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1cc1

CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM

Method: X-RAY DIFFRACTION D_max: 78.6 Å Quality: REASONABLE

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	1cc1
deposition_date	1999-03-03
title	CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM
keywords	NI-FE-SE HYDROGENASE, 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	25.14 Å
rg_electron	24.24 Å
i0	116290000.00
molecular_weight	84630.0 kDa
excluded_volume	105330 Å³
envelope_volume	116130 Å³
shell_volume	37296 Å³
envelope_diameter	84.0 Å
shell_rg	33.55 Å
envelope_rg	24.66 Å
shape_rg	24.29 Å
total_rg	24.94 Å
total_atoms	5895
n_residues	762
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	78.6 Å
rg_real	24.98 Å
rg_real_error	0.32 Å
i0_real	1.1630e+08
i0_real_error	1.4580e+06
rg_reciprocal	25.03 Å
i0_reciprocal	116300000.0000
total_estimate	0.6916
solution_quality	REASONABLE a REASONABLE solution
n_peaks	2
r_peak_primary	31.2 Å
skewness	0.146
kurtosis	-0.452
angular_range	— – 0.3150 Å⁻¹
current_alpha	0.0000
highest_alpha	28880000.0000
n_real_points	64
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.888; Stabil: 1.000; Sysdev: 0.120; Positv: 1.000; Valcen: 0.989; Smooth: 0.971

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4. Crystallography & Experiment

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5. Entities & Polymer Info (8)

Entity 1 polymer

description	HYDROGENASE (SMALL SUBUNIT)
formula_weight	30888.2 kDa
ec_number	1.18.99.1
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	S
atom_count	6214

MTEGAKKAPVIWVQGQGCTGCSVSLLNAVHPRIKEILLDVISLEFHPTVMASEGEMALAHMYEIAEKFNGNFFLLVEGAIPTAKEGRYCIVGETLDAKAHHHEVTMMELIRDLAPKSLATVAVGTCSAYGGIPAAEGNVTGSKSVRDFFADEKIEKLLVNVPGCPPHPDWMVGTLVAAWSHVLNPTEHPLPELDDDGRPLLFFGDNIHENCPYLDKYDNSEFAETFTKPGCKAELGCKGPSTYADCAKRRWNNGINWCVENAVCIGCVEPDFPDGKSPFYVAE

Entity 2 polymer

description	HYDROGENASE (LARGE SUBUNIT)
formula_weight	55217.8 kDa
ec_number	1.18.99.1
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	L

SQAATPAADGKVKISIDPLTRVEGHLKIEVEVKDGKVVDAKCSGGMFRGFEQILRGRDPRDSSQIVQRICGVCPTAHCTASVMAQDDAFGVKVTTNGRITRNLIFGANYLQSHILHFYHLAALDYVKGPDVSPFVPRYANADLLTDRIKDGAKADATNTYGLNQYLKALEIRRICHEMVAMFGGRMPHVQGMVVGGATEIPTADKVAEYAARFKEVQKFVIEEYLPLIYTLGSVYTDLFETGIGWKNVIAFGVFPEDDDYKTFLLKPGVYIDGKDEEFDSKLVKEYVGHSFFDHSAPGGLHYSVGETNPNPDKPGAYSFVKAPRYKDKPCEVGPLARMWVQNPELSPVGQKLLKELYGIEAKKFRDLGDKAFSIMGRHVLRAEETWLTAVAVEKWLKQVQPGAETYVKSEIPDAAEGTGFTEAPRGALLHYLKIKDKKIENYQIVSATLWNANPRDDMGQRGPIEEALIGVPVPDIKNPVNVGRLVRSYDPULGCAVH

Entity 3 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	3

Entity 4 non-polymer

description	NICKEL (II) ION
formula_weight	58.7 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	FE (II) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	CARBONMONOXIDE-(DICYANO) IRON
formula_weight	135.9 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	HYDROSULFURIC ACID
formula_weight	34.1 kDa
src_method	syn
entity_count	1

Entity 8 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	319

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6. Citations (2)

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length_a	110.390 Å
length_b	63.700 Å
length_c	99.580 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	4

space_group	P 21 21 21
int_tables_number	19
crystal_system	—

resolution	2.150 Å
resolution_low	8.000 Å
r_factor	—
r_work	0.1940
r_free	0.2480

fit	/app/data/saxs_computation/cc/1cc1/1cc1.fit
pddf	/app/data/pr_computation/cc/1cc1/1cc1.pr.out
profile	/app/data/saxs_computation/cc/1cc1/1cc1.dat

CRYSTAL STRUCTURE OF A REDUCED, ACTIVE FORM OF THE NI-FE-SE HYDROGENASE FROM DESULFOMICROBIUM BACULATUM

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 non-polymer

Entity 4 non-polymer

Entity 5 non-polymer

Entity 6 non-polymer

Entity 7 non-polymer

Entity 8 water

6. Citations (2)

7. Files & Curves (10)

Files (7)

Curves (3)