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- PDB-5w4c: Crystal structure of thioredoxin reductase from Cryptococcus neof... -

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Basic information

Entry
Database: PDB / ID: 5w4c
TitleCrystal structure of thioredoxin reductase from Cryptococcus neoformans in complex with FAD (FO conformation)
ComponentsThioredoxin reductase
KeywordsOXIDOREDUCTASE / Thioredoxin reductase Cryptococcus neoformans X-ray Diffraction
Function / homology
Function and homology information


thioredoxin-disulfide reductase / thioredoxin-disulfide reductase (NADPH) activity / removal of superoxide radicals / cytoplasm
Similarity search - Function
Thioredoxin reductase / Pyridine nucleotide-disulphide oxidoreductase, class-II, active site / Pyridine nucleotide-disulphide oxidoreductases class-II active site. / FAD/NAD(P)-binding domain / Pyridine nucleotide-disulphide oxidoreductase / FAD/NAD(P)-binding domain superfamily
Similarity search - Domain/homology
ACETATE ION / FLAVIN-ADENINE DINUCLEOTIDE / DI(HYDROXYETHYL)ETHER / Thioredoxin reductase
Similarity search - Component
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.255 Å
AuthorsBravo-Chaucanes, C.P. / Valadares, N.F. / Felipe, M.S.S. / Barbosa, J.A.R.G.
Funding support Brazil, 2items
OrganizationGrant numberCountry
Brazilian National Council for Scientific and Technological Development (CNPq)564007/2010-2 Brazil
FAPDF/CNPq193000569/2009 Brazil
CitationJournal: To be published
Title: Crystal structure of thioredoxin reductase from Cryptococcus neoformans in complex with FAD (FO conformation)
Authors: Bravo-Chaucanes, C.P. / Valadares, N.F. / Felipe, M.S.S. / Barbosa, J.A.R.G.
History
DepositionJun 9, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 13, 2018Provider: repository / Type: Initial release
Revision 1.1Apr 17, 2019Group: Author supporting evidence / Data collection / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2Jan 8, 2020Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Thioredoxin reductase
B: Thioredoxin reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,87211
Polymers79,8312
Non-polymers2,0419
Water5,368298
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9210 Å2
ΔGint-73 kcal/mol
Surface area27560 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.140, 108.828, 70.354
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Thioredoxin reductase


Mass: 39915.652 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (strain H99 / ATCC 208821 / CBS 10515 / FGSC 9487) (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_05847 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: J9VRX9, thioredoxin-disulfide reductase

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Non-polymers , 6 types, 307 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


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


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#6: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 298 / 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: 2.07 Å3/Da / Density % sol: 40.56 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.3
Details: 11.4% PEG 8000, 20% V/V glycerol, 80 mM MES pH 6.3 and 160 mM Calcium acetate
PH range: 6.2-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.4586 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Nov 9, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.4586 Å / Relative weight: 1
ReflectionResolution: 2.25→27.94 Å / Num. obs: 31825 / % possible obs: 99.86 % / Redundancy: 5.9 % / CC1/2: 0.766 / Rmerge(I) obs: 0.204 / Rpim(I) all: 0.09 / Rsym value: 0.204 / Net I/σ(I): 2.58
Reflection shellHighest resolution: 2.25 Å / Rmerge(I) obs: 0.829 / Rpim(I) all: 0.367 / Rsym value: 0.828

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
DENZOHKL 2000-7044data reduction
SCALEPACKHKL2000-7044data scaling
PHASER7.0.004phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ITJ

3itj


Resolution: 2.255→27.94 Å / SU ML: 0.25 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 21.88
RfactorNum. reflection% reflection
Rfree0.2275 1636 5.14 %
Rwork0.1661 --
obs0.1692 31825 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.255→27.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5144 0 132 298 5574
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0075380
X-RAY DIFFRACTIONf_angle_d0.8837324
X-RAY DIFFRACTIONf_dihedral_angle_d8.8753119
X-RAY DIFFRACTIONf_chiral_restr0.053838
X-RAY DIFFRACTIONf_plane_restr0.005930
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2546-2.3210.30491330.20252462X-RAY DIFFRACTION99
2.321-2.39580.24751320.17772476X-RAY DIFFRACTION100
2.3958-2.48140.30141380.18412463X-RAY DIFFRACTION100
2.4814-2.58070.27161380.18082489X-RAY DIFFRACTION100
2.5807-2.69810.2561550.17442474X-RAY DIFFRACTION100
2.6981-2.84020.26391350.17012487X-RAY DIFFRACTION100
2.8402-3.01790.22111290.1582514X-RAY DIFFRACTION100
3.0179-3.25060.1991310.14472504X-RAY DIFFRACTION100
3.2506-3.57710.18611450.13982516X-RAY DIFFRACTION100
3.5771-4.09340.20591430.12932535X-RAY DIFFRACTION100
4.0934-5.15190.19811240.14582580X-RAY DIFFRACTION100
5.1519-27.9460.24581330.23142689X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -4.2057 Å / Origin y: 15.5006 Å / Origin z: -0.5499 Å
111213212223313233
T0.1569 Å2-0.0126 Å20.0022 Å2-0.1851 Å20.0061 Å2--0.164 Å2
L0.1928 °2-0.1438 °2-0.0339 °2-0.9516 °20.102 °2--0.3212 °2
S-0.0123 Å °-0.0189 Å °-0.0056 Å °-0.0349 Å °0.0094 Å °0.1144 Å °0.0117 Å °-0.0353 Å °0.0054 Å °
Refinement TLS groupSelection details: all

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