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- PDB-5e59: Crystal structure of reduced state of a novel disulfide oxidoredu... -

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Basic information

Entry
Database: PDB / ID: 5.0E+59
TitleCrystal structure of reduced state of a novel disulfide oxidoreductase from Deinococcus radiodurans
ComponentsFrnE protein
KeywordsOXIDOREDUCTASE / FrnE / Deinococcus / disulfide bond / disulfide isomerase / oxidative stress
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 / MOLECULAR REPLACEMENT / Resolution: 2 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
DepositionOct 8, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 12, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Derived calculations
Category: citation / pdbx_struct_oper_list
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 / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Nov 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

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Assembly

Deposited unit
A: FrnE protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,6783
Polymers28,4941
Non-polymers1842
Water4,540252
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint0 kcal/mol
Surface area12030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.761, 62.922, 86.531
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: pET21b+ / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q9RWK7
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 252 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.28 Å3/Da / Density % sol: 46.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 10% PEG 8000 100mM Sodium Actetate 20% Glycerol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SEALED TUBE / Type: OTHER / Wavelength: 1.54056 Å
DetectorType: AGILENT TITAN CCD / Detector: CCD / Date: Aug 7, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 2→15.76 Å / Num. obs: 18231 / % possible obs: 99.8 % / Redundancy: 10.1 % / Rmerge(I) obs: 0.121 / Net I/σ(I): 19.1
Reflection shellResolution: 2→2.05 Å / Redundancy: 9 % / Rmerge(I) obs: 0.667 / Mean I/σ(I) obs: 6.1 / % possible all: 99.9

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Processing

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

5cnw


Resolution: 2→15.759 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 18.79 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2058 915 5.03 %
Rwork0.1572 --
obs0.1596 18200 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2→15.759 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 12 252 2035
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071820
X-RAY DIFFRACTIONf_angle_d0.9032466
X-RAY DIFFRACTIONf_dihedral_angle_d14.245661
X-RAY DIFFRACTIONf_chiral_restr0.041262
X-RAY DIFFRACTIONf_plane_restr0.005329
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.10530.24421430.18242415X-RAY DIFFRACTION100
2.1053-2.23680.21711460.16472402X-RAY DIFFRACTION100
2.2368-2.4090.20681380.17272426X-RAY DIFFRACTION100
2.409-2.65030.2251170.17222459X-RAY DIFFRACTION100
2.6503-3.03150.23951260.16332454X-RAY DIFFRACTION100
3.0315-3.81040.19411200.14242512X-RAY DIFFRACTION100
3.8104-15.75940.17911250.14792617X-RAY DIFFRACTION100
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)
11.85040.8250.05322.55970.03381.1209-0.166-0.2148-0.54580.18240.10740.3010.3047-0.1948-0.0110.1955-0.0030.03070.16040.09880.24860.0333143.7646105.0207
24.5656-2.3096-3.07641.18841.59152.3758-0.1402-0.6527-0.38370.13490.14730.17050.23470.0738-0.00680.2112-0.00230.03080.18660.11250.3586-3.7043141.0302112.3656
32.43090.20680.01841.9747-1.56714.4988-0.14660.7817-0.5242-0.48120.0742-0.10430.47940.33120.08830.2729-0.01550.09450.3573-0.0740.250618.1757146.420590.4396
42.3822-0.5569-0.44321.3645-0.60371.88390.04570.75660.027-0.1294-0.01710.068-0.1002-0.1477-0.00760.15450.00310.0130.25520.02490.14258.8095155.201993.0207
51.830.3647-0.47451.4694-0.12272.9795-0.0677-0.5425-0.29810.20390.05380.0403-0.08280.16040.01260.16190.01360.01330.21160.05860.137915.0929149.22109.675
61.636-0.1398-0.43460.1101-0.25591.0346-0.1251-0.6231-0.97330.1163-0.1157-0.14960.52580.5214-0.12120.32790.11320.07330.25620.26030.411317.6258138.4616111.187
70.4885-0.63730.90593.19530.66633.2218-0.05260.1068-0.6451-0.43640.29680.22630.6237-0.3991-0.09680.2817-0.06270.01760.13460.02860.3532-0.7476135.714599.9665
85.86885.9903-5.19838.3566-4.92897.1491-0.18320.3926-0.6595-0.30430.63170.38770.5366-0.6841-0.35930.2519-0.0819-0.03360.23990.09220.3984-12.1414138.4792105.2751
92.224-2.55531.88516.068-1.24231.852-0.0335-0.37260.22770.86630.01450.0753-0.3592-0.0351-0.00420.37110.05750.04860.24640.04030.3946-22.8403119.2822119.874
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 38 )
2X-RAY DIFFRACTION2chain 'A' and (resid 39 through 51 )
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 77 )
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 109 )
5X-RAY DIFFRACTION5chain 'A' and (resid 110 through 155 )
6X-RAY DIFFRACTION6chain 'A' and (resid 156 through 185 )
7X-RAY DIFFRACTION7chain 'A' and (resid 186 through 207 )
8X-RAY DIFFRACTION8chain 'A' and (resid 208 through 221 )
9X-RAY DIFFRACTION9chain 'A' and (resid 222 through 239 )

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