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9qcg

Crystal structure of Methanopyrus kandleri malate dehydrogenase mutant 4 at room temperature

Method: X-RAY DIFFRACTION D_max: 91.9 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9qcg
deposition_date	2025-03-04
last_revision	2025-03-19
title	Crystal structure of Methanopyrus kandleri malate dehydrogenase mutant 4 at room temperature
keywords	malate dehydrogenase, Rossmann-like motif, NAD(P)H binding site, 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	27.10 Å
rg_electron	26.23 Å
i0	76916400.00
molecular_weight	67784.0 kDa
excluded_volume	84691 Å³
envelope_volume	101530 Å³
shell_volume	31951 Å³
envelope_diameter	92.8 Å
shell_rg	33.82 Å
envelope_rg	26.50 Å
shape_rg	26.26 Å
total_rg	26.92 Å
total_atoms	9568
n_residues	608
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	91.9 Å
rg_real	27.08 Å
rg_real_error	0.61 Å
i0_real	7.6920e+07
i0_real_error	1.1450e+06
rg_reciprocal	27.09 Å
i0_reciprocal	76920000.0000
total_estimate	0.7994
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.6 Å
skewness	0.360
kurtosis	-0.345
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	26680000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.808; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.965; 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	34652.9 kDa
ec_number	1.1.1.299
mutation	D51H, R85Q, L146S, S228T, P232I
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	9688

MSKVAVIGATGRVGSTAAARLALLDCVNEVTLIARPKSVDKLRGLRRDILHSLAAAQKDAEITIGCERDDYVDADVIVMTAGIPQKPGQTRLDLTKDNAAIIKKYLEGVAEENPEAIVLVVTNPVDVLTYVALKVSGLPKNRVIGSGTHLDSMRFKVLIAKHFNVHMSEVHTRIIGEHGDTMVPVISSTSVGGIPVTRMPGWEDFDVEEAVREVKEAGQRIIETWGGTQFGIAQAITNLVRTILQDERRVLTVSAYLDGEIDGIRDVCIGVPARLGREGVLEIVPIELEEDEMRAFRRSVKVVKEATREAMEAISER

Source

organism	Methanopyrus kandleri
ncbi_taxonomy_id	2320
host_organism	Escherichia coli

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	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	2

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	120

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6. Citations (1)

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length_a	75.305 Å
length_b	75.305 Å
length_c	270.065 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	P 41 21 2
int_tables_number	92
crystal_system	tetragonal

resolution	2.390 Å
resolution_low	17.900 Å
r_factor	0.2651
r_work	0.2627
r_free	0.3089

fit	/app/data/saxs_computation/qc/9qcg/9qcg.fit
pddf	/app/data/pr_computation/qc/9qcg/9qcg.pr.out
profile	/app/data/saxs_computation/qc/9qcg/9qcg.dat