SAXSdb — 1e6v

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1. Structure Basics

entry_id	1e6v
deposition_date	2000-08-23
title	Methyl-coenzyme M reductase from Methanopyrus kandleri
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	38.37 Å
rg_electron	37.54 Å
i0	1150980000.00
molecular_weight	276120.0 kDa
excluded_volume	343710 Å³
envelope_volume	393330 Å³
shell_volume	80454 Å³
envelope_diameter	129.1 Å
shell_rg	47.64 Å
envelope_rg	37.92 Å
shape_rg	37.58 Å
total_rg	37.92 Å
total_atoms	19402
n_residues	2458
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	122.7 Å
rg_real	38.18 Å
rg_real_error	0.75 Å
i0_real	1.1510e+09
i0_real_error	1.8110e+07
rg_reciprocal	38.30 Å
i0_reciprocal	1151000000.0000
total_estimate	0.8804
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	47.9 Å
skewness	0.255
kurtosis	-0.330
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	556800000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.864; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.978; Smooth: 0.872

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4. Crystallography & Experiment

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5. Entities & Polymer Info (6)

Entity 1 polymer

description	METHYL-COENZYME M REDUCTASE I ALPHA SUBUNIT
formula_weight	61398.3 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	19402

MSSAEEKLFMKALKEKFEESPEEKYTKFYIFGGWKQSERKKEFKEWADKIVEERGVPHYNPDIGVPLGQRKLMSYQVSGTDVFVEGDDLTFVNNAAMQQMWDDIRRTVIVGMDTAHRVLERRLGKEVTPETINEYMETLNHALPGGAVVQEHMVEIHPGLTWDCYAKIITGDLELADEIDDKFLIDIEKLFPEEQAEQLIKAIGNRTYQVCRMPTIVGHVCDGATMYRWAAMQIAMSFICAYKIAAGEAAVSDFAFASKHAEVINMGEMLPARRARGENEPGGVPFGVLADCVQTMRKYPDDPAKVALEVIAAGAMLYDQIWLGSYMSGGVGFTQYATAVYPDNILDDYVYYGLEYVEDKYGIAEAEPSMDVVKDVATEVTLYGLEQYERYPAAMETHFGGSQRAAVCAAAAGCSTAFATGHAQAGLNGWYLSQILHKEGQGRLGFYGYALQDQCGAANSLSVRSDEGLPLELRGPNYPNYAMNVGHLGEYAGIVQAAHAARGDAFCVHPVIKVAFADENLVFDFTEPRKEFAKGALREFEPAGERDLIVPAE

Entity 2 polymer

description	METHYL-COENZYME M REDUCTASE I BETA SUBUNIT
formula_weight	48214.7 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,E

MAREAKDTVDLYDDRGNCVAEEVPIEVLSPMRNEAIQSIVNDIKRTVAVDLEGIENALQNATVGGKGMKIPGREMDVDIVDNAEAIADEIEKMIRVYQDDDTNVEPMYDGKRLLVQLPSERVKVMADPYSGTLQAGMAVVHAIIDVCEVDMWDANMVKAAVFGRYPQTIDYFGGNVASMLDVPMKQEGVGYALRNIMVNHIVAATRKNTMQAVCLAATLQQTAMFEMGDALGPFERLHLLGYAYQGLNADNMVYDIVKKHGKEGTVGTVVREVVERALEDGVIEVKEELPSFKVYKANDMDLWNAYAAAGLVAAVMVNQGAARAAQGVSATILYYNDLLEYETGLPGVDFGRAEGTAVGFSFFSHSIYGGGGPGIFHGNHIVTRHSKGFAIPPVAAAMALDAGTQMFSPEVTSKLIGDVFGEIDEFREPMKYITEAAAEEAKR

Entity 3 polymer

description	METHYL-COENZYME M REDUCTASE I GAMMA SUBUNIT
formula_weight	30114.8 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,F

MAEKAQFYYPGETDVAENRRKYMNPNYELKKLREIPDEDIVRLMGHREPGEEYPSVHPPLEEMEEPECPIRELVEPTEGAKAGDRIRYIQFTDSVYFAPIHPYIRARMYMWRYRGVDTGSLSGRQIIEVRERDLEKIAKELLETEIFDPARSGVRGATVHGHALRLDENGLMLHALRRYRLNEETGEVEYVKDQVGIELDEPIPVGAPADEDDLKERTTIYRIDGTPYREDEELLQVVQRIHELRTLAGYRPEEAEGK

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

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6. Citations (1)

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length_a	80.519 Å
length_b	115.740 Å
length_c	268.510 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	2.700 Å
resolution_low	30.000 Å
r_factor	0.2390
r_work	0.2390
r_free	0.2780

fit	/app/data/saxs_computation/e6/1e6v/1e6v.fit
pddf	/app/data/pr_computation/e6/1e6v/1e6v.pr.out
profile	/app/data/saxs_computation/e6/1e6v/1e6v.dat

Methyl-coenzyme M reductase from Methanopyrus kandleri

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 (6)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 polymer

Polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)