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- PDB-7x4e: Structure of 10635-DndE -

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Basic information

Entry
Database: PDB / ID: 7x4e
TitleStructure of 10635-DndE
ComponentsDNA sulfur modification protein DndE
KeywordsDNA BINDING PROTEIN / DNase
Function / homologyDNA sulphur modification protein DndE / DNA sulphur modification protein DndE superfamily / DNA sulphur modification protein DndE / DNA sulphur modification protein DndE / Arc Repressor Mutant / Orthogonal Bundle / Mainly Alpha / DNA sulfur modification protein DndE
Function and homology information
Biological speciesNatronorubrum bangense JCM 10635 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.32 Å
AuthorsHaiyan, G. / Wei, H. / Chen, S. / Wang, L. / Wu, G.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)2019YFA0904300 China
CitationJournal: Mbio / Year: 2022
Title: Structural and Functional Analysis of DndE Involved in DNA Phosphorothioation in the Haloalkaliphilic Archaea Natronorubrum bangense JCM10635.
Authors: He, W. / Gao, H. / Wu, D. / Jiang, S. / Huang, W. / Chen, C. / Deng, Z. / Xiong, L. / Wu, G. / Wang, L.
History
DepositionMar 2, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 20, 2022Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2022Group: Database references / Category: citation / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jun 15, 2022Group: Database references / Category: citation / citation_author
Item: _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Jul 13, 2022Group: Database references / Derived calculations / Category: atom_type / citation
Item: _atom_type.pdbx_N_electrons / _atom_type.pdbx_scat_Z / _citation.journal_volume
Revision 1.4May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA sulfur modification protein DndE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,4402
Polymers15,3481
Non-polymers921
Water30617
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20 Å2
ΔGint-0 kcal/mol
Surface area7090 Å2
Unit cell
Length a, b, c (Å)69.732, 69.732, 106.022
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number181
Space group name H-MP6422

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Components

#1: Protein DNA sulfur modification protein DndE


Mass: 15348.205 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Natronorubrum bangense JCM 10635 (archaea)
Gene: C494_06880 / Production host: Escherichia coli (E. coli) / References: UniProt: L9WJT3
#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.: 17 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.41 Å3/Da / Density % sol: 48.95 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / Details: 20% PEG 3350, 0.2 M Lithium acetate dihydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 21, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 2.31→50 Å / Num. obs: 7069 / % possible obs: 100 % / Redundancy: 34.7 % / Rmerge(I) obs: 0.458 / Rpim(I) all: 0.088 / Rrim(I) all: 0.465 / Χ2: 1.522 / Net I/σ(I): 2.6 / Num. measured all: 245237
Reflection shell

Diffraction-ID: 1 / % possible all: 100

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2
2.31-2.39297.9316770.761.4968.0740.504
2.39-2.4932.66780.8821.8120.435
2.49-2.634.84.8266860.9050.8244.8970.448
2.6-2.7434.32.0736880.9530.3582.1040.644
2.74-2.9136.32.0976900.9720.3492.1270.469
2.91-3.1339.11.2466950.9850.21.2620.52
3.13-3.4538.20.6256980.9960.1020.6330.757
3.45-3.95350.3517140.9890.0590.3561.567
3.95-4.9835.60.1767340.9950.0290.1782.766
4.98-5032.30.1448090.9850.0260.1476.539

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 2.32→35.34 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 9.627 / SU ML: 0.212 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.27 / ESU R Free: 0.218 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2486 333 4.7 %RANDOM
Rwork0.2059 ---
obs0.2079 6707 99.35 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 151.22 Å2 / Biso mean: 66.955 Å2 / Biso min: 30 Å2
Baniso -1Baniso -2Baniso -3
1-2.23 Å21.12 Å2-0 Å2
2--2.23 Å2-0 Å2
3----7.24 Å2
Refinement stepCycle: final / Resolution: 2.32→35.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms902 0 6 17 925
Biso mean--129.24 65.34 -
Num. residues----114
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.013922
X-RAY DIFFRACTIONr_bond_other_d0.0010.017855
X-RAY DIFFRACTIONr_angle_refined_deg1.6131.6581242
X-RAY DIFFRACTIONr_angle_other_deg1.3161.5791984
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5275113
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.35822.30852
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.7215158
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.997157
X-RAY DIFFRACTIONr_chiral_restr0.070.2118
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021031
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02190
LS refinement shellResolution: 2.32→2.379 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.423 25 -
Rwork0.346 428 -
obs--91.33 %

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