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9rwd

High-resolution structure of human SHMT2 with covalently bound PLP (internal aldimine)

Method: X-RAY DIFFRACTION D_max: 127.9 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9rwd
deposition_date	2025-07-09
last_revision	2025-08-13
title	High-resolution structure of human SHMT2 with covalently bound PLP (internal aldimine)
keywords	tetrahydrofolate, one-carbon metabolism, cancer therapy target, 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	40.25 Å
rg_electron	39.48 Å
i0	629702000.00
molecular_weight	204330.0 kDa
excluded_volume	255240 Å³
envelope_volume	315900 Å³
shell_volume	64883 Å³
envelope_diameter	131.7 Å
shell_rg	46.56 Å
envelope_rg	39.05 Å
shape_rg	39.47 Å
total_rg	39.87 Å
total_atoms	14515
n_residues	1815
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	127.9 Å
rg_real	40.19 Å
rg_real_error	1.03 Å
i0_real	6.2970e+08
i0_real_error	1.0720e+07
rg_reciprocal	40.25 Å
i0_reciprocal	629700000.0000
total_estimate	0.9048
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	42.6 Å
skewness	0.219
kurtosis	-0.712
angular_range	— – 0.1950 Å⁻¹
current_alpha	0.0000
highest_alpha	162000000.0000
n_real_points	40
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.933; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.992; Smooth: 0.967

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Serine hydroxymethyltransferase, mitochondrial
formula_weight	52945.0 kDa
ec_number	2.1.2.1
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	16687

SNAAQTQTGEANRGWTGQESLSDSDPEMWELLQREKDRQCRGLELIASENFCSRAALEALGSCLNNKYSEGYPGKRYYGGAEVVDEIELLCQRRALEAFDLDPAQWGVNVQPYSGSPANLAVYTALLQPHDRIMGLDLPDGGHLTHGYMSDVKRISATSIFFESMPYKLNPKTGLIDYNQLALTARLFRPRLIIAGTSAYARLIDYARMREVCDEVKAHLLADMAHISGLVAAKVIPSPFKHADIVTTTTHKTLRGARSGLIFYRKGVKAVDPKTGREIPYTFEDRINFAVFPSLQGGPHNHAIAAVAVALKQACTPMFREYSLQVLKNARAMADALLERGYSLVSGGTDNHLVLVDLRPKGLDGARAERVLELVSITANKNTCPGDRSAITPGGLRLGAPALTSRQFREDDFRRVVDFIDEGVNIGLEVKSKTAKLQDFKSFLLKDSETSQRLANLRQRVEQFARAFPMPGFDEH

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	17

Entity 3 non-polymer

description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
formula_weight	122.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	DI(HYDROXYETHYL)ETHER
formula_weight	106.1 kDa
src_method	nat
entity_count	2

Entity 5 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	nat
entity_count	4

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2113

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6. Citations (1)

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length_a	59.184 Å
length_b	125.571 Å
length_c	135.137 Å
angle_alpha	90.00 °
angle_beta	93.67 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	1.300 Å
resolution_low	59.060 Å
r_factor	0.1452
r_work	0.1452
r_free	0.1782

fit	/app/data/saxs_computation/rw/9rwd/9rwd.fit
pddf	/app/data/pr_computation/rw/9rwd/9rwd.pr.out
profile	/app/data/saxs_computation/rw/9rwd/9rwd.dat