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1dvr

STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP

Method: X-RAY DIFFRACTION D_max: 82.7 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1dvr
deposition_date	1995-12-14
title	STRUCTURE OF A MUTANT ADENYLATE KINASE LIGATED WITH AN ATP-ANALOGUE SHOWING DOMAIN CLOSURE OVER ATP
keywords	NUCLEOSIDE MONOPHOSPHATE KINASE, MYOKINASE, TRANSFERASE (PHOSPHOTRANSFERASE); TRANSFERASE (PHOSPHOTRANSFERASE)
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	24.91 Å
rg_electron	24.16 Å
i0	42217200.00
molecular_weight	49032.0 kDa
excluded_volume	60986 Å³
envelope_volume	74522 Å³
shell_volume	26021 Å³
envelope_diameter	81.2 Å
shell_rg	30.84 Å
envelope_rg	23.97 Å
shape_rg	24.21 Å
total_rg	24.77 Å
total_atoms	3432
n_residues	440
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	82.7 Å
rg_real	24.86 Å
rg_real_error	0.56 Å
i0_real	4.2220e+07
i0_real_error	5.9120e+05
rg_reciprocal	24.87 Å
i0_reciprocal	42220000.0000
total_estimate	0.8134
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	28.9 Å
skewness	0.276
kurtosis	-0.513
angular_range	— – 0.3200 Å⁻¹
current_alpha	0.0000
highest_alpha	7605000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.867; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.000

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4. Crystallography & Experiment

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5. Entities & Polymer Info (3)

Entity 1 polymer

description	ADENYLATE KINASE
formula_weight	24008.5 kDa
ec_number	2.7.4.3
mutation	D89V, R165I
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	3593

SSESIRMVLIGPPGAGKGTQAPNLQERFHAAHLATGDMLRSQIAKGTQLGLEAKKIMDQGGLVSDDIMVNMIKDELTNNPACKNGFILVGFPRTIPQAEKLDQMLKEQGTPLEKAIELKVDDELLVARITGRLIHPASGRSYHKIFNPPKEDMKDDVTGEALVQISDDNADALKKRLAAYHAQTEPIVDFYKKTGIWAGVDASQPPATVWADILNKLGKN

Source

organism	Saccharomyces cerevisiae
common_name	;baker's yeast ;
ncbi_taxonomy_id	4932
host_organism	Escherichia coli

Entity 2 non-polymer

description	PHOSPHODIFLUOROMETHYLPHOSPHONIC ACID-ADENYLATE ESTER
formula_weight	541.2 kDa
src_method	syn
entity_count	2

Entity 3 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	161

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6. Citations (7)

Structure of a mutant adenylate kinase ligated with an ATP-analogue showing domain closure over ATP.

J.Mol.Biol. (1996)

PMID: 8594191 · DOI: 10.1006/jmbi.1996.0080 PRIMARY

Stability, Activity and Structure of Adenylate Kinase Mutants

Eur.J.Biochem. (1995)

High-Resolution Structures of Adenylate Kinase from Yeast Ligated with Inhibitor Ap5A, Showing the Pathway of Phosphoryl Transfer

Protein Sci. (1995)

Movie of the Structural Changes During a Catalytic Cycle of Nucleoside Monophosphate Kinases

Structure (1995)

;The C-DNA Sequence Encoding Cytosolic Adenylate Kinase from Baker'S Yeast (Saccharomyces Cerevisiae) ;

Nucleic Acids Res. (1987)

Structure of the Complex of Yeast Adenylate Kinase with the Inhibitor Ap5A at 2.6 Angstroms Resolution

J.Mol.Biol. (1987)

;The Complete Amino Acid Sequence of Adenylate Kinase from Baker'S Yeast ;

Eur.J.Biochem. (1986)

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length_a	47.800 Å
length_b	73.400 Å
length_c	118.800 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	2.360 Å
resolution_low	10.000 Å
r_factor	0.1910
r_work	0.1910
r_free	—

fit	/app/data/saxs_computation/dv/1dvr/1dvr.fit
pddf	/app/data/pr_computation/dv/1dvr/1dvr.pr.out
profile	/app/data/saxs_computation/dv/1dvr/1dvr.dat