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- PDB-5u7n: CRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCH... -

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Basic information

Entry
Database: PDB / ID: 5u7n
TitleCRYSTAL STRUCTURE OF A CHIMERIC CUA DOMAIN (SUBUNIT II) OF CYTOCHROME BA3 FROM THERMUS THERMOPHILUS WITH THE AMICYANIN LOOP
ComponentsCytochrome c oxidase subunit 2
KeywordsOXIDOREDUCTASE / ELECTRON TRANSPORT
Function / homology
Function and homology information


cytochrome-c oxidase / cytochrome-c oxidase activity / respirasome / copper ion binding / plasma membrane
Similarity search - Function
Cytochrome C oxidase subunit IIa, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane / Ba3-like heme-copper oxidase subunit II, C-terminal / 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 II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxins - blue copper proteins ...Cytochrome C oxidase subunit IIa, transmembrane domain / Cytochrome C oxidase subunit II, transmembrane / Ba3-like heme-copper oxidase subunit II, C-terminal / 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 II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Cupredoxins - blue copper proteins / Cupredoxin / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
COPPER (II) ION / Cytochrome c oxidase subunit 2 / Cytochrome c oxidase subunit 2
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.3 Å
AuthorsOtero, L.H. / Klinke, S. / Espinoza-Cara, A. / Vila, A.J.
CitationJournal: Chem Sci / Year: 2018
Title: Engineering a bifunctional copper site in the cupredoxin fold by loop-directed mutagenesis.
Authors: Espinoza-Cara, A. / Zitare, U. / Alvarez-Paggi, D. / Klinke, S. / Otero, L.H. / Murgida, D.H. / Vila, A.J.
History
DepositionDec 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 22, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2017Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.2Dec 5, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _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: Cytochrome c oxidase subunit 2
B: Cytochrome c oxidase subunit 2
C: Cytochrome c oxidase subunit 2
D: Cytochrome c oxidase subunit 2
E: Cytochrome c oxidase subunit 2
F: Cytochrome c oxidase subunit 2
G: Cytochrome c oxidase subunit 2
H: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,39718
Polymers109,6538
Non-polymers74510
Water9,746541
1
A: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7702
Polymers13,7071
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7702
Polymers13,7071
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8883
Polymers13,7071
Non-polymers1822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7702
Polymers13,7071
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
5
E: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7702
Polymers13,7071
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
6
F: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,8883
Polymers13,7071
Non-polymers1822
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
7
G: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7702
Polymers13,7071
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
8
H: Cytochrome c oxidase subunit 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)13,7702
Polymers13,7071
Non-polymers641
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)94.352, 100.701, 101.103
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Cytochrome c oxidase subunit 2 / / Cytochrome c ba(3) subunit II / Cytochrome c oxidase polypeptide II / Cytochrome cba3 subunit 2


Mass: 13706.594 Da / Num. of mol.: 8 / Fragment: UNP residues 11-116,127-135
Source method: isolated from a genetically manipulated source
Details: THIS IS A CHIMERIC PROTEIN OF CYTOCHROME C OXIDASE SUBUNIT 2 (FRAGMENT). UNIPROT P98052. THE REGION COMPRISING THE RESIDUES 150-159 WAS MODIFIED.
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: cbaB, ctaC / Plasmid: pET28a / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: P98052, UniProt: Q5SJ80*PLUS, cytochrome-c oxidase
#2: Chemical
ChemComp-CU / COPPER (II) ION / Copper


Mass: 63.546 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Cu
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 541 / Source method: isolated from a natural source / Formula: H2O

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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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 60 % (4S)-2-METHYL-2,4-PENTANEDIOL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.5418 Å
DetectorType: BRUKER PHOTON 100 / Detector: CMOS / Date: May 30, 2014
RadiationMonochromator: Helios MX multilayer optics / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.3→45.18 Å / Num. obs: 42870 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 8 % / Biso Wilson estimate: 35.45 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.148 / Rsym value: 0.158 / Net I/σ(I): 12.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 8.2 % / Rmerge(I) obs: 0.931 / Mean I/σ(I) obs: 2.2 / Num. measured obs: 4083 / CC1/2: 0.783 / % possible all: 97.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PHASERphasing
BUSTER2.10.0refinement
PDB_EXTRACT3.22data extraction
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2CUA

2cua


Resolution: 2.3→45.18 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.9207 / SU R Cruickshank DPI: 0.328 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.36 / SU Rfree Blow DPI: 0.224 / SU Rfree Cruickshank DPI: 0.222
RfactorNum. reflection% reflectionSelection details
Rfree0.2258 2088 4.88 %RANDOM
Rwork0.1759 ---
obs0.1783 42817 98.57 %-
Displacement parametersBiso max: 117.67 Å2 / Biso mean: 34.11 Å2 / Biso min: 9.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.525 Å20 Å20 Å2
2--0.4777 Å20 Å2
3---0.0473 Å2
Refine analyzeLuzzati coordinate error obs: 0.275 Å
Refinement stepCycle: final / Resolution: 2.3→45.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7164 0 24 547 7735
Biso mean--41.82 40.01 -
Num. residues----908
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d3181SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes181HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1066HARMONIC5
X-RAY DIFFRACTIONt_it7402HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion980SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8367SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7402HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg10156HARMONIC21.07
X-RAY DIFFRACTIONt_omega_torsion3.59
X-RAY DIFFRACTIONt_other_torsion3.03
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2296 126 4.15 %
Rwork0.2072 2909 -
all0.2081 3035 -
obs--98.57 %
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)
15.5844-0.57060.4382.5249-0.56553.31810.03560.09310.33010.0178-0.04450.00730.01580.02010.0089-0.1239-0.00740.0137-0.07440.0344-0.0745116.22221.616630.2563
22.6387-1.3120.52373.16930.4752.5825-0.0719-0.0449-0.13570.32890.1136-0.0840.09880.0302-0.0417-0.06450.04-0.0458-0.07820.0015-0.068578.179317.596620.2353
31.9258-0.15640.83482.1510.1583.60150.04670.2221-0.02730.0896-0.0181-0.3354-0.070.3335-0.0285-0.11890.0214-0.0328-0.0196-0.0344-0.0377100.95943.21034.9429
42.30940.1928-0.52984.96910.57874.5979-0.0190.1240.2304-0.20620.1105-0.0144-0.0822-0.0819-0.0914-0.0992-0.00270.0122-0.06190.0221-0.1226123.48428.247110.709
52.5495-0.6275-0.86523.90790.37882.6728-0.11180.1164-0.061-0.21180.03070.2701-0.03330.00030.0811-0.05920.00440.0205-0.09350.0078-0.061598.64171.8886-5.3486
62.6703-1.3359-0.25552.25250.14691.59610.16760.3658-0.0744-0.0877-0.14510.0119-0.01580.019-0.0225-0.04730.06910.01990.018-0.0086-0.112885.4556.0654-3.0285
71.9653-1.1403-0.0282.37310.33872.3905-0.1054-0.08670.08930.27340.1379-0.02440.01090.0671-0.03240.01050.08510.0163-0.0510.0175-0.120965.610633.328.6551
84.1530.63210.06413.76450.47073.1640.14310.07140.04230.07560.0132-0.02960.08390.113-0.1563-0.109-0.0008-0.0107-0.086-0.0006-0.079696.430744.810235.9181
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|* }A49 - 163
2X-RAY DIFFRACTION2{ B|* }B48 - 163
3X-RAY DIFFRACTION3{ C|* }C48 - 163
4X-RAY DIFFRACTION4{ D|* }D50 - 163
5X-RAY DIFFRACTION5{ E|* }E51 - 163
6X-RAY DIFFRACTION6{ F|* }F55 - 163
7X-RAY DIFFRACTION7{ G|* }G53 - 163
8X-RAY DIFFRACTION8{ H|* }H50 - 163

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