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9r6z

Cubic state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus

Method: X-RAY DIFFRACTION D_max: 180.2 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9r6z
deposition_date	2025-05-13
title	Cubic state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus
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	54.94 Å
rg_electron	55.24 Å
i0	2500830000.00
molecular_weight	414970.0 kDa
excluded_volume	516490 Å³
envelope_volume	681750 Å³
shell_volume	99067 Å³
envelope_diameter	182.2 Å
shell_rg	61.23 Å
envelope_rg	54.49 Å
shape_rg	55.32 Å
total_rg	55.09 Å
total_atoms	28746
n_residues	3656
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	180.2 Å
rg_real	55.01 Å
rg_real_error	1.31 Å
i0_real	2.5010e+09
i0_real_error	4.5940e+07
rg_reciprocal	54.86 Å
i0_reciprocal	2500000000.0000
total_estimate	0.8686
solution_quality	GOOD a GOOD solution
n_peaks	1
r_peak_primary	55.9 Å
skewness	0.280
kurtosis	-0.692
angular_range	— – 0.1450 Å⁻¹
current_alpha	0.0001
highest_alpha	224900000.0000
n_real_points	30
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.903; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.585

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	F420-reducing [NiFe]-hydrogenase subunit alpha
formula_weight	45839.5 kDa
ec_number	1.12.98.1
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	A,D,G,J
atom_count	28822

MGKIVEIHPTTRHEGHTKLVLKVDDEGIVEKGAYLSVTPVRGFEKFLVGKPAEFAPIAVSRFCGICPVAHATSAVEAIEDACDITPPKDGLLLRELCGIGNKMHSHPLHQFLISPDYVPKDDSNEFIKRVQAMRRIGQYIVDAVGGEAIHSPNIKVGGMAKQITESTKAKMYYKCKEYEKLAKEQLEYLIPIFESRTLNDGTELPEKLGYHDFGYIATHPTYGDRTKIDQDKVVEYTPFDVYDKDVAIQSSTTVPTYNGRLMEVGPRARFSKFFDFKEKGAMALHIARAYEISVLVKRAMEILDELNVNGKTMSDEPIVGDGEKLGLGVHEAARGHNTHQAVIDKDGNIVYYNAIVATTWNIPVISKAVEGTHYKFAEHIVRAYDPCISCATHMIIKDYDDKIIGEKILK

Entity 2 polymer

description	F420-reducing [NiFe]-hydrogenase subunit beta
formula_weight	31091.1 kDa
ec_number	1.12.98.1
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	B,E,H,K

MDPFGKYKTVVSARAADKTILKKCQDGGIVSAAYIYGLENGLLDGVIVADKDDKLQTTPKVATTVDEVLEAAGTKYTVCPTISVIKSAVREYGCEKLGVVGTPCQIIATRKLMKYPIGFRHVPDKLALIVGIFCMENFPYNGMKTIIEEHCGIKMEDVAKTDIGKGKFWVYSKWGDVKSIKLKETHPYEQQSCHVCMDYTAELADISTGSVGSPDGWSTVFIRTAQGEEFFNKMVEAGALEVKPIEEVKPGLGLVEKLSLTKKEKNAKEIEHRKEIGLPVPY

Entity 3 polymer

description	F420-reducing [NiFe]-hydrogenase subunit gamma
formula_weight	26070.5 kDa
ec_number	1.12.98.1
src_method	nat
entity_count	4

Polymer

type	polypeptide(L)
strand_id	C,F,I,L

MVKIAHIHLCGCTGCLISLADTYEQLLDILNSVELVYALTLVDEKTEIRETDDKILIEREIPDDIDIALVEGSVCLEDEHSMKDVFDARRKSKIVVALGACAATGGITRFCRGGQMSKPVHSSFVPIGDLIKVDLALPGCPPSPEALVNLITAALNGDTEYLEIYAELAKKTEACGCDLLVNVINKSLCMGCGSCAASCPTRAIEMIDGKPNVLKELCIKCGACSLQCPRIRFPKLIEEIE

Entity 4 non-polymer

description	SULFATE ION
formula_weight	96.1 kDa
src_method	syn
entity_count	20

Entity 5 non-polymer

description	formyl[bis(hydrocyanato-1kappaC)]ironnickel(Fe-Ni)
formula_weight	195.6 kDa
src_method	syn
entity_count	4

Entity 6 non-polymer

description	FLAVIN-ADENINE DINUCLEOTIDE
formula_weight	785.5 kDa
src_method	syn
entity_count	4

Entity 7 non-polymer

description	GLYCEROL
formula_weight	92.1 kDa
src_method	syn
entity_count	15

Entity 8 non-polymer

description	IRON/SULFUR CLUSTER
formula_weight	351.6 kDa
src_method	syn
entity_count	16

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	70

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6. Citations (1)

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length_a	282.072 Å
length_b	282.072 Å
length_c	282.072 Å
angle_alpha	90.00 °
angle_beta	90.00 °
angle_gamma	90.00 °
z_pdb	48

space_group	P 21 3
int_tables_number	198
crystal_system	—

resolution	2.850 Å
resolution_low	31.340 Å
r_factor	0.1837
r_work	0.1823
r_free	0.2101

fit	/app/data/saxs_computation/r6/9r6z/9r6z.fit
pddf	/app/data/pr_computation/r6/9r6z/9r6z.pr.out
profile	/app/data/saxs_computation/r6/9r6z/9r6z.dat

Cubic state of the F420-reducing hydrogenase from Methanothermococcus thermolithotrophicus

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)