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1d5l

CRYSTAL STRUCTURE OF CYANIDE-BOUND HUMAN MYELOPEROXIDASE ISOFORM C AT PH 5.5

Method: X-RAY DIFFRACTION D_max: 111.6 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1d5l
deposition_date	1999-10-07
title	CRYSTAL STRUCTURE OF CYANIDE-BOUND HUMAN MYELOPEROXIDASE ISOFORM C AT PH 5.5
keywords	HEME-PROTEIN, PEROXIDASE, PEROXIDASE-CYANIDE 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	34.08 Å
rg_electron	33.44 Å
i0	291973000.00
molecular_weight	135250.0 kDa
excluded_volume	168160 Å³
envelope_volume	201510 Å³
shell_volume	49353 Å³
envelope_diameter	119.3 Å
shell_rg	40.95 Å
envelope_rg	33.59 Å
shape_rg	33.42 Å
total_rg	34.02 Å
total_atoms	9481
n_residues	1138
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	111.6 Å
rg_real	34.11 Å
rg_real_error	0.69 Å
i0_real	2.9200e+08
i0_real_error	4.7590e+06
rg_reciprocal	34.09 Å
i0_reciprocal	292000000.0000
total_estimate	0.8836
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	36.4 Å
skewness	0.389
kurtosis	-0.416
angular_range	— – 0.2300 Å⁻¹
current_alpha	0.0000
highest_alpha	105800000.0000
n_real_points	47
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.860; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.905

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4. Crystallography & Experiment

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5. Entities & Polymer Info (11)

Entity 1 polymer

description	MYELOPEROXIDASE
formula_weight	11903.3 kDa
ec_number	1.11.1.7
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,B
atom_count	10347

CPEQDKYRTITGMCNNRRSPTLGASNRAFVRWLPAEYEDGFSLPYGWTPGVKRNGFPVALARAVSNEIVRFPTDQLTPDQERSLMFMQWGQLLDHDLDFTPEPA

Entity 2 polymer

description	MYELOPEROXIDASE
formula_weight	53234.2 kDa
ec_number	1.11.1.7
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,D

VNCETSCVQQPPCFPLKIPPNDPRIKNQADCIPFFRSCPACPGSNITIRNQINALTSFVDASMVYGSEEPLARNLRNMSNQLGLLAVNQRFQDNGRALLPFDNLHDDPCLLTNRSARIPCFLAGDTRSSEMPELTSMHTLLLREHNRLATELKSLNPRWDGERLYQEARKIVGAMVQIITYRDYLPLVLGPTAMRKYLPTYRSYNDSVDPRIANVFTNAFRYGHTLIQPFMFRLDNRYQPMEPNPRVPLSRVFFASWRVVLEGGIDPILRGLMATPAKLNRQNQIAVDEIRERLFEQVMRIGLDLPALNMQRSRDHGLPGYNAWRRFCGLPQPETVGQLGTVLRNLKLARKLMEQYGTPNNIDIWMGGVSEPLKRKGRVGPLLACIIGTQFRKLRDGDRFWWENEGVFSMQQRQALAQISLPRIICDNTGITTVSKNNIFMSNSYPRDFVNCSTLPALNLASWREA

Entity 3 branched

description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ;
formula_weight	1057.0 kDa
src_method	man
entity_count	2

Entity 4 non-polymer

description	CHLORIDE ION
formula_weight	35.5 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	3

Entity 6 non-polymer

description	CYANIDE ION
formula_weight	26.0 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

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

Entity 8 non-polymer

description	2-acetamido-2-deoxy-beta-D-glucopyranose
formula_weight	221.2 kDa
src_method	man
entity_count	4

Entity 9 non-polymer

description	CALCIUM ION
formula_weight	40.1 kDa
src_method	syn
entity_count	2

Entity 10 non-polymer

description	ACETATE ION
formula_weight	59.0 kDa
src_method	syn
entity_count	7

Entity 11 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	866

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6. Citations (5)

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length_a	111.215 Å
length_b	63.507 Å
length_c	92.337 Å
angle_alpha	90.00 °
angle_beta	97.43 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.900 Å
resolution_low	30.000 Å
r_factor	0.1720
r_work	0.1720
r_free	0.2150

fit	/app/data/saxs_computation/d5/1d5l/1d5l.fit
pddf	/app/data/pr_computation/d5/1d5l/1d5l.pr.out
profile	/app/data/saxs_computation/d5/1d5l/1d5l.dat

CRYSTAL STRUCTURE OF CYANIDE-BOUND HUMAN MYELOPEROXIDASE ISOFORM C AT PH 5.5

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 (11)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 branched

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 water

6. Citations (5)

7. Files & Curves (10)

Files (7)

Curves (3)