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9sd3

Crystal structure of Methanocaldococcus infernus Malate dehydrogenase

Method: X-RAY DIFFRACTION D_max: 138.5 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sd3
deposition_date	2025-08-12
title	Crystal structure of Methanocaldococcus infernus 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	42.61 Å
rg_electron	42.12 Å
i0	1101930000.00
molecular_weight	284650.0 kDa
excluded_volume	360880 Å³
envelope_volume	439980 Å³
shell_volume	83243 Å³
envelope_diameter	140.9 Å
shell_rg	50.04 Å
envelope_rg	41.74 Å
shape_rg	42.12 Å
total_rg	42.46 Å
total_atoms	40521
n_residues	2496
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	138.5 Å
rg_real	42.49 Å
rg_real_error	1.17 Å
i0_real	1.1020e+09
i0_real_error	2.0040e+07
rg_reciprocal	42.61 Å
i0_reciprocal	1102000000.0000
total_estimate	0.8871
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	52.4 Å
skewness	0.248
kurtosis	-0.441
angular_range	— – 0.1850 Å⁻¹
current_alpha	0.0000
highest_alpha	419000000.0000
n_real_points	38
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.874; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.989; Smooth: 0.918

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	Malate dehydrogenase (NADP(+))
formula_weight	34515.0 kDa
ec_number	1.1.1.82
src_method	man
entity_count	8

Polymer

type	polypeptide(L)
strand_id	A,B,C,D,E,F,G,H
atom_count	41357

MKVSIIGASGKVGSAISFLLANEPYVKELVLISREKSIDKLRGLREDIYDALAGTKRDCEINVSDDKTLKFLDGSDLVIITSGVPRTPEMSRLDLAKVNAKIIGNYAKKIAEICETKLFIITNPVDVMTYKAYIDSKFERNKVFGLGTHLDSLRFKVEIAKFFGVHIDEVRTRIIGEHGDTMVPLISSTSIGGIPITRFKSFKDLPLKDIIENVKNKGSKIIALKGGSEFGPAAAVLNVVRSIANNENRLLTLSTYLDGEFGFSDVCAGVPVKVGKDGVEIVTDIVFSKEEFEAFKYSIETIKRYCEEIKEL

Source

organism	Methanocaldococcus infernus
ncbi_taxonomy_id	67760
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	8

Entity 3 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	36

Entity 4 non-polymer

description	(4S)-2-METHYL-2,4-PENTANEDIOL
formula_weight	118.2 kDa
src_method	syn
entity_count	5

Entity 5 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	8

Entity 6 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	809

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6. Citations (1)

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length_a	208.180 Å
length_b	103.680 Å
length_c	177.400 Å
angle_alpha	90.00 °
angle_beta	123.97 °
angle_gamma	90.00 °
z_pdb	32

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.200 Å
resolution_low	66.910 Å
r_factor	0.1853
r_work	0.1836
r_free	0.2175

fit	/app/data/saxs_computation/sd/9sd3/9sd3.fit
pddf	/app/data/pr_computation/sd/9sd3/9sd3.pr.out
profile	/app/data/saxs_computation/sd/9sd3/9sd3.dat