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

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Basic information

Entry
Database: PDB / ID: 5coh
TitleCrystal structure of a novel disulfide oxidoreductase from Deinococcus radiodurans crystallized in presence of beta-mercaptoethanol
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: 1.801 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 20, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jul 20, 2016Provider: repository / Type: Initial release
Revision 1.1Apr 10, 2019Group: Data collection / Database references / Derived calculations
Category: citation / citation_author / pdbx_struct_oper_list
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _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 / _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 / diffrn_radiation_wavelength / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Oct 9, 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: FrnE protein


Theoretical massNumber of molelcules
Total (without water)28,4941
Polymers28,4941
Non-polymers00
Water4,107228
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12050 Å2
Unit cell
Length a, b, c (Å)47.856, 62.350, 86.666
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-506-

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 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RWK7
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 228 / 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: 2.27 Å3/Da / Density % sol: 45.79 %
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 / Type: OTHER / Wavelength: 1.54056 Å
DetectorType: OXFORD TITAN CCD / Detector: CCD / Date: Dec 23, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54056 Å / Relative weight: 1
ReflectionResolution: 1.8→15.77 Å / Num. obs: 24630 / % possible obs: 99.6 % / Redundancy: 4.9 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 15.9
Reflection shellResolution: 1.8→1.84 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.551 / Mean I/σ(I) obs: 1.9 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine: 1.9_1682)refinement
PDB_EXTRACT3.15data extraction
CrysalisProdata processing
Aimlessdata scaling
PHASERphasing
CrysalisProdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 5CNW

5cnw


Resolution: 1.801→14.97 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2176 1255 5.11 %
Rwork0.1741 23299 -
obs0.1763 24554 99.65 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 85.1 Å2 / Biso mean: 27.9995 Å2 / Biso min: 9.57 Å2
Refinement stepCycle: final / Resolution: 1.801→14.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1771 0 0 228 1999
Biso mean---35.3 -
Num. residues----231
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071811
X-RAY DIFFRACTIONf_angle_d0.8772456
X-RAY DIFFRACTIONf_chiral_restr0.039262
X-RAY DIFFRACTIONf_plane_restr0.005329
X-RAY DIFFRACTIONf_dihedral_angle_d13.828657
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 9

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.801-1.8730.33671470.27052529267699
1.873-1.95810.26051340.2382511264599
1.9581-2.06110.26641560.214125342690100
2.0611-2.18980.25661430.188325532696100
2.1898-2.35830.24031480.181725562704100
2.3583-2.59450.25271320.186125992731100
2.5945-2.96740.23581340.172225992733100
2.9674-3.7290.19631310.158326492780100
3.729-14.97050.15781300.14627692899100
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)
13.34550.9077-1.44490.7599-0.16611.4113-0.0405-0.2652-0.40870.1568-0.03620.14380.18120.06570.16430.24620.00540.07390.14580.08810.27851.580574.5791107.6373
21.47420.1163-0.54940.3590.18450.3879-0.0397-0.0501-0.22310.01230.11660.21970.1363-0.1294-0.07560.1591-0.00290.00130.17020.08530.2398-2.532881.4023107.038
30.20170.0482-0.1320.7861-1.01281.3265-0.14950.4011-0.3218-0.41450.0627-0.08760.34910.16340.08190.3188-0.01430.10050.3357-0.01870.208718.178383.03490.4824
41.34210.069-0.04110.8455-0.13370.9611-0.03540.2027-0.1594-0.1080.05440.03210.0333-0.0102-0.00850.13650.0140.03530.17430.03220.127210.814787.647699.0406
50.53140.13870.15640.61290.01531.0154-0.1128-0.3278-0.2570.0981-0.0231-0.0605-0.01180.290.10150.14470.02970.0210.23380.07040.126916.749786.0477111.076
60.82030.06810.53720.62780.28940.4447-0.0973-0.0748-0.443-0.0793-0.0682-0.03770.37150.0753-0.36180.40810.04920.13930.09180.06920.442810.912468.6759102.2588
70.704-0.0051-0.5560.12090.07110.4774-0.04640.0543-0.4004-0.17920.13490.19660.1821-0.2477-0.02430.2476-0.084-0.02570.19750.08750.3579-7.896773.6843103.0234
80.4635-0.45030.35591.2488-0.16670.3082-0.049-0.13340.1730.3732-0.01320.0378-0.1691-0.00080.05020.38270.01920.04060.2340.05810.4505-23.059455.7325120.1927
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 9 through 22 )A0
2X-RAY DIFFRACTION2chain 'A' and (resid 23 through 51 )A0
3X-RAY DIFFRACTION3chain 'A' and (resid 52 through 77 )A0
4X-RAY DIFFRACTION4chain 'A' and (resid 78 through 122 )A0
5X-RAY DIFFRACTION5chain 'A' and (resid 123 through 172 )A0
6X-RAY DIFFRACTION6chain 'A' and (resid 173 through 192 )A0
7X-RAY DIFFRACTION7chain 'A' and (resid 193 through 221 )A0
8X-RAY DIFFRACTION8chain 'A' and (resid 222 through 239 )A0

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