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- PDB-5jy5: Crystal structure of Thioredoxin 1 from Cryptococcus neoformans a... -

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Basic information

Entry
Database: PDB / ID: 5jy5
TitleCrystal structure of Thioredoxin 1 from Cryptococcus neoformans at 1.8 Angstroms resolution
ComponentsThioredoxin
KeywordsOXIDOREDUCTASE / Thioredoxin 1 Cryptococcus neoformans X-ray crystallography
Function / homology
Function and homology information


protein-disulfide reductase activity
Similarity search - Function
Thioredoxin / Thioredoxin / Thioredoxin family active site. / Thioredoxin, conserved site / Thioredoxin domain profile. / Thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesCryptococcus neoformans var. grubii serotype A (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBravo-Chaucanes, C.P. / Abadio, A.K.R. / Kioshima, E.S. / 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/CNPq193.000.569/2009 Brazil
CitationJournal: To Be Published
Title: Crystal structure of Thioredoxin 1 from Cryptococcus neoformans at 1.8 Angstroms resolution
Authors: Bravo-Chaucanes, C.P. / Abadio, A.K.R. / Kioshima, E.S. / Felipe, M.S.S. / Barbosa, J.A.R.G.
History
DepositionMay 13, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 7, 2017Provider: 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 1.3Sep 27, 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 1.4Oct 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: Thioredoxin
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,2759
Polymers24,5882
Non-polymers6877
Water6,251347
1
A: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,5744
Polymers12,2941
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)12,7015
Polymers12,2941
Non-polymers4064
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Thioredoxin
B: Thioredoxin
hetero molecules

A: Thioredoxin
B: Thioredoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,55018
Polymers49,1774
Non-polymers1,37314
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation10_555-y,-x,-z+1/31
Buried area7090 Å2
ΔGint-73 kcal/mol
Surface area18960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)110.706, 110.706, 91.763
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number181
Space group name H-MP6422
Components on special symmetry positions
IDModelComponents
11A-312-

HOH

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Components

#1: Protein Thioredoxin


Mass: 12294.145 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Cryptococcus neoformans var. grubii serotype A (fungus)
Strain: H99 / ATCC 208821 / CBS 10515 / FGSC 9487 / Gene: CNAG_02801 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysE / References: UniProt: J9VKF2
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 347 / 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: 3.34 Å3/Da / Density % sol: 63.13 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.7 / Details: 1.6 M ammonium sulfate, 0.02 M tris hydrochloride / PH range: 7.6-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: LNLS / Beamline: W01B-MX2 / Wavelength: 1.2398 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.2398 Å / Relative weight: 1
ReflectionResolution: 1.8→25 Å / Num. obs: 31224 / % possible obs: 100 % / Redundancy: 37.1 % / Rmerge(I) obs: 0.092 / Net I/σ(I): 52.9
Reflection shellResolution: 1.8→1.86 Å / Redundancy: 34.7 % / Rmerge(I) obs: 0.581 / Mean I/σ(I) obs: 6.2 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
DENZOHKL-2000_704ydata reduction
SCALEPACKHKL-2000_704ydata scaling
PHASER7.0.004phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2J23

2j23


Resolution: 1.8→95.87 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 3.413 / SU ML: 0.056 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19549 1542 5 %RANDOM
Rwork0.15634 ---
obs0.15826 29599 99.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 37.274 Å2
Baniso -1Baniso -2Baniso -3
1--0.9 Å2-0.45 Å2-0 Å2
2---0.9 Å20 Å2
3---2.91 Å2
Refinement stepCycle: 1 / Resolution: 1.8→95.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1632 0 41 347 2020
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0191774
X-RAY DIFFRACTIONr_bond_other_d0.0030.021737
X-RAY DIFFRACTIONr_angle_refined_deg2.1891.9612421
X-RAY DIFFRACTIONr_angle_other_deg1.13934045
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6075231
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.48725.93864
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.35415315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.1450.2282
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211910
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02350
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7082.401863
X-RAY DIFFRACTIONr_mcbond_other1.6752.393861
X-RAY DIFFRACTIONr_mcangle_it2.3243.5831080
X-RAY DIFFRACTIONr_mcangle_other2.3233.5861081
X-RAY DIFFRACTIONr_scbond_it3.1372.796908
X-RAY DIFFRACTIONr_scbond_other3.0812.774900
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.6593.9981318
X-RAY DIFFRACTIONr_long_range_B_refined8.5223.6212387
X-RAY DIFFRACTIONr_long_range_B_other8.27521.2982168
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.801→1.848 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.184 109 -
Rwork0.163 2160 -
obs--99.74 %
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)
10.52520.2571-0.01830.32820.18230.428-0.02210.0367-0.0083-0.00750.04990.0304-0.01410.0427-0.02780.1152-0.0263-0.01220.1133-0.00970.0257-35.18736.16612.918
20.32040.27570.51090.84810.65441.2430.11040.0068-0.01330.1110.0085-0.05410.20890.0981-0.11890.150.0046-0.04380.1019-0.01620.0322-28.41522.49736.878
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 106
2X-RAY DIFFRACTION2B2 - 105

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