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- PDB-2qpd: An unexpected outcome of surface-engineering an integral membrane... -

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Basic information

Entry
Database: PDB / ID: 2qpd
TitleAn unexpected outcome of surface-engineering an integral membrane protein: Improved crystallization of cytochrome ba3 oxidase from Thermus thermophilus
Components
  • (Cytochrome c oxidase subunit ...) x 2
  • Cytochrome c oxidase polypeptide 2A
KeywordsOXIDOREDUCTASE / cytochrome ba3 oxidase / heme / integral membrane protein / Electron transport / Hydrogen ion transport / Ion transport / Iron / Metal-binding / Respiratory chain / Transmembrane / Transport / Formylation
Function / homology
Function and homology information


cytochrome-c oxidase / oxidative phosphorylation / cytochrome-c oxidase activity / respirasome / 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 / Copper centre Cu(A) ...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 (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: 3.25 Å
AuthorsLiu, B. / Luna, V.M. / Chen, Y. / Stout, C.D. / Fee, J.A.
Citation
Journal: Acta Crystallogr.,Sect.F / Year: 2007
Title: An unexpected outcome of surface engineering an integral membrane protein: improved crystallization of cytochrome ba(3) from Thermus thermophilus.
Authors: Liu, B. / Luna, V.M. / Chen, Y. / Stout, C.D. / Fee, J.A.
#1: Journal: Protein Expr.Purif. / Year: 2005
Title: A homologous expression system for obtaining engineered cytochrome ba3 from Thermus thermophilus
Authors: Chen, Y. / Hunsicker-Wang, L.M. / Pacoma, R.L. / Luna, E. / Fee, J.A.
History
DepositionJul 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)87,5097
Polymers85,7813
Non-polymers1,7284
Water0
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.19, 115.19, 149.14
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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 oxidase polypeptide I / Cytochrome c ba3 / subunit I / Cytochrome cba3 subunit 1


Mass: 63430.008 Da / Num. of mol.: 1 / Mutation: K258R
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: cbaA / Plasmid: PMK18 / Species (production host): Thermus thermophilus / Production host: Thermus thermophilus HB8 (bacteria) / Strain (production host): HB8 / References: UniProt: Q5SJ79, cytochrome-c oxidase
#2: Protein Cytochrome c oxidase subunit 2 / / Cytochrome c oxidase polypeptide II / Cytochrome c ba3 / subunit II / Cytochrome cba3 subunit 2


Mass: 18581.299 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: cbaB, ctaC / Plasmid: PMK18 / Species (production host): Thermus thermophilus / Production host: Thermus thermophilus HB8 (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 oxidase polypeptide IIA / Cytochrome c ba3 / subunit 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 / Plasmid: PMK18 / Species (production host): Thermus thermophilus / Production host: Thermus thermophilus HB8 (bacteria) / Strain (production host): HB8 / References: UniProt: P82543, cytochrome-c oxidase

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Non-polymers , 4 types, 4 molecules

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


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


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-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: 2.88 Å3/Da / Density % sol: 57.34 %
Crystal growTemperature: 291 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 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 6, 2007 / Details: mirrors
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: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.25→20 Å / Num. all: 13540 / Num. obs: 13540 / % possible obs: 82.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.3 % / Rmerge(I) obs: 0.032 / Net I/σ(I): 18.1
Reflection shellResolution: 3.25→3.43 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.618 / Mean I/σ(I) obs: 1.2 / Num. unique all: 2076 / % possible all: 82.8

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
Blu-Icedata collection
MOSFLMdata reduction
SCALAdata scaling
PHASESphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1XME

1xme


Resolution: 3.25→19.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.906 / SU B: 48.531 / SU ML: 0.467 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.652 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.307 780 4.9 %RANDOM
Rwork0.215 ---
all0.3067 13540 --
obs0.21982 13540 77.18 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 44.113 Å2
Baniso -1Baniso -2Baniso -3
1-0.45 Å20 Å20 Å2
2--0.45 Å20 Å2
3----0.9 Å2
Refinement stepCycle: LAST / Resolution: 3.25→19.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5966 0 111 0 6077
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0226289
X-RAY DIFFRACTIONr_angle_refined_deg2.6221.9898644
X-RAY DIFFRACTIONr_dihedral_angle_1_deg10.0655753
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.56222.213235
X-RAY DIFFRACTIONr_dihedral_angle_3_deg25.55415909
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.7161529
X-RAY DIFFRACTIONr_chiral_restr0.1530.2964
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024779
X-RAY DIFFRACTIONr_nbd_refined0.3310.24460
X-RAY DIFFRACTIONr_nbtor_refined0.3560.24197
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2330.2359
X-RAY DIFFRACTIONr_metal_ion_refined0.1410.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3430.2125
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.26
X-RAY DIFFRACTIONr_mcbond_it3.54923893
X-RAY DIFFRACTIONr_mcangle_it5.87836089
X-RAY DIFFRACTIONr_scbond_it8.53742920
X-RAY DIFFRACTIONr_scangle_it11.77962551
LS refinement shellResolution: 3.087→3.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.601 26 -
Rwork0.306 472 -
obs--34.32 %
Refinement TLS params.Method: refined / Origin x: -28.783 Å / Origin y: 22.314 Å / Origin z: -0.518 Å
111213212223313233
T0.3661 Å20.0524 Å20.0075 Å2-0.3829 Å2-0.0767 Å2--0.6728 Å2
L0.945 °2-0.4125 °2-0.6254 °2-1.0525 °20.5202 °2--1.1132 °2
S-0.039 Å °-0.2093 Å °0.1287 Å °0.0758 Å °0.2258 Å °-0.0929 Å °0.143 Å °0.2309 Å °-0.1869 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA11 - 56217 - 568
2X-RAY DIFFRACTION1BB3 - 1683 - 168
3X-RAY DIFFRACTION1CC3 - 343 - 34

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