SAXSdb — 10zb

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1. Structure Basics

entry_id	10zb
deposition_date	2026-02-12
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	;homodimer, pyridoxal-5'-phosphate, one-carbon metabolism, inactive mutant, enzyme-substrate complex, TRANSFERASE ;; TRANSFERASE
method	X-RAY DIFFRACTION

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Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

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2. SAXS Parameters (CRYSOL)

rg_guinier	27.93 Å
rg_electron	27.04 Å
i0	127257000.00
molecular_weight	89526.0 kDa
excluded_volume	112280 Å³
envelope_volume	128620 Å³
shell_volume	38556 Å³
envelope_diameter	91.5 Å
shell_rg	35.64 Å
envelope_rg	27.27 Å
shape_rg	27.03 Å
total_rg	27.88 Å
total_atoms	6308
n_residues	803
n_harmonics	20
q_range	— – 0.5000 Å⁻¹
n_points	101
shell_type	directional
solvent_density	0.3340 e/Å³
contrast_shell	0.0300 e/Å³
crysol_version	4.1.3

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3. P(r) Analysis (GNOM)

dmax	87.2 Å
rg_real	27.86 Å
rg_real_error	0.50 Å
i0_real	1.2730e+08
i0_real_error	1.6900e+06
rg_reciprocal	27.88 Å
i0_reciprocal	127300000.0000
total_estimate	0.8928
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.1 Å
skewness	0.326
kurtosis	-0.335
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	74280000.0000
n_real_points	58
gnom_version	4.1.3
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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4. Crystallography & Experiment

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5. Entities & Polymer Info (7)

Entity 1 polymer

description	Serine hydroxymethyltransferase
formula_weight	44677.0 kDa
ec_number	2.1.2.1
mutation	E53Q
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6760

STLKRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAQGYPGARYYGGCEVIDRVESLAIERAKALFGAAWANVQPHSGSQANMAVYMALMEPGDTLMGMDLAAGGHLTHGSRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGASAYPRFWDFKAFREIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGPRGGLILSNDPELGKRIDKLIFPGIQGGPLEHVIAGKAVAFFEALQPEFKEYSRLVVENAKRLAEELARRGYRIVTGGTDNHLFLVDLRPKGLTGKEAEERLDAVGITVNKNAIPFDPKPPRVTSGIRIGTPAITTRGFTPEEMPLVAELIDRALLEGPSEALREEVRRLALAHPMP

Source

organism	Thermus thermophilus
ncbi_taxonomy_id	274
host_organism	Escherichia coli

Entity 2 polymer

description	Serine hydroxymethyltransferase
formula_weight	44448.9 kDa
ec_number	2.1.2.1
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

STLKRDEALFELIALEEKRQREGLELIASENFVSKQVREAVGSVLTNKYAQGYPGARYYGGCEVIDRVESLAIERAKALFGAAWANVQPHSGSQANMAVYMALMEPGDTLMGMDLAAGGHLTHGSRVNFSGKLYKVVSYGVRPDTELIDLEEVRRLALEHRPKVIVAGASAYPRFWDFKAFREIADEVGAYLVVDMAHFAGLVAAGLHPNPLPYAHVVTSTTHKTLRGPRGGLILSNDPELGKRIDKLIFPGIQGGPLEHVIAGKAVAFFEALQPEFKEYSRLVVENAKRLAEELARRGYRIVTGGTDNHLFLVDLRPKGLTGKEAEERLDAVGITVNKNAIPFDPKPPRVTSGIRIGTPAITTRGFTPEEMPLVAELIDRALLEGPSEALREEVRRLALAHPMP

Source

organism	Thermus thermophilus
ncbi_taxonomy_id	274
host_organism	Escherichia coli

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 5 non-polymer

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

Entity 6 non-polymer

description	(6S)-5,6,7,8-TETRAHYDROFOLATE
formula_weight	445.4 kDa
src_method	syn
entity_count	1

Entity 7 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	403

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6. Citations (1)

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length_a	58.859 Å
length_b	83.602 Å
length_c	95.338 Å
angle_alpha	90.00 °
angle_beta	91.69 °
angle_gamma	90.00 °
z_pdb	2

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.800 Å
resolution_low	27.880 Å
r_factor	0.1589
r_work	0.1575
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) ;

SAXS Profile

P(r) Distribution

1. Structure Basics

Download Data

2. SAXS Parameters (CRYSOL)

3. P(r) Analysis (GNOM)

4. Crystallography & Experiment

Unit Cell

Symmetry

Refinement

Diffraction

5. Entities & Polymer Info (7)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)