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9sc9

Crystal structure of Methanocaldococcus jannaschii Malate dehydrogenase C7GP mutant

Method: X-RAY DIFFRACTION D_max: 108.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9sc9
deposition_date	2025-08-09
title	Crystal structure of Methanocaldococcus jannaschii Malate dehydrogenase C7GP mutant
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	33.85 Å
rg_electron	33.32 Å
i0	284583000.00
molecular_weight	138170.0 kDa
excluded_volume	174270 Å³
envelope_volume	214320 Å³
shell_volume	52070 Å³
envelope_diameter	117.5 Å
shell_rg	41.32 Å
envelope_rg	33.04 Å
shape_rg	33.37 Å
total_rg	33.78 Å
total_atoms	19569
n_residues	1242
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	108.2 Å
rg_real	33.69 Å
rg_real_error	0.89 Å
i0_real	2.8460e+08
i0_real_error	4.3200e+06
rg_reciprocal	33.79 Å
i0_reciprocal	284600000.0000
total_estimate	0.8955
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	46.0 Å
skewness	0.146
kurtosis	-0.440
angular_range	— – 0.2350 Å⁻¹
current_alpha	0.0000
highest_alpha	152800000.0000
n_real_points	48
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.884; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.988

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
formula_weight	35054.6 kDa
ec_number	1.1.1.375
mutation	P24S, E42K, E46M, R56G, P85A, K105N, D135E, K137G, R140K, K198R, T216G, K217Y, E219K, R223D, D266G, R277K, D289N, A295G, K305G
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	19569

MKVTIIGASGRVGSATALLLAKESFMKDLVLIGREHSINKLKGLRMDIYDALAGTGSDANIYVESDENLRIIDESDVVIITSGVARKEGMSRMDLAKTNAKIVGNYAKKIAEICDTKIFVITNPVDVMTYKALVESGFEKNQVFGLGTHLDSLRFKVAIAKFFGVHIDEVRTRIIGEHGDSMVPLLSATSIGGIPIQRFERFKELPIDEIIEDVKGYGKQIIDLKGGSEFGPAAAILNVVRCIVNNEKRLLTLSAYVDGEFDGIRGVCIGVPVKIGKDGIEEVVSIELNKDEIIGFRKSAEIIKGYCEEVKNLHHHHHH

Source

organism	Methanocaldococcus jannaschii
ncbi_taxonomy_id	2190
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	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	4

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6. Citations (1)

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length_a	73.992 Å
length_b	75.534 Å
length_c	118.502 Å
angle_alpha	90.00 °
angle_beta	95.57 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 1 21 1
int_tables_number	4
crystal_system	monoclinic

resolution	2.900 Å
resolution_low	117.940 Å
r_factor	0.2068
r_work	0.2049
r_free	0.2458

fit	/app/data/saxs_computation/sc/9sc9/9sc9.fit
pddf	/app/data/pr_computation/sc/9sc9/9sc9.pr.out
profile	/app/data/saxs_computation/sc/9sc9/9sc9.dat

Crystal structure of Methanocaldococcus jannaschii Malate dehydrogenase C7GP mutant

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