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- PDB-4txv: Crystal structure of the mixed disulfide intermediate between thi... -

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Basic information

Entry
Database: PDB / ID: 4txv
TitleCrystal structure of the mixed disulfide intermediate between thioredoxin-like TlpAs(C110S) and subunit II of cytochrome c oxidase CoxBPD (C233S)
Components
  • Cytochrome c oxidase subunit 2
  • Thiol:disulfide interchange protein TlpA
KeywordsPROTEIN BINDING / thioredoxin / mixed disulphide / cytochrome c oxidase
Function / homology
Function and homology information


cytochrome complex assembly / disulfide oxidoreductase activity / cytochrome-c oxidase / cytochrome-c oxidase activity / ATP synthesis coupled electron transport / copper ion binding / plasma membrane
Similarity search - Function
: / Redoxin / Redoxin / Cytochrome c oxidase subunit 2, C-terminal / 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/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily ...: / Redoxin / Redoxin / Cytochrome c oxidase subunit 2, C-terminal / 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/quinol oxidase subunit II / Cytochrome C oxidase subunit II, transmembrane domain superfamily / Copper centre Cu(A) / CO II and nitrous oxide reductase dinuclear copper centers signature. / Cytochrome C oxidase subunit II, periplasmic domain / Cytochrome c oxidase subunit II-like C-terminal / Cytochrome oxidase subunit II copper A binding domain profile. / Thioredoxin, conserved site / Thioredoxin family active site. / Cupredoxins - blue copper proteins / Thioredoxin domain profile. / Thioredoxin domain / Cupredoxin / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / Immunoglobulin-like / Sandwich / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Cytochrome c oxidase subunit 2 / Thiol:disulfide interchange protein TlpA
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsQuade, N. / Abicht, H.K. / Hennecke, H. / Glockshuber, R.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Promedica Foundation, Chur, SwitzerlandGHDE KXQ7-DZZ [1276/M)] Switzerland
ETH Zurich Switzerland
Swiss National Science Foundation Switzerland
CitationJournal: J.Biol.Chem. / Year: 2014
Title: How Periplasmic Thioredoxin TlpA Reduces Bacterial Copper Chaperone ScoI and Cytochrome Oxidase Subunit II (CoxB) Prior to Metallation.
Authors: Abicht, H.K. / Scharer, M.A. / Quade, N. / Ledermann, R. / Mohorko, E. / Capitani, G. / Hennecke, H. / Glockshuber, R.
History
DepositionJul 7, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Oct 1, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 15, 2014Group: Database references
Revision 1.2Dec 3, 2014Group: Database references
Revision 2.0Sep 6, 2017Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Refinement description
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / software
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_seq_id / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_2
Revision 2.1Jun 13, 2018Group: Data collection / Database references / Source and taxonomy
Category: entity_src_gen / struct_ref ...entity_src_gen / struct_ref / struct_ref_seq / struct_ref_seq_dif
Item: _entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.pdbx_gene_src_gene / _entity_src_gen.pdbx_gene_src_scientific_name / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_beg / _struct_ref_seq.seq_align_end
Revision 2.2Dec 20, 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
Revision 2.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Thiol:disulfide interchange protein TlpA
B: Cytochrome c oxidase subunit 2
C: Thiol:disulfide interchange protein TlpA
D: Cytochrome c oxidase subunit 2


Theoretical massNumber of molelcules
Total (without water)73,8914
Polymers73,8914
Non-polymers00
Water7,999444
1
A: Thiol:disulfide interchange protein TlpA
B: Cytochrome c oxidase subunit 2


Theoretical massNumber of molelcules
Total (without water)36,9452
Polymers36,9452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1990 Å2
ΔGint-10 kcal/mol
Surface area15140 Å2
MethodPISA
2
C: Thiol:disulfide interchange protein TlpA
D: Cytochrome c oxidase subunit 2


Theoretical massNumber of molelcules
Total (without water)36,9452
Polymers36,9452
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1920 Å2
ΔGint-10 kcal/mol
Surface area14670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.830, 81.640, 109.370
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 Thiol:disulfide interchange protein TlpA / Cytochrome c biogenesis protein TlpA


Mass: 19528.553 Da / Num. of mol.: 2 / Fragment: UNP residues 40-217 / Mutation: C110S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens (bacteria)
Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110 / Gene: tlpA, bll1380 / Production host: Escherichia coli (E. coli) / References: UniProt: P43221
#2: Protein Cytochrome c oxidase subunit 2


Mass: 17416.859 Da / Num. of mol.: 2 / Fragment: UNP residues 123-264 / Mutation: C233S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110) (bacteria)
Strain: JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110 / Gene: coxB / Plasmid: pProExHTa-His6-CoxBPDC233S / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: H7C6E5, cytochrome-c oxidase
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 444 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.39 Å3/Da / Density % sol: 48.45 %
Crystal growTemperature: 292 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 20% PEG2000 MME, 0.8M formic acid/NaOH, 0.1 M Na-cacodylate

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Data collection

DiffractionMean temperature: 77 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 45680 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 3.48 % / Biso Wilson estimate: 40.055 Å2 / Rmerge F obs: 0.999 / Rmerge(I) obs: 0.063 / Rrim(I) all: 0.074 / Χ2: 0.986 / Net I/σ(I): 13.57 / Num. measured all: 301989
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2-2.050.6150.8171.6222255654563230.96396.6
2.05-2.110.6850.6661.9521843631262260.78798.6
2.11-2.170.7910.5222.4120653613260580.61998.8
2.17-2.230.8330.412319850597759000.4998.7
2.23-2.310.8950.323.8319372579257320.38199
2.31-2.390.9290.2744.720130560755540.32199.1
2.39-2.480.9550.2325.4119232540253100.27298.3
2.48-2.580.9690.1787.0218473520451500.20999
2.58-2.690.9760.1428.517510498349530.16799.4
2.69-2.830.9850.10810.4915725473746980.12899.2
2.83-2.980.9910.08114.2615591453945150.09699.5
2.98-3.160.9950.06318.3715289430742850.07499.5
3.16-3.380.9970.04624.9914480402340000.05499.4
3.38-3.650.9980.03729.513115372536970.04499.2
3.65-40.9980.03133.111363344634000.03798.7
4-4.470.9990.02637.6210191312730790.03198.5
4.47-5.160.9990.02342.89621274327060.02798.7
5.16-6.320.9990.02539.48088233123050.02998.9
6.32-8.940.9990.02143.995772178317520.02698.3
8.940.9990.01954.3434369839660.02298.3

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2 Å49.25 Å
Translation2 Å49.25 Å

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
REFMAC5.8.0071refinement
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entriues 1JFU and 1m56

1jfu

1m56


Resolution: 2→65.42 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.951 / WRfactor Rfree: 0.1921 / WRfactor Rwork: 0.148 / FOM work R set: 0.8397 / SU B: 4.465 / SU ML: 0.121 / SU R Cruickshank DPI: 0.1614 / SU Rfree: 0.1504 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.161 / ESU R Free: 0.15 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2116 2304 5 %RANDOM
Rwork0.1629 43376 --
obs0.1654 45680 99.11 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 131.15 Å2 / Biso mean: 39.402 Å2 / Biso min: 20.94 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å2-0 Å2-0 Å2
2---0.65 Å20 Å2
3---1.85 Å2
Refinement stepCycle: final / Resolution: 2→65.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4823 0 0 444 5267
Biso mean---44.18 -
Num. residues----628
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0194934
X-RAY DIFFRACTIONr_bond_other_d0.0020.024824
X-RAY DIFFRACTIONr_angle_refined_deg1.8251.9686689
X-RAY DIFFRACTIONr_angle_other_deg0.882311143
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.7595623
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.66924.745196
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.15415843
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3771521
X-RAY DIFFRACTIONr_chiral_restr0.1150.2748
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215506
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021043
X-RAY DIFFRACTIONr_mcbond_it3.1463.5652507
X-RAY DIFFRACTIONr_mcbond_other3.1453.5642506
X-RAY DIFFRACTIONr_mcangle_it4.3175.3183125
LS refinement shellResolution: 1.999→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.296 169 -
Rwork0.257 3123 -
all-3292 -
obs--97.34 %

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