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

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Basic information

Entry
Database: PDB / ID: 5cnw
TitleCrystal structure of a novel disulfide oxidoreductase from Deinococcus radiodurans
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 18, 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
Water3,549197
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area260 Å2
ΔGint-1 kcal/mol
Surface area11890 Å2
Unit cell
Length a, b, c (Å)47.805, 63.032, 87.298
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221
Components on special symmetry positions
IDModelComponents
11A-592-

HOH

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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.: 197 / 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: 2.31 Å3/Da / Density % sol: 46.71 %
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 MX225HE / Detector: CCD / Date: Nov 1, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.65→32.23 Å / Num. obs: 32145 / % possible obs: 99.2 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.041 / Net I/σ(I): 17.2
Reflection shellResolution: 1.65→1.68 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.523 / Mean I/σ(I) obs: 1.9 / % possible all: 93.6

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1692)refinement
PDB_EXTRACT3.15data extraction
XDSdata processing
Aimlessdata reduction
PHASERphasing
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GL5

3gl5


Resolution: 1.65→26.42 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.22 / Phase error: 20.19 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1978 1634 5.09 %
Rwork0.1702 30460 -
obs0.1716 32094 98.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 91.17 Å2 / Biso mean: 30.8751 Å2 / Biso min: 13.55 Å2
Refinement stepCycle: final / Resolution: 1.65→26.42 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1756 0 6 197 1959
Biso mean--31.99 36.45 -
Num. residues----229
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061801
X-RAY DIFFRACTIONf_angle_d0.9192441
X-RAY DIFFRACTIONf_chiral_restr0.038260
X-RAY DIFFRACTIONf_plane_restr0.005326
X-RAY DIFFRACTIONf_dihedral_angle_d14.109653
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.65-1.69860.26821340.25512358249295
1.6986-1.75340.28521310.24382545267699
1.7534-1.8160.27131300.217124952625100
1.816-1.88870.23251430.20492522266599
1.8887-1.97460.24471320.19672525265799
1.9746-2.07870.22071610.18442514267599
2.0787-2.20890.21391440.16142495263999
2.2089-2.37930.19941430.16462542268599
2.3793-2.61860.1991300.17125662696100
2.6186-2.99710.18441340.167125972731100
2.9971-3.77420.1991270.158926042731100
3.7742-26.42320.15331250.15212697282297
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)
12.30770.7593-1.08960.7219-0.02971.8296-0.1361-0.0304-0.39850.02630.13680.21380.2159-0.2184-0.04830.1855-0.00810.01080.16930.05750.230.801181.7865104.8884
24.0606-1.4787-4.01990.82921.37253.9938-0.1619-0.6631-0.40440.040.1830.04090.16690.1790.0480.24220.00570.01940.24110.11980.3783-3.662178.1504113.1027
30.94670.2613-0.13242.3623-1.6253.3731-0.1460.4972-0.3169-0.5745-0.013-0.19690.40010.21850.18030.3373-0.00370.10720.3644-0.04610.288318.202583.866791.2294
43.4682-0.1023-0.44491.4536-0.50172.2588-0.0492-0.1766-0.1870.09110.034-0.0576-0.08040.12230.01490.1388-0.00340.01290.11450.0070.111313.677588.2616105.6542
53.99962.90231.16235.05013.02763.7035-0.2691-0.2408-0.86680.0686-0.06960.04450.93520.07710.11230.41220.08250.12390.19470.130.611514.739769.6102107.4288
61.76790.5657-0.94931.6051-0.56141.9892-0.10840.2016-0.574-0.21830.18240.35010.428-0.3775-0.04280.274-0.0899-0.01920.18850.04830.3777-5.412474.0784102.8569
71.4643-0.92061.27415.8081-1.28431.1897-0.0190.04370.31630.54520.07710.289-0.41590.0065-0.08390.34670.03340.03990.25530.01350.4133-22.786756.3537120.8913
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 11 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 169 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 170 through 185 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 186 through 221 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 222 through 239 )A0

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