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1c1d

L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE

Method: X-RAY DIFFRACTION D_max: 117.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1c1d
deposition_date	1999-07-21
title	L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE
keywords	AMINO ACID DEHYDROGENASE, OXIDATIVE DEAMINATION MECHANISM, 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	36.09 Å
rg_electron	36.01 Å
i0	90255200.00
molecular_weight	73560.0 kDa
excluded_volume	90708 Å³
envelope_volume	119290 Å³
shell_volume	27590 Å³
envelope_diameter	113.8 Å
shell_rg	42.34 Å
envelope_rg	35.28 Å
shape_rg	36.00 Å
total_rg	36.46 Å
total_atoms	5151
n_residues	697
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	117.3 Å
rg_real	36.36 Å
rg_real_error	1.00 Å
i0_real	9.0260e+07
i0_real_error	1.6160e+06
rg_reciprocal	36.20 Å
i0_reciprocal	90240000.0000
total_estimate	0.7557
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	26.7 Å
skewness	0.314
kurtosis	-0.969
angular_range	— – 0.2200 Å⁻¹
current_alpha	0.0000
highest_alpha	18190000.0000
n_real_points	45
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.481; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.503; Smooth: 0.875

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	L-PHENYLALANINE DEHYDROGENASE
formula_weight	36412.6 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6119

SIDSALNWDGEMTVTRFDAMTGAHFVIRLDSTQLGPAAGGTRAAQYSNLADALTDAGKLAGAMTLKMAVSNLPMGGGKSVIALPAPRHSIDPSTWARILRIHAENIDKLSGNYWTGPDVNTNSADMDTLNDTTEFVFGRSLERGGAGSSAFTTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCDVFAPCAMGGVITTEVARTLDCSVVAGAANNVIADEAASDILHARGILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAARTLAGRRAREASTTTATA

Source

organism	Rhodococcus sp.
ncbi_taxonomy_id	1831
host_organism	Escherichia coli BL21(DE3)

Entity 2 polymer

description	L-PHENYLALANINE DEHYDROGENASE
formula_weight	36442.7 kDa
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

SIDSALNWDGEMTVTRFDSMTGAHFVIRLDSTQLGPAAGGTRAAQYSQLADALTDAGKLAGAMTLKMAVSNLPMGGGKSVIALPAPRHSIDPSTWARILRIHAENIDKLSGNYWTGPDVNTNSADMDTLNDTTEFVFGRSLERGGAGSSAFTTAVGVFEAMKATVAHRGLGSLDGLTVLVQGLGAVGGSLASLAAEAGAQLLVADTDTERVAHAVALGHTAVALEDVLSTPCDVFAPCAMGGVITTEVARTLDCSVVAGAANNVIADEAASDILHARGILYAPDFVANAGGAIHLVGREVLGWSESVVHERAVAIGDTLNQVFEISDNDGVTPDEAARTLAGRRAREASTTTATA

Source

organism	Rhodococcus sp.
ncbi_taxonomy_id	1831
host_organism	Escherichia coli BL21(DE3)

Entity 3 non-polymer

description	POTASSIUM ION
formula_weight	39.1 kDa
src_method	syn
entity_count	4

Entity 4 non-polymer

description	PHENYLALANINE
formula_weight	165.2 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
formula_weight	665.4 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	SODIUM ION
formula_weight	23.0 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	PHOSPHATE ION
formula_weight	95.0 kDa
src_method	syn
entity_count	1

Entity 8 non-polymer

description	ISOPROPYL ALCOHOL
formula_weight	60.1 kDa
src_method	syn
entity_count	1

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	928

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6. Citations (1)

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length_a	64.800 Å
length_b	110.600 Å
length_c	113.300 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.250 Å
resolution_low	30.000 Å
r_factor	0.1950
r_work	0.1930
r_free	0.2380

fit	/app/data/saxs_computation/c1/1c1d/1c1d.fit
pddf	/app/data/pr_computation/c1/1c1d/1c1d.pr.out
profile	/app/data/saxs_computation/c1/1c1d/1c1d.dat

L-PHENYLALANINE DEHYDROGENASE STRUCTURE IN TERNARY COMPLEX WITH NADH AND L-PHENYLALANINE

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 (9)

Entity 1 polymer

Polymer

Source

Entity 2 polymer

Polymer

Source

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)