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- PDB-5wtu: Crystal structure of DndE G21/24K mutant involved in DNA phosphor... -

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Basic information

Entry
Database: PDB / ID: 5wtu
TitleCrystal structure of DndE G21/24K mutant involved in DNA phosphorothioation
ComponentsDNA sulfur modification protein DndE
KeywordsDNA BINDING PROTEIN / phosphorothioation
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 speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å
AuthorsYao, P. / Liu, Y. / Wang, C. / Cao, C.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China China
CitationJournal: To Be Published
Title: Crystal structure of DndE G21/24K mutant involved in DNA phosphorothioation
Authors: Yao, P. / Liu, Y. / Wang, C. / Cao, C.
History
DepositionDec 14, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 21, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
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: DNA sulfur modification protein DndE
B: DNA sulfur modification protein DndE
C: DNA sulfur modification protein DndE
D: DNA sulfur modification protein DndE


Theoretical massNumber of molelcules
Total (without water)50,7634
Polymers50,7634
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5510 Å2
ΔGint-33 kcal/mol
Surface area18700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.297, 57.297, 130.222
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number78
Space group name H-MP43

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Components

#1: Protein
DNA sulfur modification protein DndE


Mass: 12690.828 Da / Num. of mol.: 4 / Fragment: UNP RESIDUES 1-110
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: ACU90_25985 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0N8J336

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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: 2.11 Å3/Da / Density % sol: 41.58 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: 0.1 M Sodium citrate tribasic dihydrate pH 5.6, 0.2 M Potassium sodium tartrate tetrahydrate, 2.0 M Ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97915 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 3, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97915 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.883
11K, H, -L20.117
ReflectionResolution: 2.9→50 Å / Num. obs: 9087 / % possible obs: 97.6 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.135 / Χ2: 1.221 / Net I/σ(I): 6.3 / Num. measured all: 32212
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
2.9-33.50.5169111.04199.2
3-3.123.60.3929211.026199
3.12-3.273.60.3148911.019198.3
3.27-3.443.50.2359211.065198.2
3.44-3.653.50.1829151.213198.3
3.65-3.943.50.1489091.428198.2
3.94-4.333.50.1079101.568198
4.33-4.963.50.0978981.494196.9
4.96-6.243.50.0939021.133195.4
6.24-503.70.0499091.231195

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Processing

Software
NameVersionClassification
REFMAC5.8.0123refinement
HKL-2000data scaling
PDB_EXTRACT3.22data extraction
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
HKLdata scaling
RefinementResolution: 2.9→50.01 Å / Cor.coef. Fo:Fc: 0.896 / Cor.coef. Fo:Fc free: 0.867 / SU B: 46.928 / SU ML: 0.399 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.486 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.272 432 4.8 %RANDOM
Rwork0.2252 ---
obs0.2273 8623 97.61 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 104.74 Å2 / Biso mean: 42.31 Å2 / Biso min: 17.01 Å2
Baniso -1Baniso -2Baniso -3
1-0.61 Å2-0 Å2-0 Å2
2--0.61 Å2-0 Å2
3----1.21 Å2
Refinement stepCycle: final / Resolution: 2.9→50.01 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3114 0 0 0 3114
Num. residues----388
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0193161
X-RAY DIFFRACTIONr_angle_refined_deg1.1961.9894252
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8285376
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.87423.876129
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.98515619
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9181522
X-RAY DIFFRACTIONr_chiral_restr0.070.2497
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0212240
X-RAY DIFFRACTIONr_rigid_bond_restr2.40633137
X-RAY DIFFRACTIONr_sphericity_bonded26.97153091
LS refinement shellResolution: 2.904→2.98 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 31 -
Rwork0.259 635 -
all-666 -
obs--99.85 %
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)
10.168-0.3539-0.12741.33-0.15110.3980.0016-0.00970.0090.01660.003-0.0171-0.01040.0214-0.00460.0181-0.0071-0.00010.05740.00550.084560.57038.725-7.8968
20.7537-0.2155-0.25751.6760.35940.56140.0442-0.1094-0.0337-0.04380.0307-0.063-0.02480.0315-0.07480.0048-0.00360.0050.0373-0.00330.050938.221824.56498.3998
31.2246-0.63170.72311.2661-0.51441.3489-0.03730.08470.008-0.11630.0129-0.05890.10810.03720.02440.0343-0.01150.00590.00960.00050.043446.2131-5.37295.7065
40.4637-0.0054-0.62020.9388-0.33931.07450.0316-0.02190.05060.0727-0.0447-0.1414-0.1254-0.02680.01310.03460.0264-0.01080.0478-0.02110.08430.042514.3563-11.3006
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A3 - 107
2X-RAY DIFFRACTION2B3 - 105
3X-RAY DIFFRACTION3C4 - 109
4X-RAY DIFFRACTION4D3 - 106

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