5u7n

CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP

Method: X-RAY DIFFRACTION D_max: 95.7 Å Quality: EXCELLENT

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome c oxidase subunit 2

Thermus thermophilus

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 11–116 Chain A； UniProt 127–135	Fragment：UNP residues 11-116,127-135	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 11–116 Chain B； UniProt 127–135	Fragment：UNP residues 11-116,127-135	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 11–116 Chain C； UniProt 127–135	Fragment：UNP residues 11-116,127-135	CU COPPER (II) ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 11–116 Chain D； UniProt 127–135	Fragment：UNP residues 11-116,127-135	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
5	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain E； UniProt 11–116 Chain E； UniProt 127–135	Fragment：UNP residues 11-116,127-135	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
6	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain F； UniProt 11–116 Chain F； UniProt 127–135	Fragment：UNP residues 11-116,127-135	CU COPPER (II) ION × 1 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
7	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain G； UniProt 11–116 Chain G； UniProt 127–135	Fragment：UNP residues 11-116,127-135	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226
8	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain H； UniProt 11–116 Chain H； UniProt 127–135	Fragment：UNP residues 11-116,127-135	CU COPPER (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 7.5；295 K；60 % (4S)-2-METHYL-2,4-PENTANEDIOL	Resolution 2.30 Å R-free 0.226

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5U7N	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1XME Structure of Recombinant Cytochrome ba3 Oxidase from Thermus thermophilus Deposited 2004-10-01	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain B 1–168（168 aa）	Not recorded	BNG nonyl beta-D-glucopyranoside × 1 CU COPPER (II) ION × 1 HEM PROTOPORPHYRIN IX CONTAINING FE × 1 HAS HEME-AS × 1 GOL GLYCEROL × 1 CUA DINUCLEAR COPPER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；297 K；Peg 2000, Bis-tris, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 297K	Resolution 2.30 Å R-free 0.236
2CUA THE CUA DOMAIN OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS Deposited 1999-02-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 34–168（135 aa） Fragment：SOLUBLE CUA-CONTAINING DOMAIN	Not recorded	ZN ZINC ION × 1 CUA DINUCLEAR COPPER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.2-20% MPEG 5K 100MM NA CACODYLATE PH 6.5 1MM ZNCL2	Resolution 1.60 Å R-free 0.296
2CUA THE CUA DOMAIN OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS Deposited 1999-02-18	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 34–168（135 aa） Fragment：SOLUBLE CUA-CONTAINING DOMAIN	Not recorded	ZN ZINC ION × 1 CUA DINUCLEAR COPPER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.2-20% MPEG 5K 100MM NA CACODYLATE PH 6.5 1MM ZNCL2	Resolution 1.60 Å R-free 0.296
2FWL The cytochrome c552/CuA complex from Thermus thermophilus Deposited 2006-02-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–135（135 aa）	Not recorded	HEC HEME C × 1 CUA DINUCLEAR COPPER ION × 1	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 20mM phosphate buffer；Pressure ambient NMR sample composition 0.5mM cytochrome c552 U-15N, 20mM phosphate buffer, 2mM CuA domain, 95% H2O, 5% D2O \| 95% H2O/5% D2O NMR sample composition 0.5mM CuA domain U-15N, 20mM phosphate buffer, 2mM cytochrome c552, 95% H2O, 5% D2O \| 95% H2O/5% D2O	Resolution not provided
2LLN Solution structure of Thermus thermophilus apo-CuA Deposited 2011-11-15	Different construct Different mutation/modification Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 11–135（125 aa） Fragment：UNP residues 11-135	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 6；298 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient NMR sample composition 0.8 -1 mM [U-99% 13C; U-99% 15N] protein, 100 mM potassium phosphate, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 -1 mM [U-99% 15N] protein, 100 mM potassium phosphate, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O NMR sample composition 0.8 - 1 mM protein, 100 mM potassium phosphate, 2 mM DTT, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
6PTT Soluble model of Arabidopsis thaliana CuA (Tt3LAt) Deposited 2019-07-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 11–135（125 aa）	Not recorded	CUA DINUCLEAR COPPER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；100 mM Hepes, 1.5 M LiSO4, pH 7.5	Resolution 1.84 Å R-free 0.214
6PTT Soluble model of Arabidopsis thaliana CuA (Tt3LAt) Deposited 2019-07-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 11–135（125 aa）	Not recorded	CUA DINUCLEAR COPPER ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；100 mM Hepes, 1.5 M LiSO4, pH 7.5	Resolution 1.84 Å R-free 0.214
6PTY Soluble model of human CuA (Tt3Lh) Deposited 2019-07-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 11–135（125 aa）	Not recorded	CUA DINUCLEAR COPPER ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；100 mM Hepes, 1.6 M (NH4)2SO4, 0.1 mM NaCl, pH 7.5	Resolution 1.98 Å R-free 0.238
6PTY Soluble model of human CuA (Tt3Lh) Deposited 2019-07-16	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 11–135（125 aa）	Not recorded	CUA DINUCLEAR COPPER ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；291 K；100 mM Hepes, 1.6 M (NH4)2SO4, 0.1 mM NaCl, pH 7.5	Resolution 1.98 Å R-free 0.238

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	COX2_THETH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–110； UniProt 11–116 Author chain A； PDBConstruct 116–124； UniProt 127–135 Author chain B； PDBConstruct 5–110； UniProt 11–116 Author chain B； PDBConstruct 116–124； UniProt 127–135 Author chain C； PDBConstruct 5–110； UniProt 11–116 Author chain C； PDBConstruct 116–124； UniProt 127–135 Author chain D； PDBConstruct 5–110； UniProt 11–116 Author chain D； PDBConstruct 116–124； UniProt 127–135 Author chain E； PDBConstruct 5–110； UniProt 11–116 Author chain E； PDBConstruct 116–124； UniProt 127–135 Author chain F； PDBConstruct 5–110； UniProt 11–116 Author chain F； PDBConstruct 116–124； UniProt 127–135 Author chain G； PDBConstruct 5–110； UniProt 11–116 Author chain G； PDBConstruct 116–124； UniProt 127–135 Author chain H； PDBConstruct 5–110； UniProt 11–116 Author chain H； PDBConstruct 116–124； UniProt 127–135

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	5u7n
Deposition date deposition_date	2016-12-12
Structure title title	CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP
Keywords keywords	OXIDOREDUCTASE, ELECTRON TRANSPORT; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.17 Å
Radius of gyration Rg (electron density) rg_electron	31.20 Å
Forward intensity I(0) i0	154133000.00
Molecular weight molecular_weight	101810.0 kDa
Excluded volume excluded_volume	128600 Å³
Envelope volume envelope_volume	167090 Å³
Hydration-shell volume shell_volume	44494 Å³
Envelope diameter envelope_diameter	98.4 Å
Shell Rg shell_rg	38.60 Å
Envelope Rg envelope_rg	30.34 Å
Shape Rg shape_rg	31.19 Å
Total Rg total_rg	31.94 Å
Total atoms total_atoms	7188
Residues n_residues	908
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	95.7 Å
Rg (real space) rg_real	31.91 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	1.5410e+08
I(0) uncertainty (real space) i0_real_error	2.2820e+06
Rg (reciprocal space) rg_reciprocal	32.02 Å
I(0) (reciprocal space) i0_reciprocal	154100000.0000
Solution quality estimate total_estimate	0.9066
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	44.9 Å
Skewness Skewness skewness	0.009
Kurtosis Kurtosis kurtosis	-0.589
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	25420000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.953; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.981; Smooth: 0.941

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	Cytochrome c oxidase subunit 2
Molecular weight formula_weight	13706.6 kDa
EC 编号 ec_number	1.9.3.1,1.9.3.1
Source method src_method	man
Copy count entity_count	8

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H
Atom count atom_count	7729

GSHMVIPAGKLERVDPTTVRQEGPWADPAQAVVQTGPNQYTVYVLAFAFGYQPNPIEVPQGAEIVFKITSPDVIHGFHVEGTNINVEVLPGEVSTVRYTFKRPGEYRIICTPHPFMFGTIVVKE

来源 Source

来源生物 organism	Thermus thermophilus
NCBI Class编号 ncbi_taxonomy_id	274
宿主生物 host_organism	Escherichia coli BL21

Entity 2 Entity 2 non-polymer

Description description	COPPER (II) ION
Molecular weight formula_weight	63.5 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	(4S)-2-METHYL-2,4-PENTANEDIOL
Molecular weight formula_weight	118.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	541

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d5u7na_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d5u7nb_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d5u7nc_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d5u7nd_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d5u7ne_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d5u7nf_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d5u7ng_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

Domain ID domain_id	d5u7nh_
Class class	b — All beta proteins
Fold Fold fold	b.6 — Cupredoxin-like
Superfamily Superfamily superfamily	b.6.1 — Cupredoxins
Family Family family	b.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II

CATH v4.4 (8 domains)

Domain ID domain_id	5u7nA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5u7nB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5u7nC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5u7nD00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5u7nE00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5u7nF00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5u7nG00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

Domain ID domain_id	5u7nH00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	420 — Cupredoxins - blue copper proteins

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8. Citations (1)

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Unit-cell length a length_a	94.352 Å
Unit-cell length b length_b	100.701 Å
Unit-cell length c length_c	101.103 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	32

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	45.180 Å
R factor r_factor	0.1783
R_work r_work	0.1759
R_free r_free	0.2258

fit	/app/data/saxs_computation/u7/5u7n/5u7n.fit
pddf	/app/data/pr_computation/u7/5u7n/5u7n.pr.out
profile	/app/data/saxs_computation/u7/5u7n/5u7n.dat