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9s89

N-terminal 40kDa fragment of human PMS2 with covalent ligand NP1867

Method: X-RAY DIFFRACTION D_max: 73.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s89
deposition_date	2025-08-05
last_revision	2026-06-03
title	N-terminal 40kDa fragment of human PMS2 with covalent ligand NP1867
keywords	Mismatch Repair MMR MutL PMS2 GHKL ATPase, DNA BINDING PROTEIN; DNA BINDING PROTEIN
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	22.44 Å
rg_electron	21.79 Å
i0	33208700.00
molecular_weight	29617.0 kDa
excluded_volume	28585 Å³
envelope_volume	48193 Å³
shell_volume	19248 Å³
envelope_diameter	74.5 Å
shell_rg	27.43 Å
envelope_rg	21.89 Å
shape_rg	21.76 Å
total_rg	22.41 Å
total_atoms	2237
n_residues	288
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	73.5 Å
rg_real	22.47 Å
rg_real_error	0.47 Å
i0_real	3.3210e+07
i0_real_error	4.7090e+05
rg_reciprocal	22.47 Å
i0_reciprocal	33210000.0000
total_estimate	0.8956
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	23.4 Å
skewness	0.353
kurtosis	-0.490
angular_range	— – 0.3550 Å⁻¹
current_alpha	0.0000
highest_alpha	4394000.0000
n_real_points	67
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.958; Smooth: 0.986

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Mismatch repair endonuclease PMS2
formula_weight	40657.4 kDa
ec_number	3.1.-.-
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	2404

GSMERAESSSTEPAKAIKPIDRKSVHQICSGQVVLSLSTAVKELVENSLDAGATNIDLKLKDYGVDLIEVSDNGCGVEEENFEGLTLKHHTSKIQEFADLTQVETFGFRGEALSSLCALSDVTISTCHASAKVGTRLMFDHNGKIIQKTPYPRPRGTTVSVQQLFSTLPVRHKEFQRNIKKEYAKMVQVLHAYCIISAGIRVSCTNQLGQGKRQPVVCTGGSPSIKENIGSVFGQKQLQSLIPFVQLPPSDSVCEEYGLSCSDALHNLFYISGFISQCTHGVGRSSTDRQFFFINRRPCDPAKVCRLVNEVYHMYNRHQYPFVVLNISVDSECVDINVTPDKRQILLQEEKLLLAVLKTSLIGMFDS

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Spodoptera frugiperda

Entity 2 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	3

Entity 3 non-polymer

description	DIMETHYL SULFOXIDE
formula_weight	78.1 kDa
src_method	syn
entity_count	1

Entity 4 non-polymer

description	~{N}-[2-[2-(cyclohexylmethoxy)-3-methyl-4,6-bis(oxidanyl)phenyl]carbonyl-1,3-dihydroisoindol-4-yl]-4-(dimethylamino)butanamide
formula_weight	509.6 kDa
src_method	syn
entity_count	1

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	95

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6. Citations (1)

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length_a	82.292 Å
length_b	82.292 Å
length_c	110.801 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 31 2 1
int_tables_number	152
crystal_system	—

resolution	2.000 Å
resolution_low	38.602 Å
r_factor	—
r_work	0.2050
r_free	0.2293

fit	/app/data/saxs_computation/s8/9s89/9s89.fit
pddf	/app/data/pr_computation/s8/9s89/9s89.pr.out
profile	/app/data/saxs_computation/s8/9s89/9s89.dat