Crystal structure of Methanocaldococcus jannaschii Malate dehydrogenase C7 mutant

Method: X-RAY DIFFRACTION D_max: 98.7 Å Quality: EXCELLENT

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	9sa7
deposition_date	2025-08-07
title	Crystal structure of Methanocaldococcus jannaschii Malate dehydrogenase C7 mutant
keywords	Malate dehydrogenase, NADP binding domain, OXIDOREDUCTASE; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	33.29 Å
rg_electron	32.18 Å
i0	286402000.00
molecular_weight	137870.0 kDa
excluded_volume	173900 Å³
envelope_volume	216390 Å³
shell_volume	53628 Å³
envelope_diameter	97.1 Å
shell_rg	40.97 Å
envelope_rg	31.80 Å
shape_rg	32.18 Å
total_rg	32.90 Å
total_atoms	19562
n_residues	1233
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

▼

3. P(r) Analysis (GNOM)

dmax	98.7 Å
rg_real	33.08 Å
rg_real_error	0.59 Å
i0_real	2.8640e+08
i0_real_error	4.4560e+06
rg_reciprocal	33.22 Å
i0_reciprocal	286400000.0000
total_estimate	0.9097
solution_quality	EXCELLENT a EXCELLENT solution
n_peaks	2
r_peak_primary	45.2 Å
skewness	0.010
kurtosis	-0.655
angular_range	— – 0.2400 Å⁻¹
current_alpha	0.0000
highest_alpha	151900000.0000
n_real_points	49
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.957; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.972

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (2)

▶

6. Citations (1)

▶

length_a	87.764 Å
length_b	87.764 Å
length_c	338.338 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	24

space_group	P 32 2 1
int_tables_number	154
crystal_system	trigonal

resolution	2.800 Å
resolution_low	112.780 Å
r_factor	0.2167
r_work	0.2152
r_free	0.2464

description	L-2-hydroxycarboxylate dehydrogenase (NAD(P)(+))
formula_weight	34550.1 kDa
ec_number	1.1.1.375
mutation	E42K, E46M, K105N, D135E, R140K, K198R, K217Y, E219K, R223D, R278K, D250N, K306G
src_method	man
entity_count	4

type	polypeptide(L)
strand_id	A,B,D,C
atom_count	19562

Crystal structure of Methanocaldococcus jannaschii Malate dehydrogenase C7 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

5. Entities & Polymer Info (2)

Entity 1 polymer

Polymer

Source

Entity 2 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)

organism	Methanocaldococcaceae
ncbi_taxonomy_id	196117
host_organism	;Escherichia coli 'BL21-Gold(DE3)pLysS AG' ;

description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
formula_weight	745.4 kDa
src_method	syn
entity_count	4

fit	/app/data/saxs_computation/sa/9sa7/9sa7.fit
pddf	/app/data/pr_computation/sa/9sa7/9sa7.pr.out
profile	/app/data/saxs_computation/sa/9sa7/9sa7.dat