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- PDB-7es4: the crystral structure of DndH-C-domain -

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Basic information

Entry
Database: PDB / ID: 7es4
Titlethe crystral structure of DndH-C-domain
ComponentsDNA phosphorothioation-dependent restriction protein DptH
KeywordsTRANSLOCASE / motor protein
Function / homologyHelicase HerA-like / DNA phosphorothioation-dependent restriction protein DptH / Helicase HerA, central domain / Helicase HerA, central domain / P-loop containing nucleoside triphosphate hydrolase / DNA phosphorothioation-dependent restriction protein DptH
Function and homology information
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.3 Å
AuthorsWu, D.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31720103906 China
CitationJournal: Nat Catal / Year: 2022
Title: The functional coupling between restriction and DNA phosphorothioate modification systems underlying the DndFGH restriction complex
Authors: Wu, D. / Tang, Y. / Chen, S. / He, Y. / Chang, X. / Zheng, W. / Deng, Z. / Li, Z. / Wang, L. / Wu, G. / Chen, S.
History
DepositionMay 8, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0May 11, 2022Provider: repository / Type: Initial release
Revision 1.1Dec 14, 2022Group: Database references / Category: citation
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Dec 21, 2022Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: DNA phosphorothioation-dependent restriction protein DptH


Theoretical massNumber of molelcules
Total (without water)43,8091
Polymers43,8091
Non-polymers00
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area16120 Å2
Unit cell
Length a, b, c (Å)102.478, 102.478, 77.650
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65

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Components

#1: Protein DNA phosphorothioation-dependent restriction protein DptH


Mass: 43808.586 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: dptH / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: A0A210BW77
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.73 Å3/Da / Density % sol: 55 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / Details: PEG 4000,magnesium chloride, HEPES

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97916 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Feb 14, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
ReflectionResolution: 2.3→50 Å / Num. obs: 20708 / % possible obs: 100 % / Redundancy: 20.4 % / CC1/2: 0.972 / Net I/σ(I): 42.1
Reflection shellResolution: 2.3→2.34 Å / Num. unique obs: 1029 / CC1/2: 0.977

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Processing

Software
NameVersionClassification
HKL-3000data scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
AutoSolphasing
RefinementMethod to determine structure: SAD / Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.928 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2334 1060 5.1 %RANDOM
Rwork0.1891 ---
obs0.1913 19615 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 164.39 Å2 / Biso mean: 50.692 Å2 / Biso min: 21.4 Å2
Baniso -1Baniso -2Baniso -3
1-0.46 Å20.46 Å20 Å2
2--0.46 Å20 Å2
3----1.48 Å2
Refinement stepCycle: final / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2993 0 0 114 3107
Biso mean---44.23 -
Num. residues----373
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0193094
X-RAY DIFFRACTIONr_bond_other_d00.022951
X-RAY DIFFRACTIONr_angle_refined_deg1.3021.9684196
X-RAY DIFFRACTIONr_angle_other_deg3.59936782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6435380
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.05624.533150
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.41915513
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3811518
X-RAY DIFFRACTIONr_chiral_restr0.0690.2463
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.023535
X-RAY DIFFRACTIONr_gen_planes_other0.0060.02727
LS refinement shellResolution: 2.301→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.264 77 -
Rwork0.221 1427 -
all-1504 -
obs--99.73 %

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