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9r5i

Dimeric state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus in crystalline form 3

Method: X-RAY DIFFRACTION D_max: 118.0 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r5i
deposition_date	2025-05-08
title	Dimeric state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus in crystalline form 3
keywords	;[NiFe]-hydrogenase, redox cycle, catalysis, [4Fe-4S]-cluster, F420 cofactor, FAD, hydrogen activation, thermophilic methanogen, 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	36.92 Å
rg_electron	36.72 Å
i0	672816000.00
molecular_weight	209330.0 kDa
excluded_volume	260520 Å³
envelope_volume	310290 Å³
shell_volume	66670 Å³
envelope_diameter	127.5 Å
shell_rg	45.44 Å
envelope_rg	37.00 Å
shape_rg	36.88 Å
total_rg	36.65 Å
total_atoms	14481
n_residues	1828
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	118.0 Å
rg_real	36.80 Å
rg_real_error	0.86 Å
i0_real	6.7280e+08
i0_real_error	1.1870e+07
rg_reciprocal	36.88 Å
i0_reciprocal	672900000.0000
total_estimate	0.8933
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	43.9 Å
skewness	0.256
kurtosis	-0.410
angular_range	— – 0.2150 Å⁻¹
current_alpha	0.0000
highest_alpha	287200000.0000
n_real_points	44
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.907; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.887

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4. Crystallography & Experiment

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5. Entities & Polymer Info (13)

Entity 1 polymer

description	F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit alpha
formula_weight	45839.5 kDa
ec_number	1.12.98.1
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	A,D
atom_count	14481

MGKIVEIHPTTRHEGHTKLVLKVDDEGIVEKGAYLSVTPVRGFEKFLVGKPAEFAPIAVSRFCGICPVAHATSAVEAIEDACDITPPKDGLLLRELCGIGNKMHSHPLHQFLISPDYVPKDDSNEFIKRVQAMRRIGQYIVDAVGGEAIHSPNIKVGGMAKQITESTKAKMYYKCKEYEKLAKEQLEYLIPIFESRTLNDGTELPEKLGYHDFGYIATHPTYGDRTKIDQDKVVEYTPFDVYDKDVAIQSSTTVPTYNGRLMEVGPRARFSKFFDFKEKGAMALHIARAYEISVLVKRAMEILDELNVNGKTMSDEPIVGDGEKLGLGVHEAARGHNTHQAVIDKDGNIVYYNAIVATTWNIPVISKAVEGTHYKFAEHIVRAYDPCISCATHMIIKDYDDKIIGEKILK

Entity 2 polymer

description	F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit beta
formula_weight	31091.1 kDa
ec_number	1.12.98.1
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	B,F

MDPFGKYKTVVSARAADKTILKKCQDGGIVSAAYIYGLENGLLDGVIVADKDDKLQTTPKVATTVDEVLEAAGTKYTVCPTISVIKSAVREYGCEKLGVVGTPCQIIATRKLMKYPIGFRHVPDKLALIVGIFCMENFPYNGMKTIIEEHCGIKMEDVAKTDIGKGKFWVYSKWGDVKSIKLKETHPYEQQSCHVCMDYTAELADISTGSVGSPDGWSTVFIRTAQGEEFFNKMVEAGALEVKPIEEVKPGLGLVEKLSLTKKEKNAKEIEHRKEIGLPVPY

Entity 3 polymer

description	F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus subunit gamma
formula_weight	26070.5 kDa
ec_number	1.12.98.1
src_method	nat
entity_count	2

Polymer

type	polypeptide(L)
strand_id	C,E

MVKIAHIHLCGCTGCLISLADTYEQLLDILNSVELVYALTLVDEKTEIRETDDKILIEREIPDDIDIALVEGSVCLEDEHSMKDVFDARRKSKIVVALGACAATGGITRFCRGGQMSKPVHSSFVPIGDLIKVDLALPGCPPSPEALVNLITAALNGDTEYLEIYAELAKKTEACGCDLLVNVINKSLCMGCGSCAASCPTRAIEMIDGKPNVLKELCIKCGACSLQCPRIRFPKLIEEIE

Entity 4 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	9

Entity 5 non-polymer

description	2-(N-MORPHOLINO)-ETHANESULFONIC ACID
formula_weight	195.2 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)
formula_weight	195.6 kDa
src_method	syn
entity_count	2

Entity 7 non-polymer

description	FE (III) ION
formula_weight	55.8 kDa
src_method	syn
entity_count	2

Entity 8 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	9

Entity 9 non-polymer

description	1,2-ETHANEDIOL
formula_weight	62.1 kDa
src_method	syn
entity_count	16

Entity 10 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	2

Entity 11 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	8

Entity 12 non-polymer

description	2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
formula_weight	354.4 kDa
src_method	syn
entity_count	1

Entity 13 non-polymer

description	FE2/S2 (INORGANIC) CLUSTER
formula_weight	175.8 kDa
src_method	syn
entity_count	1

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6. Citations (1)

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length_a	196.606 Å
length_b	196.606 Å
length_c	192.072 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	120.00 °
z_pdb	12

space_group	P 31 2 1
int_tables_number	152
crystal_system	—

resolution	3.130 Å
resolution_low	77.830 Å
r_factor	0.1760
r_work	0.1744
r_free	0.2059

fit	/app/data/saxs_computation/r5/9r5i/9r5i.fit
pddf	/app/data/pr_computation/r5/9r5i/9r5i.pr.out
profile	/app/data/saxs_computation/r5/9r5i/9r5i.dat

Dimeric state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus in crystalline form 3

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 (13)

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 non-polymer

Entity 9 non-polymer

Entity 10 non-polymer

Entity 11 non-polymer

Entity 12 non-polymer

Entity 13 non-polymer

6. Citations (1)

7. Files & Curves (10)

Files (7)

Curves (3)