← Back to search

1e3d

[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774

Method: X-RAY DIFFRACTION D_max: 129.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

▼

1. Structure Basics

entry_id	1e3d
deposition_date	2000-06-14
title	[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774
keywords	HYDROGENASE, MOLECULAR MODELLING, ELECTRON TRANSFER; HYDROGENASE
method	X-RAY DIFFRACTION

▼

Download Data

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

▼

2. SAXS Parameters (CRYSOL)

rg_guinier	38.88 Å
rg_electron	39.02 Å
i0	491410000.00
molecular_weight	178050.0 kDa
excluded_volume	220790 Å³
envelope_volume	261990 Å³
shell_volume	55641 Å³
envelope_diameter	133.8 Å
shell_rg	44.87 Å
envelope_rg	38.74 Å
shape_rg	39.10 Å
total_rg	39.05 Å
total_atoms	24422
n_residues	1598
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	129.8 Å
rg_real	39.07 Å
rg_real_error	1.07 Å
i0_real	4.9140e+08
i0_real_error	7.9970e+06
rg_reciprocal	38.96 Å
i0_reciprocal	491400000.0000
total_estimate	0.8543
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	38.0 Å
skewness	0.415
kurtosis	-0.522
angular_range	— – 0.2050 Å⁻¹
current_alpha	0.0000
highest_alpha	142200000.0000
n_real_points	42
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.803; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.948; Smooth: 0.747

▶

4. Crystallography & Experiment

▶

5. Entities & Polymer Info (9)

Entity 1 polymer

description	[NiFe] hydrogenase small subunit
formula_weight	28682.6 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,C
atom_count	25867

ALTGSRPSVVYLHAAECTGCSEALLRTYQPFIDTLILDTISLDYHETIMAAAGEAAEEALQAAVNGPDGFICLVEGAIPTGMDNKYGYIAGHTMYDICKNILPKAKAVVSIGTCACYGGIQAAKPNPTAAKGINDCYADLGVKAINVPGCPPNPLNMVGTLVAFLKGQKIELDEVGRPVMFFGQSVHDLCERRKHFDAGEFAPSFNSEEARKGWCLYDVGCKGPETYNNCPKVLFNETNWPVAAGHPCIGCSEPNFWDDMTPFYQN

Entity 2 polymer

description	[NiFe] hydrogenase large subunit
formula_weight	60009.9 kDa
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,D

SQVTKTPRSNYTGPIVVDPLTRIEGHLRIEVEVEGGVIKEARSCATLFRGIETILKGRDPRDAQHFTQRTCGVCTYTHALASTRCLEDAINKPIPANATYIRNLVLGNQFMHDHLVHFYHLHALDFVDVTSALLADPAKAAKLANSISPRKATTEEFAAVQAKLKTFVASGQLGPFTNAYFLGGHEGYYMDPEANLVCTAHYLQALRAQVEVAKGMAVFGAKNPHTQFTVAGGVTCYEALTPERIKQFRELYVKARAFIEEVYIPDLLLVASYYKDWGKIGGTNNFMAFGEFPAPGGERDLNSRWYKPGVIYDRKVGSVQPFDPSKIEEHVRHSWYEGKARAPFEGETNPHFTFMGDTDKYSWNKAPRYDGHAVETGPLAQMLVAYGHNHKTIKPTIDAVLGKLNLGPEALFSTLGRTAARGIQTLVIAQQMENWLNEYENNIVKDKQIVEDYAVPTSARGVGFADVSRGGLSHWMTIEDGKIDNFQLVVPTTWNLGPRDDKGVPSAAEAALVGTPVADPKRPVEILRTIHSFDPCIACSTH

Entity 3 non-polymer

description	FE3-S4 CLUSTER
formula_weight	295.8 kDa
src_method	syn
entity_count	2

Entity 4 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	2

Entity 5 non-polymer

description	BIS-(MU-2-OXO),[(MU-3--SULFIDO)-BIS(MU-2--SULFIDO)-TRIS(CYS-S)-TRI-IRON] (AQUA)(GLU-O)IRON(II)
formula_weight	367.6 kDa
src_method	syn
entity_count	2

Entity 6 non-polymer

description	HYDROSULFURIC ACID
formula_weight	34.1 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	(MU-SULPHIDO)-BIS(MU-CYS,S)-[TRICARBONYLIRON-DI-(CYS,S)NICKEL(II)](FE-NI)
formula_weight	230.6 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	MAGNESIUM ION
formula_weight	24.3 kDa
src_method	syn
entity_count	2

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	1399

▶

6. Citations (1)

▶

length_a	64.090 Å
length_b	169.980 Å
length_c	72.620 Å
angle_alpha	90.00 °
angle_beta	92.80 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 1 21 1
int_tables_number	4
crystal_system	—

resolution	1.800 Å
resolution_low	25.000 Å
r_factor	0.1671
r_work	—
r_free	0.2231

fit	/app/data/saxs_computation/e3/1e3d/1e3d.fit
pddf	/app/data/pr_computation/e3/1e3d/1e3d.pr.out
profile	/app/data/saxs_computation/e3/1e3d/1e3d.dat

[NiFe] Hydrogenase from Desulfovibrio desulfuricans ATCC 27774

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 (9)

Entity 1 polymer

Polymer

Entity 2 polymer

Polymer

Entity 3 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 non-polymer

Entity 9 water

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)