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- PDB-5xwh: Structure of FrnE, a novel disulfide oxidoreductase from Deinococ... -

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Basic information

Entry
Database: PDB / ID: 5xwh
TitleStructure of FrnE, a novel disulfide oxidoreductase from Deinococcus radiodurans crystallized in the presence of GSH
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: 2 Å
AuthorsBihani, S.C. / Panicker, L. / Kumar, V.
CitationJournal: To Be Published
Title: Structure of FrnE, a novel disulfide oxidoreductase from Deinococcus radiodurans crystallized in the presence of GSH
Authors: Bihani, S.C. / Panicker, L. / Kumar, V.
History
DepositionJun 29, 2017Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 4, 2018Provider: repository / Type: Initial release
Revision 1.1Nov 22, 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
A: FrnE protein


Theoretical massNumber of molelcules
Total (without water)28,4941
Polymers28,4941
Non-polymers00
Water1,874104
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area11900 Å2
Unit cell
Length a, b, c (Å)47.806, 64.109, 86.333
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21221
DetailsAuthors state that dimeric biological assembly is observed in solution using SEC and light scattering experiment.

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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 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q9RWK7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 2.32 Å3/Da / Density % sol: 47.02 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 10% PEG8000, 100mM sodium acetate, pH 5.0 20% glycerol 5mM GSH

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: RRCAT INDUS-2 / Beamline: PX-BL21 / Wavelength: 0.97947 Å
DetectorType: RAYONIX MX225HE / Detector: CCD / Date: Oct 29, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97947 Å / Relative weight: 1
ReflectionResolution: 2→47.81 Å / Num. obs: 17317 / % possible obs: 94.4 % / Redundancy: 3.4 % / CC1/2: 0.999 / Rmerge(I) obs: 0.052 / Net I/σ(I): 13
Reflection shellResolution: 2→2.05 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.427 / CC1/2: 0.745 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CO3

5co3


Resolution: 2→41.822 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / Phase error: 23.82
RfactorNum. reflection% reflection
Rfree0.2228 874 5.06 %
Rwork0.1693 --
obs0.1719 17273 93.17 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2→41.822 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1749 0 0 104 1853
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071797
X-RAY DIFFRACTIONf_angle_d0.8382437
X-RAY DIFFRACTIONf_dihedral_angle_d14.614654
X-RAY DIFFRACTIONf_chiral_restr0.035261
X-RAY DIFFRACTIONf_plane_restr0.004325
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0001-2.12540.30411580.2462704X-RAY DIFFRACTION96
2.1254-2.28940.25861710.2222748X-RAY DIFFRACTION95
2.2894-2.51980.26581490.19382723X-RAY DIFFRACTION95
2.5198-2.88440.25841240.18462755X-RAY DIFFRACTION94
2.8844-3.63370.24661350.16452732X-RAY DIFFRACTION92
3.6337-41.83140.16681370.13992737X-RAY DIFFRACTION88
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)
14.4694-0.163-0.62291.79730.61930.9143-0.2561-0.55-0.66210.38970.16480.25750.3274-0.07640.07520.34290.02270.04750.30120.09450.4223-0.492210.2699106.9788
20.69970.9071-1.16952.0929-1.70751.962-0.52050.6713-0.8692-0.48830.1282-0.5710.3888-0.13420.33010.4173-0.04090.14490.5833-0.11780.561218.4968212.855390.6441
35.37660.7297-0.33251.9567-0.53232.68310.0232-0.0208-0.32750.12850.02290.0557-0.094-0.0338-0.03760.2256-0.00710.01240.1740.02560.215412.6366218.67103.0228
43.2136-0.27350.16120.10320.36833.54520.0637-0.7777-1.56890.6826-0.2792-0.07370.90330.9117-0.02120.47150.09640.00320.46770.35180.650718.2636205.5304111.6782
51.93931.3245-0.68921.5446-0.88642.5449-0.13010.4548-1.2836-0.16330.120.59760.6524-0.74510.07790.3983-0.10070.03520.38140.07040.7664-5.5288202.9562103.2424
64.542-1.96950.3648.1971-2.90993.23020.2389-0.31420.84050.6094-0.11940.7354-0.69380.1392-0.0440.5293-0.02270.03090.4263-0.08260.6015-22.2931183.8252119.9112
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 11 through 51 )
2X-RAY DIFFRACTION2chain 'A' and (resid 52 through 77 )
3X-RAY DIFFRACTION3chain 'A' and (resid 78 through 156 )
4X-RAY DIFFRACTION4chain 'A' and (resid 157 through 185 )
5X-RAY DIFFRACTION5chain 'A' and (resid 186 through 223 )
6X-RAY DIFFRACTION6chain 'A' and (resid 224 through 247 )

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