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- PDB-6pw0: Cytochrome C oxidase delta 6 mutant -

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Basic information

Entry
Database: PDB / ID: 6pw0
TitleCytochrome C oxidase delta 6 mutant
Components(Cytochrome c oxidase subunit ...) x 2
KeywordsOXIDOREDUCTASE / Oxidase / Proton pumping / Electron transfer / MEMBRANE PROTEIN
Function / homology
Function and homology information


respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / electron transport coupled proton transport / respirasome / copper ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome c oxidase, subunit I bacterial type / Helix Hairpins - #90 / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. ...Cytochrome c oxidase, subunit I bacterial type / Helix Hairpins - #90 / Cytochrome c oxidase subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c/quinol oxidase subunit II / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Cytochrome c oxidase, subunit I, copper-binding site / Heme-copper oxidase catalytic subunit, copper B binding region signature. / Cytochrome c oxidase-like, subunit I domain / Cytochrome oxidase subunit I profile. / Cytochrome c oxidase subunit I / Cytochrome c oxidase-like, subunit I superfamily / Cytochrome C and Quinol oxidase polypeptide I / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxins - blue copper proteins / Cupredoxin / Helix Hairpins / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
alpha-maltose / : / COPPER (II) ION / HEME-A / (2S,3R)-heptane-1,2,3-triol / HYDROXIDE ION / TRIDECANE / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesRhodobacter sphaeroides 2.4.1 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsLiu, J. / Ferguson-Miller, S.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) United States
CitationJournal: Biochim Biophys Acta Bioenerg / Year: 2019
Title: Structural changes at the surface of cytochrome c oxidase alter the proton-pumping stoichiometry.
Authors: Berg, J. / Liu, J. / Svahn, E. / Ferguson-Miller, S. / Brzezinski, P.
History
DepositionJul 21, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 27, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 11, 2019Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 2.0Jul 29, 2020Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / entity_name_com / pdbx_branch_scheme / pdbx_chem_comp_identifier / pdbx_entity_branch / pdbx_entity_branch_descriptor / pdbx_entity_branch_link / pdbx_entity_branch_list / pdbx_entity_nonpoly / pdbx_molecule_features / pdbx_nonpoly_scheme / pdbx_struct_assembly_gen / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_asym / struct_conn / struct_conn_type / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_asym_id / _atom_site.auth_atom_id / _atom_site.auth_comp_id / _atom_site.auth_seq_id / _atom_site.label_asym_id / _atom_site.label_atom_id / _atom_site.label_comp_id / _atom_site.label_entity_id / _atom_site.occupancy / _atom_site.type_symbol / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _entity.formula_weight / _entity.pdbx_description / _entity.pdbx_number_of_molecules / _entity.src_method / _entity.type / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_unobs_or_zero_occ_atoms.label_asym_id / _struct_asym.entity_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 2.1Oct 11, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 1
D: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)196,41153
Polymers183,7944
Non-polymers12,61749
Water8,215456
1
A: Cytochrome c oxidase subunit 1
B: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)99,59932
Polymers91,8972
Non-polymers7,70230
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7830 Å2
ΔGint-56 kcal/mol
Surface area27650 Å2
MethodPISA
2
C: Cytochrome c oxidase subunit 1
D: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,81121
Polymers91,8972
Non-polymers4,91419
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7660 Å2
ΔGint-57 kcal/mol
Surface area27180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)124.905, 131.477, 176.601
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22
13
23

NCS domain segments:

Component-ID: 1 / End auth comp-ID: HIS / End label comp-ID: HIS

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11TRPTRP(chain 'A' and (resid 20 through 21 or (resid 22...AA20 - 54920 - 549
21TRPTRP(chain 'C' and ((resid 20 and (name N or name...CC20 - 54920 - 549
12LEULEU(chain 'B' and (resid 30 through 85 or (resid 86...BB30 - 2855 - 260
22LEULEU(chain 'D' and (resid 30 through 130 or (resid 131...DD30 - 2855 - 260

NCS ensembles :
ID
1
2
3

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Components

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Cytochrome c oxidase subunit ... , 2 types, 4 molecules ACBD

#1: Protein Cytochrome c oxidase subunit 1 /


Mass: 62531.645 Da / Num. of mol.: 2 / Mutation: 6 residues were deleted at C-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: coxI, RSP_1877 / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / References: UniProt: Q3J5A7, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 /


Mass: 29365.385 Da / Num. of mol.: 2 / Mutation: 6 histidine tag added to the C-terminus
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rhodobacter sphaeroides 2.4.1 (bacteria)
Strain: ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158 / Gene: coxII, RSP_1826 / Production host: Rhodobacter sphaeroides 2.4.1 (bacteria) / References: UniProt: Q3J5G0, cytochrome-c oxidase

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Sugars , 2 types, 11 molecules

#3: Polysaccharide alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose / alpha-maltose


Type: oligosaccharide, Oligosaccharide / Class: Nutrient / Mass: 342.297 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: oligosaccharide / References: alpha-maltose
DescriptorTypeProgram
DGlcpa1-4DGlcpa1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1a_1-5]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][a-D-Glcp]{[(4+1)][a-D-Glcp]{}}LINUCSPDB-CARE
#6: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 10 types, 494 molecules

#4: Chemical ChemComp-OH / HYDROXIDE ION / Hydroxide


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#5: Chemical
ChemComp-HEA / HEME-A / Heme A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6 / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical
ChemComp-TRD / TRIDECANE / LIPID FRAGMENT / Tridecane


Mass: 184.361 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: C13H28
#8: Chemical ChemComp-HTH / (2S,3R)-heptane-1,2,3-triol / heptane-1,2,3-triol


Mass: 148.200 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H16O3
#9: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Cu
#10: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#11: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: Ca
#12: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#13: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C4H12NO3 / Comment: pH buffer*YM
#14: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 456 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.13 Å3/Da / Density % sol: 70.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 100 mM MES, pH 6.3, 27 % PEG-400 2.5 % heptanetriol, 16 mM MgCl2, 0.65 mM CdCl2 and 0.013 % Dodecyl maltoside

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Apr 8, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→42.84 Å / Num. obs: 117531 / % possible obs: 90 % / Redundancy: 5.7 % / Biso Wilson estimate: 46.81 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 22.5
Reflection shellResolution: 2.3→2.38 Å / Rmerge(I) obs: 0.491 / Num. unique obs: 7044

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Processing

Software
NameVersionClassification
PHENIX1.14_3260refinement
PHENIX1.14_3260refinement
JBluIce-EPICSdata collection
HKL-2000data scaling
PHENIXmodel building
PHASERphasing
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2GSM

2gsm


Resolution: 2.5→42.84 Å / SU ML: 0.2486 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 20.0085
RfactorNum. reflection% reflection
Rfree0.2077 2984 3.02 %
Rwork0.1727 --
obs0.1738 98707 97.73 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 51.19 Å2
Refinement stepCycle: LAST / Resolution: 2.5→42.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12299 0 789 456 13544
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006113522
X-RAY DIFFRACTIONf_angle_d1.253818457
X-RAY DIFFRACTIONf_chiral_restr0.06612037
X-RAY DIFFRACTIONf_plane_restr0.00652206
X-RAY DIFFRACTIONf_dihedral_angle_d9.19997469
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5-2.540.27921220.21133821X-RAY DIFFRACTION82.71
2.54-2.580.25151390.20194033X-RAY DIFFRACTION87.83
2.58-2.630.28831340.20144258X-RAY DIFFRACTION92.44
2.63-2.680.21741490.18554409X-RAY DIFFRACTION95.82
2.68-2.740.23331530.17974507X-RAY DIFFRACTION98.23
2.74-2.80.23171340.17194588X-RAY DIFFRACTION99.06
2.8-2.860.2131440.16974607X-RAY DIFFRACTION99.33
2.86-2.930.19321530.16014602X-RAY DIFFRACTION99.69
2.93-3.010.2051440.16534609X-RAY DIFFRACTION99.75
3.01-3.10.20281510.16374613X-RAY DIFFRACTION99.85
3.1-3.20.18211410.15994650X-RAY DIFFRACTION99.83
3.2-3.320.22691490.16164605X-RAY DIFFRACTION99.81
3.32-3.450.24751200.16664658X-RAY DIFFRACTION99.94
3.45-3.610.18741450.17244672X-RAY DIFFRACTION99.9
3.61-3.80.23111420.17344652X-RAY DIFFRACTION99.94
3.8-4.030.19321330.16614689X-RAY DIFFRACTION99.98
4.03-4.340.2091440.15954680X-RAY DIFFRACTION100
4.34-4.780.17321410.15214722X-RAY DIFFRACTION100
4.78-5.470.18991480.16024723X-RAY DIFFRACTION100
5.47-6.890.18111580.18224761X-RAY DIFFRACTION100
6.89-42.840.22531400.20394864X-RAY DIFFRACTION97.93

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