- PDB-2yev: Structure of caa3-type cytochrome oxidase -
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Open data
ID or keywords:
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Basic information
Entry
Database: PDB / ID: 2yev
Title
Structure of caa3-type cytochrome oxidase
Components
(CYTOCHROME C OXIDASE ...) x 2
CAA3-TYPE CYTOCHROME OXIDASE SUBUNIT IV
Keywords
ELECTRON TRANSPORT
Function / homology
Function and homology information
oxidative phosphorylation / cytochrome-c oxidase / cytochrome-c oxidase activity / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / respiratory electron transport chain / copper ion binding / heme binding / membrane ...oxidative phosphorylation / cytochrome-c oxidase / cytochrome-c oxidase activity / electron transport coupled proton transport / : / ATP synthesis coupled electron transport / respiratory electron transport chain / copper ion binding / heme binding / membrane / metal ion binding / plasma membrane Similarity search - Function
Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #110 / Cytochrome oxidase Caa3-type, subunit IV / Caa3-type Cytochrome c oxidase subunit II, cupredoxin domain / Cytochrome oxidase Caa3-type, subunit IV superfamily / CAA3-type cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit I bacterial type / Cytochrome c oxidase, subunit III, four-helix bundle / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain ...Methane Monooxygenase Hydroxylase; Chain G, domain 1 - #110 / Cytochrome oxidase Caa3-type, subunit IV / Caa3-type Cytochrome c oxidase subunit II, cupredoxin domain / Cytochrome oxidase Caa3-type, subunit IV superfamily / CAA3-type cytochrome c oxidase subunit IV / Cytochrome c oxidase, subunit I bacterial type / Cytochrome c oxidase, subunit III, four-helix bundle / Helix Hairpins - #90 / Cytochrome C Oxidase; Chain A / Cytochrome c oxidase-like, subunit I domain / Methane Monooxygenase Hydroxylase; Chain G, domain 1 / Cytochrome c oxidase, subunit II / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane domain / Cytochrome oxidase subunit II transmembrane region profile. / Cytochrome c oxidase subunit III-like / Cytochrome c oxidase, subunit III, 4-helical bundle / Cytochrome c oxidase subunit III / Heme-copper oxidase subunit III family profile. / Cytochrome c oxidase subunit III-like superfamily / Cytochrome c/quinol oxidase subunit II / 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. / Helix Hairpins - #70 / Cytochrome c / Cupredoxins - blue copper proteins / Cytochrome c family profile. / Cytochrome c-like domain / Cytochrome c-like domain superfamily / Four Helix Bundle (Hemerythrin (Met), subunit A) / Cupredoxin / Helix non-globular / Special / Helix Hairpins / Up-down Bundle / Immunoglobulin-like / Sandwich / Orthogonal Bundle / Mainly Beta / Mainly Alpha Similarity search - Domain/homology
(2R)-3-HYDROXYPROPANE-1,2-DIYL DIHEXADECANOATE / Chem-5PL / (2R)-2,3-DIHYDROXYPROPYL (7Z)-TETRADEC-7-ENOATE / 1,3-DIHYDROXYPROPAN-2-YL (Z)-TETRADEC-7-ENOATE / COPPER (II) ION / DINUCLEAR COPPER ION / HEME-AS / HEME C / Cytochrome c oxidase polypeptide I+III / Cytochrome oxidase Caa3-type subunit IV domain-containing protein / Cytochrome c oxidase subunit 2 Similarity search - Component
Mass: 18.015 Da / Num. of mol.: 392 / Source method: isolated from a natural source / Formula: H2O
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Details
Nonpolymer details
HEME C (HEC): THIOETHER CROSSLINKS BETWEEN ATOMS CAB AND SG OF CYS 247 IN CHAINS B AND E. THIOETHER ...HEME C (HEC): THIOETHER CROSSLINKS BETWEEN ATOMS CAB AND SG OF CYS 247 IN CHAINS B AND E. THIOETHER CROSSLINKS BETWEEN ATOMS CAC AND SG OF CYS 250 IN CHAINS B AND E.
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Experimental details
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Experiment
Experiment
Method: X-RAY DIFFRACTION / Number of used crystals: 21
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Sample preparation
Crystal
Density Matthews: 2.78 Å3/Da / Density % sol: 55.83 % / Description: NONE
Crystal grow
Method: lipidic cubic phase / pH: 5 Details: 16-21% PEG 400, 0.1 M NA CITRATE PH 4.5-5.0, 0-0.1 M LITHIUM SULPHATE, 0.1 M NACL. CRYSTALLISED USING THE LIPIDIC CUBIC PHASE USING 7.7 MAG AS THE HOSTING LIPID.
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Data collection
Diffraction
ID
Mean temperature (K)
Crystal-ID
1
100
1
2
100
1
Diffraction source
Source
Site
Beamline
ID
Wavelength
SYNCHROTRON
APS
23-ID-B
1
0.97777
SYNCHROTRON
Diamond
I24
2
Detector
Type
ID
Detector
Date
Details
MARRESEARCH
1
CCD
Jun 17, 2010
TWO K-B PAIRS OF BIMORPH TYPE MIRRORS
MARRESEARCH
2
CCD
Radiation
ID
Monochromator
Protocol
Monochromatic (M) / Laue (L)
Scattering type
Wavelength-ID
1
ACCELFIXEDEXITDOUBLECRYSTALSI(111)
SINGLEWAVELENGTH
M
x-ray
1
2
SINGLEWAVELENGTH
M
x-ray
1
Radiation wavelength
Wavelength: 0.97777 Å / Relative weight: 1
Reflection
Resolution: 2.36→53.48 Å / Num. obs: 118251 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.4 % / Rmerge(I) obs: 0.16 / Net I/σ(I): 9.5
Reflection shell
Resolution: 2.36→2.49 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.98 / Mean I/σ(I) obs: 2.3 / % possible all: 100