SAXSdb — 1e6y

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1. Structure Basics

entry_id	1e6y
deposition_date	2000-08-23
title	Methyl-coenzyme M reductase from Methanosarcina barkeri
keywords	BIOLOGICAL METHANOGENESIS, NI-ENZYME, OXIDOREDUCTASE, NI ENZYME; 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	38.00 Å
rg_electron	37.23 Å
i0	1148310000.00
molecular_weight	272400.0 kDa
excluded_volume	338030 Å³
envelope_volume	379170 Å³
shell_volume	78398 Å³
envelope_diameter	128.3 Å
shell_rg	47.20 Å
envelope_rg	37.55 Å
shape_rg	37.23 Å
total_rg	37.66 Å
total_atoms	19113
n_residues	2485
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	122.1 Å
rg_real	37.81 Å
rg_real_error	0.58 Å
i0_real	1.1480e+09
i0_real_error	1.8620e+07
rg_reciprocal	37.93 Å
i0_reciprocal	1148000000.0000
total_estimate	0.8837
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	46.5 Å
skewness	0.250
kurtosis	-0.368
angular_range	— – 0.2100 Å⁻¹
current_alpha	0.0001
highest_alpha	421300000.0000
n_real_points	43
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.916

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	METHYL-COENZYME M REDUCTASE SUBUNIT ALPHA
formula_weight	61951.7 kDa
ec_number	2.8.4.1
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	21340

AADIFSKFKKDMEVKFAQEFGSNKQTGGDITDKTAKFLRLGPEQDPRKVEMIKAGKEIAEKRGIAFYNPMMHSGAPLGQRAITPYTISGTDIVCEPDDLHYVNNAAMQQMWDDIRRTCIVGLDMAHETLEKRLGKEVTPETINHYLEVLNHAMPGAAVVQEMMVETHPALVDDCYVKVFTGDDALADEIDKQFLIDINKEFSEEQAAQIKASIGKTSWQAIHIPTIVSRTTDGAQTSRWAAMQIGMSFISAYAMCAGEAAVADLSFAAKHAALVSMGEMLPARRARGPNEPGGLSFGHLSDIVQTSRVSEDPAKIALEVVGAGCMLYDQIWLGSYMSGGVGFTQYATAAYTDDILDNNTYYDVDYINDKYNGAATVGKDNKVKASLEVVKDIATESTLYGIETYEKFPTALEDHFGGSQRATVLAAAAGVACSLATGNANAGLSGWYLSMYLHKEAWGRLGFFGFDLQDQCGATNVLSYQGDEGLPDELRGPNYPNYAMNVGHQGGYAGIAQAAHSGRGDAFTVNPLLKVCFADDLLPFNFAEPRREFGRGAIREFVPAGERSLVIPAK

Entity 2 polymer

description	METHYL-COENZYME M REDUCTASE I BETA SUBUNIT
formula_weight	45328.3 kDa
ec_number	2.8.4.1
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

SDTVDIYDDRGKLLESNVDIMSLAPTRNAAIQSIIMDTKRSVAVNLAGIQGALASGKMGGKGRQILGRGLNYDIVGNADAIAENVKKLVQVDEGDDTNVIKVKGGKSLLIQSPKSRIIAGADFMSATTVGAAAVTQTIMDMFGTDPYDAPIVKSAVWGSYPQTMDLMGGQVQGILSIPQNNEGLGFSLRNIMANHVAAISNRNAMNASALSSIYEQSGIFEMGGAVGMFERHQLLGLAYQGLNANNLLYDIVKENGKDGTIGTVIESVVRRAIEAGIISVDKTAPSGYNFYKANDVPKWNACAAVGTLAATLVNCGAGRAAQNVSSTLLYFNDILEKETGLPGCDYGKVEGTAVGFSFFSHSIYGGGGPGVFNGNHVVTRHSRGFAIPCVCAAVALDAGTQMFSIESTSGLIGDVFGAIPEFREPIKAVAGVL

Entity 3 polymer

description	METHYL-COENZYME M REDUCTASE SUBUNIT GAMMA
formula_weight	27769.2 kDa
ec_number	2.8.4.1
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,F

AYERQYYPGATSVAANRRKHMSGKLEKLREISDEDLTAVLGHRAPGSDYPSTHPPLAEMGEPACSTRENVAATPGAAAGDRVRYIQFADSMYNAPATPYFRSYFAAINFRGVDPGTLSGRQIVEARERDMEQCAKVQMETEITDHALAGVRGATVHGHSVRLQEDGVMFDMLDRRRLENGTIIMDKDQVAIPLDRKVDLGKPMSSEEAAKRTTIYRVDNVAFRDDAEVVEWVHRIFDQRTKFGFQPK

Entity 4 non-polymer

description	FACTOR 430
formula_weight	906.6 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	Coenzyme B
formula_weight	343.3 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	1-THIOETHANESULFONIC ACID
formula_weight	142.2 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	3

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	2195

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6. Citations (1)

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length_a	113.678 Å
length_b	153.099 Å
length_c	153.288 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	1.600 Å
resolution_low	30.000 Å
r_factor	0.1600
r_work	0.1600
r_free	0.1790

fit	/app/data/saxs_computation/e6/1e6y/1e6y.fit
pddf	/app/data/pr_computation/e6/1e6y/1e6y.pr.out
profile	/app/data/saxs_computation/e6/1e6y/1e6y.dat

Methyl-coenzyme M reductase from Methanosarcina barkeri

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 (8)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)