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1f06

;THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE ;

Method: X-RAY DIFFRACTION D_max: 88.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1f06
deposition_date	2000-05-14
title	;THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE ;
keywords	Enzyme-NADPH-inhibitor ternary complex, 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	27.71 Å
rg_electron	26.83 Å
i0	92774000.00
molecular_weight	71924.0 kDa
excluded_volume	88315 Å³
envelope_volume	106040 Å³
shell_volume	33203 Å³
envelope_diameter	94.0 Å
shell_rg	33.97 Å
envelope_rg	27.07 Å
shape_rg	26.83 Å
total_rg	27.51 Å
total_atoms	5059
n_residues	640
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	88.6 Å
rg_real	27.70 Å
rg_real_error	0.60 Å
i0_real	9.2770e+07
i0_real_error	1.4070e+06
rg_reciprocal	27.70 Å
i0_reciprocal	92770000.0000
total_estimate	0.8933
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	31.1 Å
skewness	0.363
kurtosis	-0.311
angular_range	— – 0.2850 Å⁻¹
current_alpha	0.0000
highest_alpha	17910000.0000
n_real_points	58
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.894

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	MESO-DIAMINOPIMELATE D-DEHYDROGENASE
formula_weight	35242.3 kDa
ec_number	1.4.1.16
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5175

MTNIRVAIVGYGNLGRSVEKLIAKQPDMDLVGIFSRRATLDTKTPVFDVADVDKHADDVDVLFLCMGSATDIPEQAPKFAQFACTVDTYDNHRDIPRHRQVMNEAATAAGNVALVSTGWDPGMFSINRVYAAAVLAEHQQHTFWGPGLSQGHSDALRRIPGVQKAVQYTLPSEDALEKARRGEAGDLTGKQTHKRQCFVVADAADHERIENDIRTMPDYFVGYEVEVNFIDEATFDSEHTGMPHGGHVITTGDTGGFNHTVEYILKLDRNPDFTASSQIAFGRAAHRMKQQGQSGAFTVLEVAPYLLSPENLDDLIARDV

Source

organism	Corynebacterium glutamicum
ncbi_taxonomy_id	1718
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	L-2-AMINO-6-METHYLENE-PIMELIC ACID
formula_weight	187.2 kDa
src_method	syn
entity_count	1

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	116

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6. Citations (1)

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length_a	75.547 Å
length_b	65.591 Å
length_c	84.281 Å
angle_alpha	90.00 °
angle_beta	106.52 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	2.100 Å
resolution_low	48.600 Å
r_factor	0.1850
r_work	0.1790
r_free	0.2090

fit	/app/data/saxs_computation/f0/1f06/1f06.fit
pddf	/app/data/pr_computation/f0/1f06/1f06.pr.out
profile	/app/data/saxs_computation/f0/1f06/1f06.dat

;THREE DIMENSIONAL STRUCTURE OF THE TERNARY COMPLEX OF CORYNEBACTERIUM GLUTAMICUM DIAMINOPIMELATE DEHYDROGENASE NADPH-L-2-AMINO-6-METHYLENE-PIMELATE ;

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