- PDB-1ehk: CRYSTAL STRUCTURE OF THE ABERRANT BA3-CYTOCHROME-C OXIDASE FROM T... -
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Basic information
Entry
Database: PDB / ID: 1ehk
Title
CRYSTAL STRUCTURE OF THE ABERRANT BA3-CYTOCHROME-C OXIDASE FROM THERMUS THERMOPHILUS
Components
(BA3-TYPE CYTOCHROME-C ...) x 3
Keywords
OXIDOREDUCTASE / 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 species
Thermus thermophilus (bacteria)
Method
X-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
Resolution: 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
Name
Version
Classification
SHARP
phasing
CNS
0.3
refinement
DENZO
datareduction
SCALEPACK
datascaling
Refinement
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 ...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
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.264
1972
5 %
RANDOM
Rwork
0.222
-
-
-
obs
0.222
39379
96.3 %
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Displacement parameters
Biso mean: 50.6 Å2
Baniso -1
Baniso -2
Baniso -3
1-
9.46 Å2
0 Å2
0 Å2
2-
-
9.46 Å2
0 Å2
3-
-
-
-18.92 Å2
Refine analyze
Luzzati coordinate error obs: 0.28 Å / Luzzati d res low obs: 4 Å / Luzzati sigma a obs: 0.2 Å
Refinement step
Cycle: LAST / Resolution: 2.4→20 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
5851
0
174
119
6144
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
X-RAY DIFFRACTION
c_bond_d
0.008
X-RAY DIFFRACTION
c_bond_d_na
X-RAY DIFFRACTION
c_bond_d_prot
X-RAY DIFFRACTION
c_angle_d
X-RAY DIFFRACTION
c_angle_d_na
X-RAY DIFFRACTION
c_angle_d_prot
X-RAY DIFFRACTION
c_angle_deg
1.6
X-RAY DIFFRACTION
c_angle_deg_na
X-RAY DIFFRACTION
c_angle_deg_prot
X-RAY DIFFRACTION
c_dihedral_angle_d
19.7
X-RAY DIFFRACTION
c_dihedral_angle_d_na
X-RAY DIFFRACTION
c_dihedral_angle_d_prot
X-RAY DIFFRACTION
c_improper_angle_d
1.09
X-RAY DIFFRACTION
c_improper_angle_d_na
X-RAY DIFFRACTION
c_improper_angle_d_prot
X-RAY DIFFRACTION
c_mcbond_it
3.1
1.5
X-RAY DIFFRACTION
c_mcangle_it
4.37
2
X-RAY DIFFRACTION
c_scbond_it
4.43
2
X-RAY DIFFRACTION
c_scangle_it
5.41
2.5
LS refinement shell
Resolution: 2.4→2.49 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 10
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