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- PDB-6zmu: Crystal structure of the germline-specific thioredoxin protein De... -

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Basic information

Entry
Database: PDB / ID: 6zmu
TitleCrystal structure of the germline-specific thioredoxin protein Deadhead (Thioredoxin-1) from Drospohila melanogaster, P43212
ComponentsThioredoxin-1
KeywordsOXIDOREDUCTASE / homeostasis / sperm / oocyte-to-embryo / DNA-binding / redox / protamine
Function / homology
Function and homology information


sperm DNA decondensation / head development / glutathione disulfide oxidoreductase activity / female meiotic nuclear division / protein-disulfide reductase activity / nucleus / cytosol
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin, conserved site / Thioredoxin family active site. / Thioredoxin domain profile. / Thioredoxin domain / Thioredoxin-like superfamily
Similarity search - Domain/homology
Biological speciesDrosophila melanogaster (fruit fly)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsBaginski, B. / Pluta, R. / Macias, M.J.
Funding support Spain, European Union, 3items
OrganizationGrant numberCountry
Spanish Ministry of Economy and CompetitivenessBFU2014-53787-P Spain
European Commission754510European Union
European Commission754558European Union
Citation
Journal: Iucrj / Year: 2021
Title: Structures of the germline-specific Deadhead and thioredoxin T proteins from Drosophila melanogaster reveal unique features among thioredoxins.
Authors: Freier, R. / Aragon, E. / Baginski, B. / Pluta, R. / Martin-Malpartida, P. / Ruiz, L. / Condeminas, M. / Gonzalez, C. / Macias, M.J.
#1: Journal: Biorxiv / Year: 2020
Title: Structures of the germline-specific Deadhead and Thioredoxin T proteins from Drosophila melanogaster reveal unique features among Thioredoxins
Authors: Freier, R. / Aragon, E. / Baginski, B. / Pluta, R. / Martin-Malpartida, P. / Ruiz, L. / Condeminas, M. / Gonzaez, C. / Macias, M.
History
DepositionJul 3, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 21, 2020Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2021Group: Database references / Category: citation / citation_author
Revision 1.2Jan 31, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.journal_id_ISSN / _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: Thioredoxin-1
B: Thioredoxin-1
C: Thioredoxin-1
D: Thioredoxin-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,70720
Polymers50,2434
Non-polymers1,46416
Water1,69394
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6750 Å2
ΔGint-193 kcal/mol
Surface area20840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.827, 111.827, 106.991
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein
Thioredoxin-1 / DmTrx-1 / Protein deadhead


Mass: 12560.693 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Drosophila melanogaster (fruit fly) / Gene: dhd, Trx-1, CG4193 / Production host: Escherichia coli (E. coli) / References: UniProt: P47938
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 15 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 3.33 Å3/Da / Density % sol: 63.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 0.1 M sodium citrate, pH 5.0, 3.2 M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 7, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.95→77.43 Å / Num. obs: 43714 / % possible obs: 96.7 % / Redundancy: 10.8 % / CC1/2: 1 / Net I/σ(I): 18.1
Reflection shellResolution: 1.97→2.054 Å / Mean I/σ(I) obs: 1.5 / Num. unique obs: 2187 / CC1/2: 0.617

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1xwa

1xwa


Resolution: 1.95→77.43 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.951 / SU B: 7.461 / SU ML: 0.1 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.22035 2119 4.8 %RANDOM
Rwork0.18532 ---
obs0.187 41617 87.73 %-
Solvent computationIon probe radii: 0.9 Å / Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: MASK
Displacement parametersBiso mean: 58.161 Å2
Baniso -1Baniso -2Baniso -3
1--0.2 Å20 Å20 Å2
2---0.2 Å20 Å2
3---0.4 Å2
Refinement stepCycle: LAST / Resolution: 1.95→77.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3428 0 76 94 3598
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193554
X-RAY DIFFRACTIONr_bond_other_d0.0010.023425
X-RAY DIFFRACTIONr_angle_refined_deg1.7531.8934770
X-RAY DIFFRACTIONr_angle_other_deg1.1732.9397907
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.55421
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.70522.549153
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.56515699
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.2961533
X-RAY DIFFRACTIONr_chiral_restr0.1020.2524
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.023763
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02750
X-RAY DIFFRACTIONr_mcbond_it3.8663.3541690
X-RAY DIFFRACTIONr_mcbond_other3.8623.3521689
X-RAY DIFFRACTIONr_mcangle_it4.8565.0052106
X-RAY DIFFRACTIONr_mcangle_other4.8565.0072107
X-RAY DIFFRACTIONr_scbond_it7.664.2071864
X-RAY DIFFRACTIONr_scbond_other6.6634.0181805
X-RAY DIFFRACTIONr_scangle_other8.7395.7272574
X-RAY DIFFRACTIONr_long_range_B_refined10.90939.3323840
X-RAY DIFFRACTIONr_long_range_B_other10.88939.2373828
LS refinement shellResolution: 1.952→2.003 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.372 20 -
Rwork0.341 436 -
obs--12.59 %
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)
12.1548-0.8665-0.93970.94690.02663.5199-0.0223-0.19270.1643-0.00660.10850.04680.0478-0.0169-0.08620.0306-0.00910.00470.0305-0.00550.0465128.43141.395109.037
23.49411.057-0.8734.31-1.57023.03060.13680.55790.4352-0.13730.01040.3706-0.3513-0.296-0.14710.10810.06320.04280.20120.04280.1232102.58948.737107.23
36.4438-1.25931.3375.85670.32912.94450.19520.2312-1.06460.3447-0.1335-0.40580.65140.3927-0.06170.20030.05930.03120.1963-0.07140.3713111.66918.472119.962
44.37871.56980.55832.86540.25951.8512-0.14190.6408-0.043-0.47810.233-0.07930.1129-0.2196-0.0910.118-0.06220.01850.2648-0.02540.01883.92326.135108.705
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 107
2X-RAY DIFFRACTION2B1 - 105
3X-RAY DIFFRACTION3C1 - 105
4X-RAY DIFFRACTION4D1 - 106

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