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9vdj

Serial synchrotron crystallography structure of a ba3-type cytochrome c oxidase using a goniometer-compatible chip-based platform

Method: X-RAY DIFFRACTION D_max: 88.8 Å Quality: GOOD

SAXS Profile

P(r) Distribution

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1. Structure Basics

entry_id	9vdj
deposition_date	2025-06-08
title	Serial synchrotron crystallography structure of a ba3-type cytochrome c oxidase using a goniometer-compatible chip-based platform
keywords	Proton-pump, Bioenergetics, complex IV, serial crystallography, lipidic cubic phase, MEMBRANE PROTEIN; MEMBRANE PROTEIN
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	27.38 Å
rg_electron	26.08 Å
i0	91259400.00
molecular_weight	88769.0 kDa
excluded_volume	116550 Å³
envelope_volume	129750 Å³
shell_volume	39414 Å³
envelope_diameter	91.1 Å
shell_rg	35.19 Å
envelope_rg	26.52 Å
shape_rg	26.06 Å
total_rg	27.15 Å
total_atoms	6291
n_residues	752
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	88.8 Å
rg_real	27.31 Å
rg_real_error	0.55 Å
i0_real	9.1260e+07
i0_real_error	1.3090e+06
rg_reciprocal	27.33 Å
i0_reciprocal	91260000.0000
total_estimate	0.8891
solution_quality	GOOD a GOOD solution
n_peaks	2
r_peak_primary	32.1 Å
skewness	0.321
kurtosis	-0.303
angular_range	— – 0.2900 Å⁻¹
current_alpha	0.0000
highest_alpha	24390000.0000
n_real_points	59
gnom_version	4.1.3
quality_criteria	AN1: 0.000; Oscil: 0.863; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.968

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4. Crystallography & Experiment

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5. Entities & Polymer Info (9)

Entity 1 polymer

description	Cytochrome c oxidase subunit 1
formula_weight	63540.1 kDa
ec_number	7.1.1.9
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	A
atom_count	6426

MHHHHHHHAVRASEISRVYEAYPEKKATLYFLVLGFLALIVGSLFGPFQALNYGNVDAYPLLKRLLPFVQSYYQGLTLHGVLNAIVFTQLFAQAIMVYLPARELNMRPNMGLMWLSWWMAFIGLVVAALPLLANEATVLYTFYPPLKGHWAFYLGASVFVLSTWVSIYIVLDLWRRWKAANPGKVTPLVTYMAVVFWLMWFLASLGLVLEAVLFLLPWSFGLVEGVDPLVARTLFWWTGHPIVYFWLLPAYAIIYTILPKQAGGKLVSDPMARLAFLLFLLLSTPVGFHHQFADPGIDPTWKMIHSVLTLFVAVPSLMTAFTVAASLEFAGRLRGGRGLFGWIRALPWDNPAFVAPVLGLLGFIPGGAGGIVNASFTLDYVVHNTAWVPGHFHLQVASLVTLTAMGSLYWLLPNLTGKPISDAQRRLGLAVVWLWFLGMMIMAVGLHWAGLLNVPRRAYIAQVPDAYPHAAVPMVFNVLAGIVLLVALLLFIYGLFSVLLSRERKPELAEAPLPFAEVISGPEDRRLVLAMDRIGFWFAVAAILVVLAYGPTLVQLFGHLNPVPGWRLW

Source

organism	Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
ncbi_taxonomy_id	300852
host_organism	Thermus thermophilus

Entity 2 polymer

description	Cytochrome c oxidase subunit 2
formula_weight	18581.3 kDa
ec_number	7.1.1.9
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	B

MVDEHKAHKAILAYEKGWLAFSLAMLFVFIALIAYTLATHTAGVIPAGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIICNQYCGLGHQNMFGTIVVKE

Source

organism	Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
ncbi_taxonomy_id	300852
host_organism	Thermus thermophilus

Entity 3 polymer

description	Cytochrome c oxidase polypeptide 2A
formula_weight	3769.6 kDa
ec_number	7.1.1.9
src_method	man
entity_count	1

Polymer

type	polypeptide(L)
strand_id	C

MEEKPKGALAVILVLTLTILVFWLGVYAVFFARG

Source

organism	Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8)
ncbi_taxonomy_id	300852
host_organism	Thermus thermophilus

Entity 4 non-polymer

description	COPPER (II) ION
formula_weight	63.5 kDa
src_method	syn
entity_count	1

Entity 5 non-polymer

description	PROTOPORPHYRIN IX CONTAINING FE
formula_weight	616.5 kDa
src_method	syn
entity_count	1

Entity 6 non-polymer

description	HEME-AS
formula_weight	921.0 kDa
src_method	syn
entity_count	1

Entity 7 non-polymer

description	(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
formula_weight	356.5 kDa
src_method	syn
entity_count	15

Entity 8 non-polymer

description	DINUCLEAR COPPER ION
formula_weight	127.1 kDa
src_method	syn
entity_count	1

Entity 9 water

description	water
formula_weight	18.0 kDa
src_method	nat
entity_count	135

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6. Citations (1)

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length_a	145.850 Å
length_b	100.320 Å
length_c	96.620 Å
angle_alpha	90.00 °
angle_beta	126.76 °
angle_gamma	90.00 °
z_pdb	4

space_group	C 1 2 1
int_tables_number	5
crystal_system	monoclinic

resolution	2.300 Å
resolution_low	32.150 Å
r_factor	0.2118
r_work	0.2091
r_free	0.2640

fit	/app/data/saxs_computation/vd/9vdj/9vdj.fit
pddf	/app/data/pr_computation/vd/9vdj/9vdj.pr.out
profile	/app/data/saxs_computation/vd/9vdj/9vdj.dat

Serial synchrotron crystallography structure of a ba3-type cytochrome c oxidase using a goniometer-compatible chip-based platform

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

Source

Entity 2 polymer

Polymer

Source

Entity 3 polymer

Polymer

Source

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)