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9r52

Dimeric state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus in crystalline form 2

Method: X-RAY DIFFRACTION D_max: 103.3 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r52
deposition_date	2025-05-08
title	Dimeric state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus in crystalline form 2
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	30.13 Å
rg_electron	29.86 Å
i0	170745000.00
molecular_weight	103500.0 kDa
excluded_volume	129060 Å³
envelope_volume	151900 Å³
shell_volume	41680 Å³
envelope_diameter	108.8 Å
shell_rg	37.58 Å
envelope_rg	30.38 Å
shape_rg	29.96 Å
total_rg	30.14 Å
total_atoms	14325
n_residues	910
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	103.3 Å
rg_real	30.20 Å
rg_real_error	1.03 Å
i0_real	1.7070e+08
i0_real_error	2.9070e+06
rg_reciprocal	30.17 Å
i0_reciprocal	170700000.0000
total_estimate	0.8633
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	33.1 Å
skewness	0.466
kurtosis	-0.189
angular_range	— – 0.2650 Å⁻¹
current_alpha	0.0000
highest_alpha	67870000.0000
n_real_points	54
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.759; Stabil: 0.997; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.980

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus alpha subunit
formula_weight	45839.5 kDa
ec_number	1.12.98.1
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	15123

MGKIVEIHPTTRHEGHTKLVLKVDDEGIVEKGAYLSVTPVRGFEKFLVGKPAEFAPIAVSRFCGICPVAHATSAVEAIEDACDITPPKDGLLLRELCGIGNKMHSHPLHQFLISPDYVPKDDSNEFIKRVQAMRRIGQYIVDAVGGEAIHSPNIKVGGMAKQITESTKAKMYYKCKEYEKLAKEQLEYLIPIFESRTLNDGTELPEKLGYHDFGYIATHPTYGDRTKIDQDKVVEYTPFDVYDKDVAIQSSTTVPTYNGRLMEVGPRARFSKFFDFKEKGAMALHIARAYEISVLVKRAMEILDELNVNGKTMSDEPIVGDGEKLGLGVHEAARGHNTHQAVIDKDGNIVYYNAIVATTWNIPVISKAVEGTHYKFAEHIVRAYDPCISCATHMIIKDYDDKIIGEKILK

Entity 2 polymer

description	F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus beta subunit
formula_weight	31091.1 kDa
ec_number	1.12.98.1
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MDPFGKYKTVVSARAADKTILKKCQDGGIVSAAYIYGLENGLLDGVIVADKDDKLQTTPKVATTVDEVLEAAGTKYTVCPTISVIKSAVREYGCEKLGVVGTPCQIIATRKLMKYPIGFRHVPDKLALIVGIFCMENFPYNGMKTIIEEHCGIKMEDVAKTDIGKGKFWVYSKWGDVKSIKLKETHPYEQQSCHVCMDYTAELADISTGSVGSPDGWSTVFIRTAQGEEFFNKMVEAGALEVKPIEEVKPGLGLVEKLSLTKKEKNAKEIEHRKEIGLPVPY

Entity 3 polymer

description	F420-reducing [NiFe]-hydrogenase from Methanothermococcus thermolithotrophicus gamma subunit
formula_weight	26070.5 kDa
ec_number	1.12.98.1
src_method	nat
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MVKIAHIHLCGCTGCLISLADTYEQLLDILNSVELVYALTLVDEKTEIRETDDKILIEREIPDDIDIALVEGSVCLEDEHSMKDVFDARRKSKIVVALGACAATGGITRFCRGGQMSKPVHSSFVPIGDLIKVDLALPGCPPSPEALVNLITAALNGDTEYLEIYAELAKKTEACGCDLLVNVINKSLCMGCGSCAASCPTRAIEMIDGKPNVLKELCIKCGACSLQCPRIRFPKLIEEIE

Entity 4 non-polymer

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

Entity 5 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	10

Entity 6 non-polymer

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

Entity 7 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	4

Entity 8 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	1

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	725

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6. Citations (1)

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length_a	95.028 Å
length_b	163.482 Å
length_c	128.826 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	8

space_group	C 2 2 21
int_tables_number	20
crystal_system	—

resolution	1.650 Å
resolution_low	64.410 Å
r_factor	0.1432
r_work	0.1411
r_free	0.1826

fit	/app/data/saxs_computation/r5/9r52/9r52.fit
pddf	/app/data/pr_computation/r5/9r52/9r52.pr.out
profile	/app/data/saxs_computation/r5/9r52/9r52.dat

Dimeric state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus in crystalline form 2

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 polymer

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)