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- PDB-7dka: Crystal structure of DsbA-like protein DR2335 from Deinococcus ra... -

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Basic information

Entry
Database: PDB / ID: 7dka
TitleCrystal structure of DsbA-like protein DR2335 from Deinococcus radiodurans R1, C24S mutant protein
ComponentsDSBA domain-containing protein
KeywordsOXIDOREDUCTASE / DsbA / thioredoxin fold / Thiol:disulfide interchange protein
Function / homology
Function and homology information


oxidoreductase activity
Similarity search - Function
DSBA-like thioredoxin domain / DSBA-like thioredoxin domain / Glutaredoxin / Glutaredoxin / Thioredoxin-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / DI(HYDROXYETHYL)ETHER / DSBA-like thioredoxin domain-containing protein
Similarity search - Component
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.56 Å
AuthorsKim, M.-K. / Zhang, J. / Zhao, L.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
National Research Foundation (NRF, Korea)NRF-2020R1F1A1057780 Korea, Republic Of
CitationJournal: To Be Published
Title: Crystal structure of DsbA-like protein DR2335 from Deinococcus radiodurans R1, native protein
Authors: Kim, M.-K. / Zhang, J. / Zhao, L.
History
DepositionNov 23, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 24, 2021Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 2.0Sep 17, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Data collection / Derived calculations / Structure summary
Category: atom_site / pdbx_entry_details ...atom_site / pdbx_entry_details / pdbx_nonpoly_scheme / pdbx_validate_close_contact / struct_conn
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _pdbx_entry_details.has_protein_modification / _pdbx_nonpoly_scheme.auth_seq_num

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DSBA domain-containing protein
B: DSBA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,74719
Polymers52,4762
Non-polymers1,27117
Water9,476526
1
A: DSBA domain-containing protein
hetero molecules

B: DSBA domain-containing protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,74719
Polymers52,4762
Non-polymers1,27117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_444-x-1,y-1/2,-z-11
Buried area6780 Å2
ΔGint-6 kcal/mol
Surface area19020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.084, 84.177, 63.898
Angle α, β, γ (deg.)90.000, 91.540, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein DSBA domain-containing protein


Mass: 26238.105 Da / Num. of mol.: 2 / Mutation: C24S
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_2335 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RRZ4
#2: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H3O2
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C4H10O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 526 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN
Has protein modificationN

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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: 46.75 %
Crystal growTemperature: 295 K / Method: microbatch
Details: Ammonium acetate, Sodium acetate trihydrate pH 4.6, 30% w/v PEG 4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97933 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: May 15, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97933 Å / Relative weight: 1
ReflectionResolution: 1.56→50 Å / Num. obs: 67292 / % possible obs: 99.9 % / Redundancy: 7.4 % / CC1/2: 0.986 / Rmerge(I) obs: 0.139 / Rpim(I) all: 0.055 / Rrim(I) all: 0.15 / Rsym value: 0.139 / Net I/σ(I): 37.635
Reflection shellResolution: 1.56→1.59 Å / Rmerge(I) obs: 0.782 / Mean I/σ(I) obs: 4.845 / Num. unique obs: 3334 / CC1/2: 0.839 / Rpim(I) all: 0.31 / Rrim(I) all: 0.842 / Rsym value: 0.782

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
HKL-2000data scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DK9

7dk9


Resolution: 1.56→29.86 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 18.89 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1805 1998 2.97 %
Rwork0.1554 65258 -
obs0.1562 67256 99.82 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 83.4 Å2 / Biso mean: 19.9027 Å2 / Biso min: 6.16 Å2
Refinement stepCycle: final / Resolution: 1.56→29.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3362 0 85 526 3973
Biso mean--38.66 32.64 -
Num. residues----421
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 14

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.56-1.60.2231390.20324567470698
1.6-1.650.20841500.189846634813100
1.65-1.690.22741330.188746034736100
1.69-1.750.2061470.184246634810100
1.75-1.810.23531430.176346534796100
1.81-1.880.24521410.171546684809100
1.88-1.970.18941430.161246484791100
1.97-2.070.20571410.160346734814100
2.07-2.20.1841420.150746774819100
2.2-2.370.19031480.151746644812100
2.37-2.610.13871440.150246474791100
2.61-2.990.18361390.151947074846100
2.99-3.760.14661470.139946964843100
3.77-29.860.17081410.14644729487099

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