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- PDB-3omi: Catalytic core subunits (I and II) of cytochrome C oxidase from R... -

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Basic information

Entry
Database: PDB / ID: 3omi
TitleCatalytic core subunits (I and II) of cytochrome C oxidase from Rhodobacter sphaeroides with D132A mutation
Components(Cytochrome c ...) x 2
KeywordsOXIDOREDUCTASE / TRANSMEMBRANE PROTEIN COMPLEX
Function / homology
Function and homology information


respiratory chain complex IV / cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / electron transport coupled proton transport / ATP synthesis coupled electron transport / respiratory electron transport chain / 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; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit I domain / 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 ...Cytochrome c oxidase, subunit I bacterial type / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Cytochrome c oxidase, subunit II / Cytochrome c oxidase subunit I domain / 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 / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / 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 / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
: / COPPER (II) ION / COPPER (I) 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: 2.15 Å
AuthorsLiu, J. / Qin, L. / Ferguson-Miller, S.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Crystallographic and online spectral evidence for role of conformational change and conserved water in cytochrome oxidase proton pump.
Authors: Liu, J. / Qin, L. / Ferguson-Miller, S.
History
DepositionAug 27, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2May 2, 2012Group: Structure summary
Revision 1.3Nov 19, 2014Group: Non-polymer description
Revision 1.4Nov 8, 2017Group: Refinement description / Category: software
Revision 1.5Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / pdbx_validate_chiral / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_entry_details.has_protein_modification / _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.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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_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, aa3 type, subunit I
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase, aa3 type, subunit I
D: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)187,82047
Polymers176,2284
Non-polymers11,59243
Water8,845491
1
A: Cytochrome c oxidase, aa3 type, subunit I
B: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,50226
Polymers88,1142
Non-polymers6,38824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17920 Å2
ΔGint-185 kcal/mol
Surface area25880 Å2
MethodPISA
2
C: Cytochrome c oxidase, aa3 type, subunit I
D: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,31821
Polymers88,1142
Non-polymers5,20419
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area15900 Å2
ΔGint-196 kcal/mol
Surface area26210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)125.064, 131.519, 175.674
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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

#1: Protein Cytochrome c oxidase, aa3 type, subunit I


Mass: 59496.344 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 17-551 / Mutation: D132A
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, CTAD, RHOS4_04590, RSP_1877 / Plasmid: pRK415-1 / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: Q3J5A7, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2


Mass: 28617.637 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 30-281
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, CTAB, CTAC, RHOS4_04060, RSP_1826 / Plasmid: pRK415-1 / Production host: Rhodobacter sphaeroides (bacteria) / References: UniProt: Q3J5G0, cytochrome-c oxidase

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Sugars , 1 types, 11 molecules

#4: Sugar
ChemComp-DMU / DECYL-BETA-D-MALTOPYRANOSIDE / DECYLMALTOSIDE


Type: D-saccharide / Mass: 482.562 Da / Num. of mol.: 11
Source method: isolated from a genetically manipulated source
Formula: C22H42O11 / Comment: detergent*YM

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Non-polymers , 11 types, 523 molecules

#3: Chemical ChemComp-OH / HYDROXIDE ION


Mass: 17.007 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: HO
#5: Chemical
ChemComp-TRD / TRIDECANE / LIPID FRAGMENT


Mass: 184.361 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C13H28
#6: Chemical
ChemComp-HEA / HEME-A


Mass: 852.837 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C49H56FeN4O6
#7: Chemical
ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cu
#8: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#10: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#11: Chemical ChemComp-HTH / (2S,3R)-heptane-1,2,3-triol / heptane-1,2,3-triol


Mass: 148.200 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C7H16O3
#12: Chemical ChemComp-CU1 / COPPER (I) ION


Mass: 63.546 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cu
#13: Chemical
ChemComp-CD / CADMIUM ION


Mass: 112.411 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cd
#14: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 491 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer detailsLIGANDS LABELLED AS TRD ARE ALL ALKYL CHAINS WITH DIFFERENT LENGTHS OF EITHER DMU OR NATIVE ...LIGANDS LABELLED AS TRD ARE ALL ALKYL CHAINS WITH DIFFERENT LENGTHS OF EITHER DMU OR NATIVE MEMBRANE LIPIDS SUCH AS PHOSPHATIDYL ETHANOLAMINE OR CARDIOLIPIN. THE AUTHORS DO NOT KNOW FOR SURE THE IDENTITIES OF THE COMPLETE MOLECULES.

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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: 4.1 Å3/Da / Density % sol: 69.99 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 26-29% PEG 400, pH 6.3, VAPOR DIFFUSION, SITTING DROP, temperature 277K, vapor diffusion, sitting drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 15, 2009
RadiationMonochromator: Diamond / Protocol: SINGLE WEAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97872 Å / Relative weight: 1
ReflectionResolution: 2.15→50 Å / Num. obs: 151816 / % possible obs: 97.3 % / Redundancy: 6.9 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 12
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsDiffraction-ID% possible all
2.15-2.2450.556181.6
2.24-2.335.80.451193.4
2.33-2.436.40.361198.9
2.43-2.567.10.2771100
2.56-2.727.30.1971100
2.72-2.937.40.1441100
2.93-3.237.50.1071100
3.23-3.697.50.0861100
3.69-4.657.50.0721100
4.65-507.20.049198.8

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
MD2data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→35.84 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.937 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 3.594 / SU ML: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: THERE IS RESIDUAL DENSITY IN (FO-FC) DIFFERENCE FOURIER MAP AT THE MAGNESIUM SITES IN BOTH MOLECULES AND THE B-FACTOR FOR EACH MAGNESIUM ION IS UNUSUALLY LOW. THESE OBSERVATIONS SUGGEST THAT ...Details: THERE IS RESIDUAL DENSITY IN (FO-FC) DIFFERENCE FOURIER MAP AT THE MAGNESIUM SITES IN BOTH MOLECULES AND THE B-FACTOR FOR EACH MAGNESIUM ION IS UNUSUALLY LOW. THESE OBSERVATIONS SUGGEST THAT THIS MAGNESIUM SITE MAY BE PARTIALLY OCCUPIED BY A HEAVIER META ION IN THE PROTEIN CRYSTAL. THERE ARE RESIDUAL DENSITIES IN (FO-FC) DIFFERENCE FOURIER MAP AT THE SITE OF CU AND HEMEA FE. THESE DENSITIES SUGGEST THAT THE METEAL CENTER OF THIS MUTATNT MIGHT BE IN A STATE DIFFERENT FROM WILD TYPE IN CRYSTAL.
RfactorNum. reflection% reflection
Rfree0.215 4574 3 %
Rwork0.192 --
obs0.193 151679 96.5 %
Solvent computationSolvent model: MASK
Displacement parametersBiso mean: 38.49 Å2
Baniso -1Baniso -2Baniso -3
1--1.61 Å20 Å20 Å2
2---0.37 Å20 Å2
3---1.99 Å2
Refinement stepCycle: LAST / Resolution: 2.15→35.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms12279 0 646 491 13416
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.02213333
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1641.97518197
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.5451573
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20822.769502
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.436151804
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.2271537
X-RAY DIFFRACTIONr_chiral_restr0.0840.22011
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0210036
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.20.27023
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3130.29302
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1390.2656
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1210.221
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1820.251
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0730.25
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.6571.58027
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.072212608
X-RAY DIFFRACTIONr_scbond_it1.48436264
X-RAY DIFFRACTIONr_scangle_it2.1124.55587
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.21 Å
RfactorNum. reflection% reflection
Rfree0.293 231 -
Rwork0.252 7705 -
obs--69.36 %

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