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- PDB-1ehk: CRYSTAL STRUCTURE OF THE ABERRANT BA3-CYTOCHROME-C OXIDASE FROM T... -

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Basic information

Entry
Database: PDB / ID: 1ehk
TitleCRYSTAL STRUCTURE OF THE ABERRANT BA3-CYTOCHROME-C OXIDASE FROM THERMUS THERMOPHILUS
Components(BA3-TYPE CYTOCHROME-C ...) x 3
KeywordsOXIDOREDUCTASE / cytochrome-c oxidase / membrane protein / Thermus thermophilus
Function / homology
Function and homology information


cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / : / copper ion binding / heme binding / metal ion binding / plasma membrane
Similarity search - Function
Cytochrome c oxidase polypeptide 2A / Cytochrome c oxidase polypeptide 2A, ba3 type / Cytochrome c oxidase subunit IIa family / Ba3-like heme-copper oxidase subunit I / Cytochrome C oxidase subunit IIa, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane / Ba3-like heme-copper oxidase subunit II, C-terminal / : / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain ...Cytochrome c oxidase polypeptide 2A / Cytochrome c oxidase polypeptide 2A, ba3 type / Cytochrome c oxidase subunit IIa family / Ba3-like heme-copper oxidase subunit I / Cytochrome C oxidase subunit IIa, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane / Ba3-like heme-copper oxidase subunit II, C-terminal / : / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / 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. / Rhopdopsin 7-helix transmembrane proteins / Rhodopsin 7-helix transmembrane proteins / Cupredoxins - blue copper proteins / Cupredoxin / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha
Similarity search - Domain/homology
COPPER (II) ION / DINUCLEAR COPPER ION / HEME-AS / PROTOPORPHYRIN IX CONTAINING FE / Cytochrome c oxidase polypeptide 2A / Cytochrome c oxidase subunit 1 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / THE STRUCTURE WAS SOLVED BY MULTIPLE ANOMALOUS DISPERSION (MAD) USING 5 DIFFERENT WAVELENGTH (2X FE-EDGE, 2X CU-EDGE, 1 REMOTE). THE DATA STATISTICS GIVEN CORRESPOND TO THE REFERENCE WAVELENGTH WHICH WAS USED FOR REFINEMENT. THE STRUCTURE WAS SOLVED WITH SHARP. / Resolution: 2.4 Å
AuthorsSoulimane, T. / Buse, G. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R. / Than, M.E.
CitationJournal: EMBO J. / Year: 2000
Title: Structure and mechanism of the aberrant ba(3)-cytochrome c oxidase from thermus thermophilus.
Authors: Soulimane, T. / Buse, G. / Bourenkov, G.P. / Bartunik, H.D. / Huber, R. / Than, M.E.
History
DepositionFeb 21, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 22, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Jul 29, 2020Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / pdbx_struct_conn_angle / pdbx_unobs_or_zero_occ_atoms / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.mon_nstd_flag / _chem_comp.name ..._chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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.pdbx_leaving_atom_flag / _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
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Nov 13, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_unobs_or_zero_occ_atoms / pdbx_validate_chiral
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: BA3-TYPE CYTOCHROME-C OXIDASE
B: BA3-TYPE CYTOCHROME-C OXIDASE
C: BA3-TYPE CYTOCHROME-C OXIDASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,44010
Polymers84,7933
Non-polymers2,6477
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area13690 Å2
ΔGint-142 kcal/mol
Surface area25170 Å2
MethodPISA
Unit cell
Length a, b, c (Å)112.110, 112.110, 161.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

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BA3-TYPE CYTOCHROME-C ... , 3 types, 3 molecules ABC

#1: Protein BA3-TYPE CYTOCHROME-C OXIDASE


Mass: 62573.098 Da / Num. of mol.: 1 / Fragment: SUBUNIT I / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJ79, cytochrome-c oxidase
#2: Protein BA3-TYPE CYTOCHROME-C OXIDASE


Mass: 18581.299 Da / Num. of mol.: 1 / Fragment: SUBUNIT II / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: Q5SJ80, cytochrome-c oxidase
#3: Protein/peptide BA3-TYPE CYTOCHROME-C OXIDASE


Mass: 3638.407 Da / Num. of mol.: 1 / Fragment: SUBUNIT IIA / Source method: isolated from a natural source / Source: (natural) Thermus thermophilus (bacteria) / Strain: HB8 / References: UniProt: P82543, cytochrome-c oxidase

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Sugars , 1 types, 3 molecules

#4: Sugar ChemComp-BNG / nonyl beta-D-glucopyranoside / Beta-NONYLGLUCOSIDE / nonyl beta-D-glucoside / nonyl D-glucoside / nonyl glucoside


Type: D-saccharide / Mass: 306.395 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C15H30O6 / Comment: detergent*YM
IdentifierTypeProgram
b-nonylglucosideIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0

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Non-polymers , 5 types, 123 molecules

#5: Chemical ChemComp-CU / COPPER (II) ION


Mass: 63.546 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu
#6: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#7: Chemical ChemComp-HAS / HEME-AS


Mass: 920.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H64FeN4O6
#8: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2
#9: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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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: 3.02 Å3/Da / Density % sol: 59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7
Details: PEG 2000, Bis-Tris buffer, nonyl-beta-D-glucoside, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
114 %PEG20001reservoir
220 mMBis-Tris1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MPG/DESY, HAMBURG / Beamline: BW6 / Wavelength: 1.05
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.05 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 39379 / Num. obs: 39379 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 46.3 Å2 / Rmerge(I) obs: 0.043
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.147 / Num. unique all: 7703 / % possible all: 100
Reflection
*PLUS

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.3refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: THE STRUCTURE WAS SOLVED BY MULTIPLE ANOMALOUS DISPERSION (MAD) USING 5 DIFFERENT WAVELENGTH (2X FE-EDGE, 2X CU-EDGE, 1 REMOTE). THE DATA STATISTICS GIVEN CORRESPOND TO ...Method to determine structure: THE STRUCTURE WAS SOLVED BY MULTIPLE ANOMALOUS DISPERSION (MAD) USING 5 DIFFERENT WAVELENGTH (2X FE-EDGE, 2X CU-EDGE, 1 REMOTE). THE DATA STATISTICS GIVEN CORRESPOND TO THE REFERENCE WAVELENGTH WHICH WAS USED FOR REFINEMENT. THE STRUCTURE WAS SOLVED WITH SHARP.
Resolution: 2.4→20 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 3262390.49 / Data cutoff high rms absF: 3262390.49 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Details: bulk solvent & overall anisotropic B-factors used
RfactorNum. reflection% reflectionSelection details
Rfree0.264 1972 5 %RANDOM
Rwork0.222 ---
obs0.222 39379 96.3 %-
Displacement parametersBiso mean: 50.6 Å2
Baniso -1Baniso -2Baniso -3
1-9.46 Å20 Å20 Å2
2--9.46 Å20 Å2
3----18.92 Å2
Refine analyzeLuzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 4 Å / Luzzati sigma a obs: 0.2 Å
Refinement stepCycle: LAST / Resolution: 2.4→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5851 0 174 119 6144
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d19.7
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.09
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it3.11.5
X-RAY DIFFRACTIONc_mcangle_it4.372
X-RAY DIFFRACTIONc_scbond_it4.432
X-RAY DIFFRACTIONc_scangle_it5.412.5
LS refinement shellResolution: 2.4→2.49 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.299 198 5.2 %
Rwork0.254 3623 -
obs--95 %
Software
*PLUS
Name: CNS / Version: 0.3 / Classification: refinement
Refinement
*PLUS
σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 50.6 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg19.7
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.09
X-RAY DIFFRACTIONc_mcbond_it1.5
X-RAY DIFFRACTIONc_scbond_it2
X-RAY DIFFRACTIONc_mcangle_it2
X-RAY DIFFRACTIONc_scangle_it2.5
LS refinement shell
*PLUS
Rfactor Rfree: 0.299 / % reflection Rfree: 5.2 % / Rfactor Rwork: 0.254 / Rfactor obs: 0.254

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