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3hb3

High resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase

Method: X-RAY DIFFRACTION Dmax: 114.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Cytochrome c oxidase subunit 1-beta

Paracoccus denitrificans

UniProt P98002

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–558 Not recorded Cytochrome c oxidase subunit 2 × 1 （P08306） ANTIBODY FV FRAGMENT × 1 ANTIBODY FV FRAGMENT × 1 HEA HEME-A × 2 CU1 COPPER (I) ION × 3 MN MANGANESE (II) ION × 1 CA CALCIUM ION × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 10 LMT DODECYL-BETA-D-MALTOSIDE × 14 PEO HYDROGEN PEROXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.5；277 K；25% glycerol, pH 5.5, VAPOR DIFFUSION, temperature 277K Resolution 2.25 Å R-free 0.280

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 3HB3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AR1 Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans two-subunit Cytochrome C Oxidase Complexed with an Antibody Fv Fragment Deposited 1997-08-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–558（558 aa）
Not recorded CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 HEA HEME-A × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 9 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；pH 5.5
Resolution 2.70 Å R-free 0.261
1QLE CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT Deposited 1999-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain A 17–554（538 aa）
Not recorded HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 MN MANGANESE (II) ION × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.00
Resolution 3.00 Å R-free 0.309
3EHB A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate Deposited 2008-09-12 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–558（558 aa） Fragment：UNP residues 17-545
Mutation：N131D HEA HEME-A × 2 CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 9 LMT DODECYL-BETA-D-MALTOSIDE × 12 PER PEROXIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；291 K；MPEG 2000 is contained in the crystallization buffer pH 5.5, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.32 Å R-free 0.242
7ATE Cytochrome c oxidase structure in P-state Deposited 2020-10-30 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–558（558 aa）
Not recorded MN MANGANESE (II) ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 PEO HYDROGEN PEROXIDE × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；4 second before plunging
Resolution 2.40 Å
7ATN Cytochrome c oxidase structure in R-state Deposited 2020-10-30 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–558（558 aa）
Not recorded MN MANGANESE (II) ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；4 seconds before plunging
Resolution 2.66 Å
7AU3 Cytochrome c oxidase structure in F-state Deposited 2020-11-02 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–558（558 aa）
Not recorded MN MANGANESE (II) ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 O OXYGEN ATOM × 1 2FK SUPEROXO ION × 1 CUA DINUCLEAR COPPER ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；4 seconds before plunging
Resolution 2.56 Å
7AU6 Cytochrome c oxidase structure in O-state Deposited 2020-11-02 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain A 1–558（558 aa）
Not recorded HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 OXY OXYGEN MOLECULE × 6 PEO HYDROGEN PEROXIDE × 1 MN MANGANESE (II) ION × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；4 seconds before plunging
Resolution 2.40 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COX1B_PARDE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–558； UniProt 1–558

Cytochrome c oxidase subunit 2

Paracoccus denitrificans

UniProt P08306

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 1–298 Not recorded Cytochrome c oxidase subunit 1-beta × 1 （P98002） ANTIBODY FV FRAGMENT × 1 ANTIBODY FV FRAGMENT × 1 HEA HEME-A × 2 CU1 COPPER (I) ION × 3 MN MANGANESE (II) ION × 1 CA CALCIUM ION × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 10 LMT DODECYL-BETA-D-MALTOSIDE × 14 PEO HYDROGEN PEROXIDE × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 5.5；277 K；25% glycerol, pH 5.5, VAPOR DIFFUSION, temperature 277K Resolution 2.25 Å R-free 0.280

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 3HB3 Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1AR1 Structure at 2.7 Angstrom Resolution of the Paracoccus Denitrificans two-subunit Cytochrome C Oxidase Complexed with an Antibody Fv Fragment Deposited 1997-08-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–298（298 aa）
Not recorded CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 HEA HEME-A × 2 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 9 X-RAY DIFFRACTION
X-ray crystallization conditions pH 5.5；pH 5.5
Resolution 2.70 Å R-free 0.261
1QLE CRYO-STRUCTURE OF THE PARACOCCUS DENITRIFICANS FOUR-SUBUNIT CYTOCHROME C OXIDASE IN THE COMPLETELY OXIDIZED STATE COMPLEXED WITH AN ANTIBODY FV FRAGMENT Deposited 1999-08-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric
Chain B 30–281（252 aa）
Not recorded HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 MN MANGANESE (II) ION × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions pH 8；pH 8.00
Resolution 3.00 Å R-free 0.309
3EHB A D-Pathway Mutation Decouples the Paracoccus Denitrificans Cytochrome c Oxidase by Altering the side chain orientation of a distant, conserved Glutamate Deposited 2008-09-12 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–298（298 aa）
Not recorded HEA HEME-A × 2 CU COPPER (II) ION × 3 MG MAGNESIUM ION × 1 CA CALCIUM ION × 1 LDA LAURYL DIMETHYLAMINE-N-OXIDE × 9 LMT DODECYL-BETA-D-MALTOSIDE × 12 PER PEROXIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；291 K；MPEG 2000 is contained in the crystallization buffer pH 5.5, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 2.32 Å R-free 0.242
7ATE Cytochrome c oxidase structure in P-state Deposited 2020-10-30 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–298（298 aa）
Not recorded MN MANGANESE (II) ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 PEO HYDROGEN PEROXIDE × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；4 second before plunging
Resolution 2.40 Å
7ATN Cytochrome c oxidase structure in R-state Deposited 2020-10-30 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–298（298 aa）
Not recorded MN MANGANESE (II) ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；4 seconds before plunging
Resolution 2.66 Å
7AU3 Cytochrome c oxidase structure in F-state Deposited 2020-11-02 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–298（298 aa）
Not recorded MN MANGANESE (II) ION × 1 HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 O OXYGEN ATOM × 1 2FK SUPEROXO ION × 1 CUA DINUCLEAR COPPER ION × 1 PGV (1R)-2-{[{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-1-[(PALMITOYLOXY)METHYL]ETHYL (11E)-OCTADEC-11-ENOATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；4 seconds before plunging
Resolution 2.56 Å
7AU6 Cytochrome c oxidase structure in O-state Deposited 2020-11-02 Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 1–298（298 aa）
Not recorded HEA HEME-A × 2 CU COPPER (II) ION × 1 CA CALCIUM ION × 1 OXY OXYGEN MOLECULE × 6 PEO HYDROGEN PEROXIDE × 1 MN MANGANESE (II) ION × 1 CUA DINUCLEAR COPPER ION × 1 PC1 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 8
cryo-EM vitrification conditions Cryogen ETHANE；4 seconds before plunging
Resolution 2.40 Å

7 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name COX2_PARDE
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–298； UniProt 1–298

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

SAXS profile for 3hb3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3hb3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3hb3
Deposition date deposition_date2009-05-04
Structure title titleHigh resolution crystal structure of Paracoccus denitrificans cytochrome c oxidase
Keywords keywords;Electron transfer, Proton transfer, Proton pumping, Membrane protein, Cell inner membrane, Cell membrane, Copper, Disulfide bond, Electron transport, Heme, Hydrogen ion transport, Ion transport, Iron, Membrane, Metal-binding, Oxidoreductase, Respiratory chain, Transmembrane, Transport, Pyrrolidone carboxylic acid ;; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier34.08 Å
Radius of gyration Rg (electron density) rg_electron33.17 Å
Forward intensity I(0) i0188949000.00
Molecular weight molecular_weight123500.0 kDa
Excluded volume excluded_volume159590 ų
Envelope volume envelope_volume182980 ų
Hydration-shell volume shell_volume46451 ų
Envelope diameter envelope_diameter122.4 Å
Shell Rg shell_rg39.59 Å
Envelope Rg envelope_rg33.47 Å
Shape Rg shape_rg33.16 Å
Total Rg total_rg33.70 Å
Total atoms total_atoms8699
Residues n_residues1007
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax114.0 Å
Rg (real space) rg_real34.22 Å
Rg uncertainty (real space) rg_real_error0.86 Å
I(0) (real space) i0_real1.8890e+08
I(0) uncertainty (real space) i0_real_error2.9150e+06
Rg (reciprocal space) rg_reciprocal34.14 Å
I(0) (reciprocal space) i0_reciprocal188900000.0000
Solution quality estimate total_estimate0.8668
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary34.7 Å
Skewness Skewness skewness0.482
Kurtosis Kurtosis kurtosis-0.286
Angular range angular_range— – 0.2300 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha41640000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.833; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.794
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (12)

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7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (5 domains)

Domain ID domain_idd3hb3a_
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.24 — Cytochrome c oxidase subunit I-like
Superfamily Superfamily superfamilyf.24.1 — Cytochrome c oxidase subunit I-like
Family Family familyf.24.1.1 — Cytochrome c oxidase subunit I-like
Domain ID domain_idd3hb3b1
Class classf — Membrane and cell surface proteins and peptides
Fold Fold foldf.17 — Transmembrane helix hairpin
Superfamily Superfamily superfamilyf.17.2 — Cytochrome c oxidase subunit II-like, transmembrane region
Family Family familyf.17.2.1 — Cytochrome c oxidase subunit II-like, transmembrane region
Domain ID domain_idd3hb3b2
Class classb — All beta proteins
Fold Fold foldb.6 — Cupredoxin-like
Superfamily Superfamily superfamilyb.6.1 — Cupredoxins
Family Family familyb.6.1.2 — Periplasmic domain of cytochrome c oxidase subunit II
Domain ID domain_idd3hb3c_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)
Domain ID domain_idd3hb3d_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.1 — V set domains (antibody variable domain-like)

CATH v4.4 (5 domains)

Domain ID domain_id3hb3A00
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology210 — Cytochrome C Oxidase; Chain A
Homologous superfamily homologous superfamily10 — Cytochrome c oxidase-like, subunit I domain
Domain ID domain_id3hb3B01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily420 — Cupredoxins - blue copper proteins
Domain ID domain_id3hb3B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily90 —
Domain ID domain_id3hb3C00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3hb3D00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
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8. Citations (1)

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9. Files and Curves (10)