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- PDB-5co3: Crystal structure of a novel disulfide oxidoreductase from Deinoc... -

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Basic information

Entry
Database: PDB / ID: 5co3
TitleCrystal structure of a novel disulfide oxidoreductase from Deinococcus radiodurans crystallized in presence of DTT
ComponentsFrnE protein
KeywordsOXIDOREDUCTASE / Disulfide oxidoreductase / Disulfide isomerase / FrnE
Function / homologyDSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / oxidoreductase activity / 3-Layer(aba) Sandwich / Alpha Beta / FrnE protein
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsBihani, S.C. / Panicker, L. / Kumar, V.
CitationJournal: Antioxid. Redox Signal. / Year: 2018
Title: drFrnE Represents a Hitherto Unknown Class of Eubacterial Cytoplasmic Disulfide Oxido-Reductases.
Authors: Bihani, S.C. / Panicker, L. / Rajpurohit, Y.S. / Misra, H.S. / Kumar, V.
History
DepositionJul 19, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 4, 2018Group: Data collection / Database references / Derived calculations
Category: citation / diffrn_source / pdbx_struct_oper_list
Item: _citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_beamline ..._citation.journal_id_CSD / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.type / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Apr 10, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.3Nov 8, 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

Downloads & links

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Assembly

Deposited unit
A: FrnE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,5862
Polymers28,4941
Non-polymers921
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-1 kcal/mol
Surface area11910 Å2
Unit cell
Length a, b, c (Å)47.729, 63.520, 86.247
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Protein FrnE protein


Mass: 28493.875 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422) (radioresistant)
Strain: ATCC 13939 / DSM 20539 / JCM 16871 / LMG 4051 / NBRC 15346 / NCIMB 9279 / R1 / VKM B-1422
Gene: DR_0659 / Plasmid: pET21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q9RWK7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / 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: 2.29 Å3/Da / Density % sol: 46.39 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5 / Details: PEG 8000, Glycerol, Sodium acetate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→38.16 Å / Num. obs: 31826 / % possible obs: 98.7 % / Redundancy: 5 % / Rmerge(I) obs: 0.034 / Net I/σ(I): 23.5
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.574 / Mean I/σ(I) obs: 2.2 / % possible all: 88.7

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Processing

Software
NameVersionClassification
PHENIXrefinement
PDB_EXTRACT3.15data extraction
XDSdata processing
Aimlessdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CNW

5cnw


Resolution: 1.65→38.158 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.03 / Phase error: 25.02 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2149 1587 5.05 %
Rwork0.1861 29860 -
obs0.1876 31447 97.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 104.64 Å2 / Biso mean: 39.5825 Å2 / Biso min: 17.28 Å2
Refinement stepCycle: final / Resolution: 1.65→38.158 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1758 0 6 146 1910
Biso mean--43.26 41.57 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061838
X-RAY DIFFRACTIONf_angle_d0.8672498
X-RAY DIFFRACTIONf_chiral_restr0.037268
X-RAY DIFFRACTIONf_plane_restr0.004333
X-RAY DIFFRACTIONf_dihedral_angle_d15.113680
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 11

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.70330.32171270.24012486261391
1.7033-1.76410.29311520.25312697284998
1.7641-1.83480.24341340.225227282862100
1.8348-1.91830.30491470.26282687283498
1.9183-2.01940.27341450.23712680282598
2.0194-2.14590.26841540.22162692284698
2.1459-2.31160.22651700.20652643281397
2.3116-2.54420.2521360.19652776291299
2.5442-2.91220.21881400.19042771291199
2.9122-3.66860.21191390.16562826296599
3.6686-38.16770.15851430.15572874301796
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)
12.23051.3938-1.00941.0362-0.32141.2085-0.1823-0.1618-0.51430.14680.09020.16940.2726-0.16560.0540.24930.00410.04480.20880.08530.34420.4957145.855104.6878
23.5428-1.2477-3.2221.01920.95772.9271-0.1507-0.9107-0.11020.22190.1164-0.01240.34980.1821-0.01530.36660.01460.04950.35250.12340.5469-3.6349142.4589112.488
30.87460.71810.32531.6024-1.21782.7753-0.30410.9333-0.84-0.3951-0.0371-0.32460.38290.29080.19580.37550.00980.15260.4963-0.11110.40618.3476147.421590.2904
45.05770.3096-0.90831.4765-0.09982.2129-0.017-0.3111-0.37760.12210.03020.0075-0.06370.1593-0.00520.1861-0.00240.01920.15610.04010.152114.019152.1663105.059
50.38420.0303-0.84130.7019-0.21012.1114-0.4480.5908-1.6062-0.11080.13810.00770.8098-0.5897-0.14340.4357-0.05540.0820.08650.11230.8190.1723136.4544103.447
60.9186-1.55640.0735.7342-2.53511.88920.03570.12760.41421.2461-0.25590.6984-0.65880.12460.15130.5430.0263-0.02040.401-0.04240.6782-22.0134119.9582119.4338
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 10 through 38 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 51 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 77 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 172 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 173 through 222 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 223 through 247 )A0

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