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Basic information

Entry
Database: PDB / ID: 3qjt
TitleThe structure of and photolytic induced changes of carbon monoxide binding to the cytochrome ba3-oxidase from Thermus thermophilus
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • Cytochrome c oxidase polypeptide 2A
KeywordsOXIDOREDUCTASE / CYTOCHROME BA3 OXIDASE / Carbon monoxide / CO photodissociation
Function / homology
Function and homology information


oxidative phosphorylation / cytochrome-c oxidase / 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
CARBON MONOXIDE / COPPER (I) 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 / MOLECULAR REPLACEMENT / Resolution: 2.95 Å
AuthorsLiu, B. / Zhang, Y. / Sage, J.T. / Doukov, T. / Chen, Y. / Stout, C.D. / Fee, J.A.
Citation
Journal: Biochim.Biophys.Acta / Year: 2012
Title: Structural changes that occur upon photolysis of the Fe(II)(a3)-CO complex in the cytochrome ba(3)-oxidase of Thermus thermophilus: A combined X-ray crystallographic and infrared spectral ...Title: Structural changes that occur upon photolysis of the Fe(II)(a3)-CO complex in the cytochrome ba(3)-oxidase of Thermus thermophilus: A combined X-ray crystallographic and infrared spectral study demonstrates CO binding to Cu(B).
Authors: Liu, B. / Zhang, Y. / Sage, J.T. / Soltis, S.M. / Doukov, T. / Chen, Y. / Stout, C.D. / Fee, J.A.
#1: Journal: Biochemistry / Year: 2009
Title: Combined microspectrophotometric and crystallographic examination of chemically-reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: Structure of the ...Title: Combined microspectrophotometric and crystallographic examination of chemically-reduced and X-ray radiation-reduced forms of cytochrome ba3 oxidase from Thermus thermophilus: Structure of the reduced form of the enzyme
Authors: Liu, B. / Chen, Y. / Doukov, T. / Soltis, S.M. / Stout, C.D. / Fee, J.A.
#2: Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba3 from Thermus thermophilus
Authors: Liu, B. / Luna, V.M. / Chen, Y. / Stout, C.D. / Fee, J.A.
History
DepositionJan 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 4, 2012Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation
Item: _audit_author.name / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / pdbx_struct_special_symmetry / 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_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_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_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_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 subunit 1
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase polypeptide 2A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,5368
Polymers85,7803
Non-polymers1,7565
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12850 Å2
ΔGint-148 kcal/mol
Surface area25440 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.964, 114.964, 148.562
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-499-

PRO

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Components

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Cytochrome c oxidase subunit ... , 2 types, 2 molecules AB

#1: Protein Cytochrome c oxidase subunit 1 / Cytochrome c ba(3) subunit I / Cytochrome c oxidase polypeptide I / Cytochrome cba3 subunit 1


Mass: 63430.008 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: cbaA, TTHA1135 / Plasmid: PMK18 / Production host: thermus thermophilus (bacteria) / Strain (production host): HB8 / References: UniProt: Q5SJ79, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / Cytochrome c ba(3) subunit II / Cytochrome c oxidase polypeptide II / Cytochrome cba3 subunit 2


Mass: 18580.314 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: cbaB, ctaC, TTHA1134 / Plasmid: PMK18 / Production host: thermus thermophilus (bacteria) / Strain (production host): HB8 / References: UniProt: Q5SJ80, cytochrome-c oxidase

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Protein/peptide , 1 types, 1 molecules C

#3: Protein/peptide Cytochrome c oxidase polypeptide 2A / Cytochrome c ba(3) subunit IIA / Cytochrome c oxidase polypeptide IIA / Cytochrome cba3 subunit 2A


Mass: 3769.602 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: cbaD, TTHA1133 / Plasmid: PMK18 / Production host: thermus thermophilus (bacteria) / Strain (production host): HB8 / References: UniProt: P82543, cytochrome-c oxidase

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Non-polymers , 5 types, 5 molecules

#4: Chemical ChemComp-CU1 / COPPER (I) ION


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


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


Mass: 920.954 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C54H64FeN4O6
#7: Chemical ChemComp-CMO / CARBON MONOXIDE


Mass: 28.010 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CO
#8: Chemical ChemComp-CUA / DINUCLEAR COPPER ION


Mass: 127.092 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cu2

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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: 2.86 Å3/Da / Density % sol: 57.01 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 7% PEK 2K, 50 mM KCl, 20 mM Bis-Tris pH 7.0, 6.5 mM n-nonyl-beta-D-glucopyranoside , VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97946 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Apr 3, 2008
RadiationMonochromator: FLAT MIRROR (VERTICAL FOCUSING), SINGLE CRYSTAL FOCUSING, SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 2.95→20 Å / Num. all: 19662 / Num. obs: 19662 / % possible obs: 92.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rsym value: 0.074 / Net I/σ(I): 3.5
Reflection shellResolution: 2.95→3.11 Å / Redundancy: 2.9 % / Mean I/σ(I) obs: 1.8 / Num. unique all: 6677 / Rsym value: 0.383 / % possible all: 92.1

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
REFMAC5.5.0072refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1XME

1xme


Resolution: 2.95→19.62 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.856 / SU B: 55.389 / SU ML: 0.481 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.57 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.3232 976 5 %RANDOM
Rwork0.25784 ---
all0.26101 19662 --
obs0.26101 18674 91.33 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 75.428 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.95→19.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5966 0 113 0 6079
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0226290
X-RAY DIFFRACTIONr_angle_refined_deg2.0221.9898644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.0875753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.39722.213235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg23.47715909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.0241529
X-RAY DIFFRACTIONr_chiral_restr0.1380.2961
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0214778
X-RAY DIFFRACTIONr_mcbond_it0.2781.53607
X-RAY DIFFRACTIONr_mcangle_it0.53225827
X-RAY DIFFRACTIONr_scbond_it0.97632416
X-RAY DIFFRACTIONr_scangle_it1.5854.52456
LS refinement shellResolution: 2.95→3.025 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 53 -
Rwork0.273 1065 -
obs--72.04 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.7838-0.541-0.46591.46980.5121.7268-0.1302-0.2446-0.10820.19130.2169-0.14290.2970.4192-0.08670.11080.07580.00310.121-0.0260.0514-24.827916.44920.4603
21.7877-0.7621-0.6472.30230.71142.09380.13090.00410.3072-0.09150.046-0.1206-0.33380.0099-0.17690.0942-0.01770.04410.0363-0.03720.1109-40.114440.91150.5982
35.5498-2.76242.23633.665-1.9011.17940.23250.12480.0111-1.5026-0.04370.46370.53260.0131-0.18881.04820.1624-0.10220.14390.15720.2639-33.860326.4138-20.6635
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A6 - 562
2X-RAY DIFFRACTION2B3 - 168
3X-RAY DIFFRACTION3C2 - 34

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