SAXSdb — 10zb

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

Serine hydroxymethyltransferase

Thermus thermophilus

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 3–407 Chain B； UniProt 3–407	Mutation：E53Q Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 1 SO4 SULFATE ION × 3 KOU (E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine × 1 THG (6S)-5,6,7,8-TETRAHYDROFOLATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；40 mM NaOAc, pH 5.5, 1M ammonium sulfate, 0.5M lithium sulfate	Resolution 1.80 Å R-free 0.185

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 10ZB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
10YN Joint X-ray/neutron structure of E53Q mutant of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT) Deposited 2026-02-12	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–407（405 aa） Chain B 3–407（405 aa）	Mutation：E53Q Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：E53Q Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 2	Experimental method not declared X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；40 mM NaOAc, pH 5.5, 1M ammonium sulfate, 0.5 M lithium sulfate	Resolution not provided
9O50 Room-temperature X-ray structure of Thermus thermophilus SHMT in complex with tetrahydrofolate (THF) Deposited 2025-04-09	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–407（405 aa） Chain B 3–407（405 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	SO4 SULFATE ION × 3 THG (6S)-5,6,7,8-TETRAHYDROFOLATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；40 mM sodium acetate pH 5.5, 1M ammonium sulfate and 0.5 M lithium sulfate	Resolution 1.80 Å R-free 0.175
9O5G Room-temperature joint X-ray/Neutron structure of Thermus thermophilus SHMT in complex with PLP-Gly external aldimine and 5-methyl-tetrahydrofolate (5MTHF) Deposited 2025-04-10	Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 3–407（405 aa） Chain B 3–407（405 aa）	Not recorded	SO4 SULFATE ION × 5 PLG N-GLYCINE-[3-HYDROXY-2-METHYL-5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] × 1 C2F 5-METHYL-5,6,7,8-TETRAHYDROFOLIC ACID × 1	Experimental method not declared X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5.5；289 K；50mM NaOAc, 0.5M Li2SO4, 1.0M Ammonium SO4	Resolution not provided

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

View Construct and Data Evidence

UniProt name	A0AAD1KUU5_THETH
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–405； UniProt 3–407 Author chain B； PDBConstruct 1–405； UniProt 3–407

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	10zb
Deposition date deposition_date	2026-02-12
Structure title title	Room-temperature X-ray structure of E53Q mutant of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT) in complex with PLP-L-Ser external aldimine and tetrahydrofolate (THF)
Keywords keywords	;homodimer, pyridoxal-5'-phosphate, one-carbon metabolism, inactive mutant, enzyme-substrate complex, 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	27.93 Å
Radius of gyration Rg (electron density) rg_electron	27.04 Å
Forward intensity I(0) i0	127257000.00
Molecular weight molecular_weight	89526.0 kDa
Excluded volume excluded_volume	112280 Å³
Envelope volume envelope_volume	128620 Å³
Hydration-shell volume shell_volume	38556 Å³
Envelope diameter envelope_diameter	91.5 Å
Shell Rg shell_rg	35.64 Å
Envelope Rg envelope_rg	27.27 Å
Shape Rg shape_rg	27.03 Å
Total Rg total_rg	27.88 Å
Total atoms total_atoms	6308
Residues n_residues	803
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	87.2 Å
Rg (real space) rg_real	27.86 Å
Rg uncertainty (real space) rg_real_error	0.50 Å
I(0) (real space) i0_real	1.2730e+08
I(0) uncertainty (real space) i0_real_error	1.6900e+06
Rg (reciprocal space) rg_reciprocal	27.88 Å
I(0) (reciprocal space) i0_reciprocal	127300000.0000
Solution quality estimate total_estimate	0.8928
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	32.1 Å
Skewness Skewness skewness	0.326
Kurtosis Kurtosis kurtosis	-0.335
Angular range angular_range	— – 0.2850 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	74280000.0000
Real-space data points n_real_points	58
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.858

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Serine hydroxymethyltransferase
Molecular weight formula_weight	44677.0 kDa
EC 编号 ec_number	2.1.2.1
Mutation mutation	E53Q
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	6760

STLKRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAQGYPGARYYGGCEVIDRVESLAIERAKALFGAAWANVQPHSGSQANMAVYMALMEPGDTLMGMDLAAGGHLTHGSRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGASAYPRFWDFKAFREIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGPRGGLILSNDPELGKRIDKLIFPGIQGGPLEHVIAGKAVAFFEALQPEFKEYSRLVVENAKRLAEELARRGYRIVTGGTDNHLFLVDLRPKGLTGKEAEERLDAVGITVNKNAIPFDPKPPRVTSGIRIGTPAITTRGFTPEEMPLVAELIDRALLEGPSEALREEVRRLALAHPMP

来源 Source

来源生物 organism	Thermus thermophilus
NCBI Class编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Serine hydroxymethyltransferase
Molecular weight formula_weight	44448.9 kDa
EC 编号 ec_number	2.1.2.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

STLKRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAQGYPGARYYGGCEVIDRVESLAIERAKALFGAAWANVQPHSGSQANMAVYMALMEPGDTLMGMDLAAGGHLTHGSRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGASAYPRFWDFKAFREIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGPRGGLILSNDPELGKRIDKLIFPGIQGGPLEHVIAGKAVAFFEALQPEFKEYSRLVVENAKRLAEELARRGYRIVTGGTDNHLFLVDLRPKGLTGKEAEERLDAVGITVNKNAIPFDPKPPRVTSGIRIGTPAITTRGFTPEEMPLVAELIDRALLEGPSEALREEVRRLALAHPMP

来源 Source

来源生物 organism	Thermus thermophilus
NCBI Class编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 5 Entity 5 non-polymer

Description description	(E)-N-({3-hydroxy-2-methyl-5-[(phosphonooxy)methyl]pyridin-4-yl}methylidene)-L-serine
Molecular weight formula_weight	334.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	(6S)-5,6,7,8-TETRAHYDROFOLATE
Molecular weight formula_weight	445.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	403

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8. Citations (1)

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Unit-cell length a length_a	58.859 Å
Unit-cell length b length_b	83.602 Å
Unit-cell length c length_c	95.338 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.69 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.800 Å
Low-resolution limit resolution_low	27.880 Å
R factor r_factor	0.1589
R_work r_work	0.1575
R_free r_free	0.1850

fit	/app/data/saxs_computation/0z/10zb/10zb.fit
pddf	/app/data/pr_computation/0z/10zb/10zb.pr.out
profile	/app/data/saxs_computation/0z/10zb/10zb.dat

Room-temperature X-ray structure of E53Q mutant of Thermus thermophilus serine hydroxymethyltransferase (TthSHMT) in complex with PLP-L-Ser external aldimine and tetrahydrofolate (THF)

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

Serine hydroxymethyltransferase

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

6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)