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- PDB-4txo: Crystal structure of the mixed disulfide complex of thioredoxin-l... -

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Basic information

Entry
Database: PDB / ID: 4txo
TitleCrystal structure of the mixed disulfide complex of thioredoxin-like TlpAs(C110S) and copper chaperone ScoIs(C74S)
Components
  • Blr1131 protein
  • Thiol:disulfide interchange protein TlpA
KeywordsOXIDODREDUCTASE/COPPER BINDING PROTEIN / mixed disulfide / soluble domain of membrane protein / thioredoxin fold / copper protein / protein binding / OXIDODREDUCTASE-COPPER BINDING PROTEIN complex
Function / homology
Function and homology information


cytochrome complex assembly / disulfide oxidoreductase activity / membrane / metal ion binding / plasma membrane
Similarity search - Function
Copper chaperone SCO1/SenC / SCO1/SenC / Redoxin / Redoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin ...Copper chaperone SCO1/SenC / SCO1/SenC / Redoxin / Redoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
DI(HYDROXYETHYL)ETHER / THIOCYANATE ION / Thiol:disulfide interchange protein TlpA / Blr1131 protein
Similarity search - Component
Biological speciesBradyrhizobium diazoefficiens USDA 110 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å
AuthorsScharer, M.A. / Abicht, H.K. / Glockshuber, R. / Hennecke, H.
Funding support Switzerland, 3items
OrganizationGrant numberCountry
Swiss National Science Foundation Switzerland
Promedica Foundation, Chur, SwitzerlandGHDE KXQ7-DZZ [1276/M)] Switzerland
ETH Zurich 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 4, 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 / Derived calculations / Refinement description
Category: atom_site / pdbx_audit_support ...atom_site / pdbx_audit_support / pdbx_distant_solvent_atoms / pdbx_validate_close_contact / pdbx_validate_symm_contact / software / struct_site_gen
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 / _pdbx_audit_support.funding_organization / _pdbx_distant_solvent_atoms.auth_seq_id / _pdbx_validate_close_contact.auth_seq_id_1 / _pdbx_validate_close_contact.auth_seq_id_2 / _pdbx_validate_symm_contact.auth_seq_id_1 / _pdbx_validate_symm_contact.auth_seq_id_2 / _struct_site_gen.auth_seq_id
Revision 2.1Dec 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
C: Thiol:disulfide interchange protein TlpA
D: Blr1131 protein
A: Thiol:disulfide interchange protein TlpA
B: Blr1131 protein
E: Thiol:disulfide interchange protein TlpA
F: Blr1131 protein
G: Thiol:disulfide interchange protein TlpA
H: Blr1131 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,68613
Polymers155,4188
Non-polymers2685
Water10,629590
1
C: Thiol:disulfide interchange protein TlpA
D: Blr1131 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,0194
Polymers38,8542
Non-polymers1642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-6 kcal/mol
Surface area15230 Å2
MethodPISA
2
A: Thiol:disulfide interchange protein TlpA
B: Blr1131 protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)38,9595
Polymers38,8542
Non-polymers1043
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1970 Å2
ΔGint-25 kcal/mol
Surface area15110 Å2
MethodPISA
3
E: Thiol:disulfide interchange protein TlpA
F: Blr1131 protein


Theoretical massNumber of molelcules
Total (without water)38,8542
Polymers38,8542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1570 Å2
ΔGint-9 kcal/mol
Surface area15450 Å2
MethodPISA
4
G: Thiol:disulfide interchange protein TlpA
H: Blr1131 protein


Theoretical massNumber of molelcules
Total (without water)38,8542
Polymers38,8542
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1430 Å2
ΔGint-15 kcal/mol
Surface area15060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.030, 173.220, 66.690
Angle α, β, γ (deg.)90.000, 89.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 2 types, 8 molecules CAEGDBFH

#1: Protein
Thiol:disulfide interchange protein TlpA / Cytochrome c biogenesis protein TlpA


Mass: 19528.553 Da / Num. of mol.: 4 / Fragment: UNP Residues 38-221 / Mutation: C110S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria)
Gene: tlpA, bll1380 / Plasmid: pMal-p/TlpASC110S / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P43221
#2: Protein
Blr1131 protein / ScoI S


Mass: 19325.930 Da / Num. of mol.: 4 / Fragment: UNP Residues 30-196 / Mutation: C74S, WSHPQFEK: StrepII purification tag
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bradyrhizobium diazoefficiens USDA 110 (bacteria)
Gene: blr1131 / Plasmid: pRJ8336 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q89VB6

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Non-polymers , 4 types, 595 molecules

#3: Chemical ChemComp-SCN / THIOCYANATE ION / Thiocyanate


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#5: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 590 / 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: 2.23 Å3/Da / Density % sol: 44.87 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 8
Details: Crystals were grown with the sitting-drop vapor diffusion technique by mixing 0.75 ul of the TlpA-ScoI complex (10 mg/ml in 10 mM Tris-HCl, pH 8) with 0.75 ul of precipitant solution (final ...Details: Crystals were grown with the sitting-drop vapor diffusion technique by mixing 0.75 ul of the TlpA-ScoI complex (10 mg/ml in 10 mM Tris-HCl, pH 8) with 0.75 ul of precipitant solution (final concentration: 3% glycerol, 0.2 M NaSCN and 16.0% (w/v) PEG 3350) and equilibration over 100 ul of well solution (3% Glycerol, 0.2 M NaSCN, 28% PEG 3350).

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.97941 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: May 26, 2013
RadiationMonochromator: Barrtels MONOCHROMATOR WITH DUAL CHANNEL CUT CRYSTALS
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97941 Å / Relative weight: 1
Reflection twinOperator: h,-k,-l / Fraction: 0.5
ReflectionResolution: 2.2→50 Å / Num. obs: 68110 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / Biso Wilson estimate: 40.4 Å2 / Rmerge F obs: 0.996 / Rmerge(I) obs: 0.147 / Rrim(I) all: 0.158 / Χ2: 0.911 / Net I/σ(I): 10.55 / Num. measured all: 512163
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
2.2-2.30.4821.1651.3236432862081611.31994.7
2.3-2.40.5740.9931.7737030720870781.10498.2
2.4-2.50.7180.7732.4935453608660160.84898.8
2.5-30.9090.4764.5614324219751196680.51299.6
3-3.50.9860.18511.778809010021100000.19799.8
3.5-40.9960.1120.0657643566156600.116100
4-60.9980.07128.4479261809880980.075100
6-80.9980.06131.9920066196419640.064100
8-100.9990.04743.0875807237230.049100
10-200.9990.04347.6366086516510.045100
20-3010.03942.7461769690.041100
30-4010.03343.4811014140.035100
4010.03332.38311480.03857.1

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Phasing

PhasingMethod: molecular replacement
Phasing MRPacking: 0

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.14data extraction
PHASERphasing
PHENIX(phenix.refine: 1.8.4_1496)refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entries 1jfu, 1xzo

1jfu

1xzo


Resolution: 2.2→49.338 Å / FOM work R set: 0.8556 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.95 / Stereochemistry target values: TWIN_LSQ_F
RfactorNum. reflection% reflectionSelection details
Rfree0.2068 1371 2.01 %Random
Rwork0.1742 66738 --
obs0.1749 68109 98.89 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 128.77 Å2 / Biso mean: 43.43 Å2 / Biso min: 6.54 Å2
Refinement stepCycle: final / Resolution: 2.2→49.338 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10193 0 15 590 10798
Biso mean--34.98 30.58 -
Num. residues----1335
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00610434
X-RAY DIFFRACTIONf_angle_d1.0814132
X-RAY DIFFRACTIONf_chiral_restr0.0421602
X-RAY DIFFRACTIONf_plane_restr0.0061835
X-RAY DIFFRACTIONf_dihedral_angle_d12.1363909
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.2001-2.27880.34171300.27836332646292
2.2788-2.370.30381350.24816606674196
2.37-2.47790.30081350.22666654678997
2.4779-2.60850.26721360.22556666680297
2.6085-2.77190.26091370.2136704684198
2.7719-2.98590.21231380.19396746688498
2.9859-3.28630.22411360.17376676681298
3.2863-3.76160.18611390.15746798693798
3.7616-4.73840.16091370.13326743688098
4.7384-44.63850.14871400.14326813695398
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)
12.3678-0.13111.05680.9131-0.05791.34090.09690.1023-0.19240.02870.0034-0.10980.10880.1418-0.09560.13020.0026-0.02120.3969-0.02190.387641.1585-12.6935-2.9235
21.6250.2638-1.48161.150.11941.4823-0.007-0.112-0.04580.0488-0.0402-0.02210.10320.0960.04510.11790.0176-0.0190.35270.01860.281317.3423-13.0093-19.7317
32.9049-0.83-0.50372.6086-0.15773.23710.04940.04350.3128-0.02030.1058-0.0039-0.1713-0.4098-0.12920.151-0.02080.01070.21130.01370.3084-11.28851.688330.536
42.6532-0.27350.17070.3397-0.09511.9695-0.06290.0070.17180.15650.03830.0748-0.16520.0650.01710.2205-0.0113-0.00110.0984-0.01240.292412.76992.286313.6185
52.8611-1.02190.40630.3953-0.25021.90510.16670.1513-0.3553-0.0246-0.0958-0.10510.3285-0.0685-0.05390.5107-0.0211-0.01810.2126-0.01960.52776.0403-37.818618.3928
61.92660.1821-0.74243.78050.46013.3786-0.0278-0.0344-0.58690.0428-0.0399-0.06340.31650.36090.05780.29710.07880.01350.24860.03340.492921.1348-39.864743.6191
72.3689-0.1848-0.80693.92812.66373.15850.15580.06980.4254-0.27880.0066-0.3343-0.4488-0.0351-0.15320.3731-0.01870.0390.27020.06940.424223.985827.1095-14.881
81.2362-0.2793-0.00283.33210.62933.7141-0.0997-0.03340.3237-0.07160.10090.2067-0.2950.17520.01490.33280.00110.02210.19090.01680.60918.361929.071510.3352
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain AA39 - 215
2X-RAY DIFFRACTION2chain BB39 - 196
3X-RAY DIFFRACTION3chain CC40 - 216
4X-RAY DIFFRACTION4chain DD38 - 196
5X-RAY DIFFRACTION5chain EE39 - 216
6X-RAY DIFFRACTION6chain FF39 - 196
7X-RAY DIFFRACTION7chain GG40 - 215
8X-RAY DIFFRACTION8chain HH40 - 196

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