 1, MYCOBACTERIUM TUBERCULOSIS, HYDROLASE ;; HYDROLASE
Experimental Method method	ELECTRON MICROSCOPY

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

Radius of gyration Rg (Guinier) rg_guinier	44.25 Å
Radius of gyration Rg (electron density) rg_electron	43.25 Å
Forward intensity I(0) i0	659424000.00
Molecular weight molecular_weight	208640.0 kDa
Excluded volume excluded_volume	260250 Å³
Envelope volume envelope_volume	374960 Å³
Hydration-shell volume shell_volume	70523 Å³
Envelope diameter envelope_diameter	125.9 Å
Shell Rg shell_rg	51.57 Å
Envelope Rg envelope_rg	40.65 Å
Shape Rg shape_rg	43.28 Å
Total Rg total_rg	43.53 Å
Total atoms total_atoms	14610
Residues n_residues	1880
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	118.4 Å
Rg (real space) rg_real	43.95 Å
Rg uncertainty (real space) rg_real_error	0.69 Å
I(0) (real space) i0_real	6.5940e+08
I(0) uncertainty (real space) i0_real_error	1.0560e+07
Rg (reciprocal space) rg_reciprocal	44.25 Å
I(0) (reciprocal space) i0_reciprocal	659600000.0000
Solution quality estimate total_estimate	0.8451
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	69.1 Å
Skewness Skewness skewness	-0.069
Kurtosis Kurtosis kurtosis	-0.761
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	107600000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.994; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.002

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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8. Citations (1)

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	—

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

Resolution resolution	2.770 Å
Low-resolution limit resolution_low	— Å
R factor r_factor	—
R_work r_work	—
R_free r_free	—

Resolution resolution	2.77 Å
Resolution测定方法 resolution_method	—
颗粒数 num_particles	565880

Description description	GTP cyclohydrolase 1
Molecular weight formula_weight	24717.2 kDa
EC 编号 ec_number	3.5.4.16
Source method src_method	man
Copy count entity_count	10

Cryo EM Structure of GTP cyclohydrolase 1 (FolE) from Mycobacterium tuberculosis

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

GTP cyclohydrolase 1

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

冷冻电镜 EM 3D

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J
Atom count atom_count	14610

来源生物 organism	Mycobacterium tuberculosis H37Rv
NCBI Class编号 ncbi_taxonomy_id	83332
宿主生物 host_organism	Escherichia coli BL21(DE3)

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	10

fit	/app/data/saxs_computation/1y/11yz/11yz.fit
pddf	/app/data/pr_computation/1y/11yz/11yz.pr.out
profile	/app/data/saxs_computation/1y/11yz/11yz.dat