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1bdm

;THE STRUCTURE AT 1.8 ANGSTROMS RESOLUTION OF A SINGLE SITE MUTANT (T189I) OF MALATE DEHYDROGENASE FROM THERMUS FLAVUS WITH INCREASED ENZYMATIC ACTIVITY ;

Method: X-RAY DIFFRACTION D_max: 87.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1bdm
deposition_date	1993-02-16
title	;THE STRUCTURE AT 1.8 ANGSTROMS RESOLUTION OF A SINGLE SITE MUTANT (T189I) OF MALATE DEHYDROGENASE FROM THERMUS FLAVUS WITH INCREASED ENZYMATIC ACTIVITY ;
keywords	OXIDOREDUCTASE(NAD(A)-CHOH(D)); OXIDOREDUCTASE(NAD(A)-CHOH(D))
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	26.37 Å
i0	82216500.00
molecular_weight	70860.0 kDa
excluded_volume	88742 Å³
envelope_volume	104740 Å³
shell_volume	32862 Å³
envelope_diameter	93.3 Å
shell_rg	33.96 Å
envelope_rg	26.45 Å
shape_rg	26.39 Å
total_rg	27.09 Å
total_atoms	4975
n_residues	645
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	87.8 Å
rg_real	27.08 Å
rg_real_error	0.57 Å
i0_real	8.2220e+07
i0_real_error	1.1680e+06
rg_reciprocal	27.09 Å
i0_reciprocal	82220000.0000
total_estimate	0.8186
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	29.8 Å
skewness	0.334
kurtosis	-0.407
angular_range	— – 0.2950 Å⁻¹
current_alpha	0.0000
highest_alpha	31900000.0000
n_real_points	60
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.883; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	MALATE DEHYDROGENASE
formula_weight	35464.7 kDa
ec_number	1.1.1.37
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5197

MKAPVRVAVTGAAGQIGYSLLFRIAAGEMLGKDQPVILQLLEIPQAMKALEGVVMELEDCAFPLLAGLEATDDPDVAFKDADYALLVGAAPRKAGMERRDLLQVNGKIFTEQGRALAEVAKKDVKVLVVGNPANTNALIAYKNAPGLNPRNFTAMTRLDHNRAKAQLAKKTGTGVDRIRRMTVWGNHSSIMFPDLFHAEVDGRPALELVDMEWYEKVFIPTVAQRGAAIIQARGASSAASAANAAIEHIRDWALGTPEGDWVSMAVPSQGEYGIPEGIVYSFPVTAKDGAYRVVEGLEINEFARKRMEITAQELLDEMEQVKALGLI

Source

organism	Thermus thermophilus
ncbi_taxonomy_id	274

Entity 2 non-polymer

description	BETA-6-HYDROXY-1,4,5,6-TETRHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
formula_weight	683.5 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	202

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6. Citations (7)

;Determinants of protein thermostability observed in the 1.9-A crystal structure of malate dehydrogenase from the thermophilic bacterium Thermus flavus. ;

Biochemistry (1993)

PMID: 8471603 · DOI: 10.1021/bi00066a010 PRIMARY

Preliminary X-Ray Diffraction Analysis of a Crystallizable Mutant of Malate Dehydrogenase from the Thermophile Thermus Flavus

J.Mol.Biol. (1991)

Role of Threonine 190 in Modulating the Catalytic Function of Malate Dehydrogenase from a Thermophile Thermus Flavus

J.Biol.Chem. (1991)

Refined Crystal Structure of Cytoplasmic Malate Dehydrogenase at 2.5-Angstroms Resolution

Biochemistry (1989)

Nucleotide Sequence of the Malate Dehydrogenase Gene of Thermus Flavus and its Mutation Directing an Increase in Enzyme Activity

J.Biol.Chem. (1986)

Chemistry and Solution Conformation of the Pyridine Coenzymes

The Pyridine Nucleotide Coenzymes (1982)

Malate Dehydrogenase

The Enzymes,Third Edition (1975)

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length_a	71.750 Å
length_b	88.640 Å
length_c	118.970 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.800 Å
resolution_low	— Å
r_factor	0.1690
r_work	0.1690
r_free	—

fit	/app/data/saxs_computation/bd/1bdm/1bdm.fit
pddf	/app/data/pr_computation/bd/1bdm/1bdm.pr.out
profile	/app/data/saxs_computation/bd/1bdm/1bdm.dat