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9s3k

Crystal structure of ancestral (Methanocaldococcaceae/A34) Malate dehydrogenase

Method: X-RAY DIFFRACTION D_max: 91.6 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9s3k
deposition_date	2025-07-24
title	Crystal structure of ancestral (Methanocaldococcaceae/A34) 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	31.73 Å
rg_electron	30.41 Å
i0	287931000.00
molecular_weight	138510.0 kDa
excluded_volume	174680 Å³
envelope_volume	199150 Å³
shell_volume	51508 Å³
envelope_diameter	92.7 Å
shell_rg	39.79 Å
envelope_rg	30.45 Å
shape_rg	30.43 Å
total_rg	31.09 Å
total_atoms	19605
n_residues	1239
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	91.6 Å
rg_real	31.45 Å
rg_real_error	0.38 Å
i0_real	2.8790e+08
i0_real_error	4.0150e+06
rg_reciprocal	31.57 Å
i0_reciprocal	288000000.0000
total_estimate	0.9055
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	42.1 Å
skewness	0.023
kurtosis	-0.640
angular_range	— – 0.2500 Å⁻¹
current_alpha	0.0000
highest_alpha	176900000.0000
n_real_points	51
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.973; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.868

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	Malate dehydrogenase
formula_weight	34538.9 kDa
ec_number	1.1.1.299
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	19708

MKVSVIGASGRIGSAVSFLLAKEPYIKDLVLISREKSLNKLKGLKMDIYDALAGTRSDANIEVHSDKDLSVVDGSDIVIITAGVPRKEDMSRLDLAKINAKIVGNYAREIAKVCDTKLFIITNPVDVMTYKALIESNYERNQVFGLGTHLDSLRFKVAIAKFFGVHIDDVRTRIIGEHGDTMVPLLSATSIGGIPINRLPNFENFPYEEVIDDVKNKGKKIIKLKGGSEFGPASAIINIVRCIANDEKRLLTLSAYLDGEIDGIRDVCIGVPVKVGKNGIEEVVPIKLEDDEFEAFRHSVEVVKEYCEEVKDI

Source

organism	Methanocaldococcaceae
ncbi_taxonomy_id	196117
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	4

Entity 3 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	4

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	103

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6. Citations (1)

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length_a	91.904 Å
length_b	102.990 Å
length_c	129.853 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 21 21 21
int_tables_number	19
crystal_system	orthorhombic

resolution	2.700 Å
resolution_low	80.690 Å
r_factor	0.2009
r_work	0.1985
r_free	0.2489

fit	/app/data/saxs_computation/s3/9s3k/9s3k.fit
pddf	/app/data/pr_computation/s3/9s3k/9s3k.pr.out
profile	/app/data/saxs_computation/s3/9s3k/9s3k.dat

Crystal structure of ancestral (Methanocaldococcaceae/A34) Malate dehydrogenase

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