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1do8

CRYSTAL STRUCTURE OF A CLOSED FORM OF HUMAN MITOCHONDRIAL NAD(P)+-DEPENDENT MALIC ENZYME

Method: X-RAY DIFFRACTION D_max: 142.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1do8
deposition_date	1999-12-19
title	CRYSTAL STRUCTURE OF A CLOSED FORM OF HUMAN MITOCHONDRIAL NAD(P)+-DEPENDENT MALIC ENZYME
keywords	;Oxidative Decarboxylase, Four domains: one with Rossmann fold, one with parallel alpha-beta fold, one mostly helical, and one mostly extended, 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	44.20 Å
rg_electron	44.12 Å
i0	975471000.00
molecular_weight	256760.0 kDa
excluded_volume	319850 Å³
envelope_volume	395310 Å³
shell_volume	74975 Å³
envelope_diameter	148.3 Å
shell_rg	48.39 Å
envelope_rg	44.06 Å
shape_rg	44.14 Å
total_rg	44.21 Å
total_atoms	17848
n_residues	2156
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	142.6 Å
rg_real	44.17 Å
rg_real_error	1.07 Å
i0_real	9.7550e+08
i0_real_error	1.6790e+07
rg_reciprocal	44.20 Å
i0_reciprocal	975500000.0000
total_estimate	0.8711
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	51.5 Å
skewness	0.290
kurtosis	-0.382
angular_range	— – 0.1800 Å⁻¹
current_alpha	0.0000
highest_alpha	185000000.0000
n_real_points	37
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.920; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.561

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4. Crystallography & Experiment

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5. Entities & Polymer Info (5)

Entity 1 polymer

description	MALIC ENZYME
formula_weight	63893.2 kDa
ec_number	1.1.1.39
mutation	METHIONINES REPLACED BY SELENOMETHIONINES
src_method	man
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,B,C,D
atom_count	18807

IKEKGKPLMLNPRTNKGMAFTLQERQMLGLQGLLPPKIETQDIQALRFHRNLKKMTSPLEKYIYIMGIQERNEKLFYRILQDDIESLMPIVYTPTVGLACSQYGHIFRRPKGLFISISDRGHVRSIVDNWPENHVKAVVVTDGERILGLGDLGVYGMGIPVGKLCLYTACAGIRPDRCLPVCIDVGTDNIALLKDPFYMGLYQKRDRTQQYDDLIDEFMKAITDRYGRNTLIQFEDFGNHNAFRFLRKYREKYCTFNDDIQGTAAVALAGLLAAQKVISKPISEHKILFLGAGEAALGIANLIVMSMVENGLSEQEAQKKIWMFDKYGLLVKGRKAKIDSYQEPFTHSAPESIPDTFEDAVNILKPSTIIGVAGAGRLFTPDVIRAMASINERPVIFALSNPTAQAECTAEEAYTLTEGRCLFASGSPFGPVKLTDGRVFTPGQGNNVYIFPGVALAVILCNTRHISDSVFLEAAKALTSQLTDEELAQGRLYPPLANIQEVSINIAIKVTEYLYANKMAFRYPEPEDKAKYVKERTWRSEYDSLLPDVYEWPESASSPPVITE

Source

organism	Homo sapiens
common_name	human
ncbi_taxonomy_id	9606
host_organism	Escherichia coli

Entity 2 non-polymer

description	OXALATE ION
formula_weight	88.0 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	MANGANESE (II) ION
formula_weight	54.9 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	NICOTINAMIDE-ADENINE-DINUCLEOTIDE
formula_weight	663.4 kDa
src_method	syn
entity_count	8

Entity 5 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	959

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6. Citations (1)

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length_a	229.000 Å
length_b	118.700 Å
length_c	113.000 Å
angle_alpha	90.00 °
angle_beta	109.60 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 1 2 1
int_tables_number	5
crystal_system	—

resolution	2.200 Å
resolution_low	20.000 Å
r_factor	0.2140
r_work	0.2040
r_free	0.2630

fit	/app/data/saxs_computation/do/1do8/1do8.fit
pddf	/app/data/pr_computation/do/1do8/1do8.pr.out
profile	/app/data/saxs_computation/do/1do8/1do8.dat