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9s3y

Crystal structure of ancestral (Methanococcaceae/A19) Malate dehydrogenase

Method: X-RAY DIFFRACTION D_max: 84.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s3y
deposition_date	2025-07-25
title	Crystal structure of ancestral (Methanococcaceae/A19) Malate dehydrogenase
keywords	Malate dehydrogenase, NADP binding domain, OXIDOREDUCTASE; OXIDOREDUCTASE
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	26.88 Å
rg_electron	26.04 Å
i0	81440800.00
molecular_weight	70523.0 kDa
excluded_volume	88214 Å³
envelope_volume	103990 Å³
shell_volume	32743 Å³
envelope_diameter	88.0 Å
shell_rg	34.05 Å
envelope_rg	26.32 Å
shape_rg	26.08 Å
total_rg	26.75 Å
total_atoms	9878
n_residues	623
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	84.5 Å
rg_real	26.84 Å
rg_real_error	0.56 Å
i0_real	8.1440e+07
i0_real_error	1.1010e+06
rg_reciprocal	26.85 Å
i0_reciprocal	81440000.0000
total_estimate	0.8250
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	30.1 Å
skewness	0.327
kurtosis	-0.384
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	26850000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.910; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	Malate dehydrogenase
formula_weight	34317.5 kDa
ec_number	1.1.1.299
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	10438

MKVSVIGASGRIGSAVSFLLAKEPYINHINLISREKSLNKLKGLKMDIYDALAASGRDADIEVHSDKDLSVVDGSDITIITAGVPRNGNMSRLDLAKENAKIVKNYARDIAKVCDTKLFMITNPVDVMTYKALIESGYEKNQVFGLGTHLDSMRFKVAIAKYFGVHIDDVRTRIIGEHGDTMVPLLSATAIGGIPINRLPNFENFPYEEVIDSVKNGGKKIIELKGGSEYGPASAIVNIVRCIANDEKRLLTLSAYLDGEIDGIKDVCIGVPVKVGKNGIEEVVPIKLEDDEFEAFKHSVEVVKEYCKEVKDI

Source

organism	Methanococcales
ncbi_taxonomy_id	2182
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 non-polymer

description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
formula_weight	745.4 kDa
src_method	syn
entity_count	2

Entity 3 non-polymer

description	MALONATE ION
formula_weight	102.0 kDa
src_method	syn
entity_count	12

Entity 4 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	436

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6. Citations (1)

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length_a	189.500 Å
length_b	189.500 Å
length_c	143.020 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	32

space_group	I 41 2 2
int_tables_number	98
crystal_system	tetragonal

resolution	2.050 Å
resolution_low	29.960 Å
r_factor	0.1697
r_work	0.1684
r_free	0.1950

fit	/app/data/saxs_computation/s3/9s3y/9s3y.fit
pddf	/app/data/pr_computation/s3/9s3y/9s3y.pr.out
profile	/app/data/saxs_computation/s3/9s3y/9s3y.dat