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1d3v

;CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH 2(S)-AMINO-6-BORONOHEXANOIC ACID, AN L-ARGININE ANALOG ;

Method: X-RAY DIFFRACTION D_max: 117.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d3v
deposition_date	1999-10-01
title	;CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH 2(S)-AMINO-6-BORONOHEXANOIC ACID, AN L-ARGININE ANALOG ;
keywords	BINUCLEAR MANGANESE CLUSTER, BORONIC ACID INHIBITOR, PERFECTLY TWINNED CRYSTAL, HYDROLASE; HYDROLASE
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	38.28 Å
rg_electron	38.23 Å
i0	64683300.00
molecular_weight	67112.0 kDa
excluded_volume	84709 Å³
envelope_volume	112000 Å³
shell_volume	23820 Å³
envelope_diameter	117.2 Å
shell_rg	45.68 Å
envelope_rg	37.09 Å
shape_rg	38.23 Å
total_rg	38.65 Å
total_atoms	4718
n_residues	616
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	117.6 Å
rg_real	38.69 Å
rg_real_error	1.26 Å
i0_real	6.4680e+07
i0_real_error	1.2040e+06
rg_reciprocal	38.45 Å
i0_reciprocal	64670000.0000
total_estimate	0.5955
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	22.9 Å
skewness	0.222
kurtosis	-1.274
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	56510000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.041; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.248; Smooth: 0.367

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4. Crystallography & Experiment

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5. Entities & Polymer Info (4)

Entity 1 polymer

description	PROTEIN (ARGINASE)
formula_weight	35019.1 kDa
ec_number	3.5.3.1
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5015

MSSKPKPIEIIGAPFSKGQPRGGVEKGPAALRKAGLVEKLKETEYNVRDHGDLAFVDVPNDSPFQIVKNPRSVGKANEQLAAVVAETQKNGTISVVLGGDHSMAIGSISGHARVHPDLCVIWVDAHTDINTPLTTSSGNLHGQPVAFLLKELKGKFPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYIIKTLGIKYFSMTEVDKLGIGKVMEETFSYLLGRKKRPIHLSFDVDGLDPVFTPATGTPVVGGLSYREGLYITEEIYKTGLLSGLDIMEVNPTLGKTPEEVTRTVNTAVALTLSCFGTKREGNHKPETDYLKPPK

Source

organism	Rattus norvegicus
common_name	Norway rat
ncbi_taxonomy_id	10116
host_organism	Escherichia coli

Entity 2 non-polymer

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

Entity 3 non-polymer

description	2(S)-AMINO-6-BORONOHEXANOIC ACID
formula_weight	192.0 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	297

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6. Citations (1)

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length_a	91.300 Å
length_b	91.300 Å
length_c	69.900 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	6

space_group	P 3
int_tables_number	143
crystal_system	—

resolution	1.700 Å
resolution_low	20.000 Å
r_factor	0.1570
r_work	0.1570
r_free	0.1790

fit	/app/data/saxs_computation/d3/1d3v/1d3v.fit
pddf	/app/data/pr_computation/d3/1d3v/1d3v.pr.out
profile	/app/data/saxs_computation/d3/1d3v/1d3v.dat

;CRYSTAL STRUCTURE OF THE BINUCLEAR MANGANESE METALLOENZYME ARGINASE COMPLEXED WITH 2(S)-AMINO-6-BORONOHEXANOIC ACID, AN L-ARGININE ANALOG ;

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