SAXSdb — 1b85

▼

1. Structure Basics

entry_id	1b85
deposition_date	1999-02-05
title	LIGNIN PEROXIDASE
keywords	;LIGNIN DEGRADATION, HEME, RADICAL REACTION, ELECTRON TRANSFER, OXIDOREDUCTASE, Calcium, Cleavage on pair of basic residues, Disulfide bond, Glycoprotein, Hydrogen peroxide, Iron, Metal-binding, Peroxidase, Zymogen ;; OXIDOREDUCTASE
method	X-RAY DIFFRACTION

▼

Download Data

SAXS curve (.dat) P(r) distribution (.pr.out) Structure (CIF)

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	35.53 Å
rg_electron	35.64 Å
i0	89909500.00
molecular_weight	75320.0 kDa
excluded_volume	93582 Å³
envelope_volume	116420 Å³
shell_volume	29066 Å³
envelope_diameter	125.7 Å
shell_rg	38.89 Å
envelope_rg	35.38 Å
shape_rg	35.63 Å
total_rg	35.91 Å
total_atoms	5300
n_residues	693
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

▼

3. P(r) Analysis (GNOM)

dmax	123.5 Å
rg_real	35.99 Å
rg_real_error	1.08 Å
i0_real	8.9910e+07
i0_real_error	1.3080e+06
rg_reciprocal	35.71 Å
i0_reciprocal	89890000.0000
total_estimate	0.7240
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	27.4 Å
skewness	0.522
kurtosis	-0.632
angular_range	— – 0.2250 Å⁻¹
current_alpha	0.0000
highest_alpha	22050000.0000
n_real_points	46
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.402; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.384; Smooth: 0.817

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (4)

Entity 1 polymer

description	Ligninase H8
formula_weight	37441.7 kDa
ec_number	1.11.1.14
mutation	W171F SUBSTITUTION
src_method	man
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	5938

AAVIEKRATCSNGKTVGDASCCAWFDVLDDIQQNLFHGGQCGAEAHESIRLVFHDSIAISPAMEAQGKFGGGGADGSIMIFDDIETAFHPNIGLDEIVKLQKPFVQKHGVTPGDFIAFAGAVALSNCPGAPQMNFFTGRAPATQPAPDGLVPEPFHTVDQIINRVNDAGEFDELELVFMLSAHSVAAVNDVDPTVQGLPFDSTPGIFDSQFFVETQLRGTAFPGSGGNQGEVESPLPGEIRIQSDHTIARDSRTACEWQSFVNNQSKLVDDFQFIFLALTQLGQDPNAMTDCSDVIPQSKPIPGNLPFSFFPAGKTIKDVEQACAETPFPTLTTLPGPETSVQRIPPPPGA

Source

organism	Phanerochaete chrysosporium
common_name	White-rot fungus
ncbi_taxonomy_id	5306
host_organism	Escherichia coli

Entity 2 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	4

Entity 3 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	2

Entity 4 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	636

▶

6. Citations (3)

▶

length_a	73.400 Å
length_b	94.400 Å
length_c	230.990 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	16

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	1.850 Å
resolution_low	12.000 Å
r_factor	—
r_work	0.1420
r_free	0.1810

fit	/app/data/saxs_computation/b8/1b85/1b85.fit
pddf	/app/data/pr_computation/b8/1b85/1b85.pr.out
profile	/app/data/saxs_computation/b8/1b85/1b85.dat

LIGNIN PEROXIDASE

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