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- PDB-6vsx: X-ray crystal structure of the C-terminal domain of Bacillus subt... -

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Basic information

Entry
Database: PDB / ID: 6vsx
TitleX-ray crystal structure of the C-terminal domain of Bacillus subtilis RNA polymerase binding helicase HelD
ComponentsDNA helicaseHelicase
KeywordsTRANSCRIPTION / RNA polymerase / Helicase
Function / homology
Function and homology information


recombinational repair / 3'-5' DNA helicase activity / DNA helicase / DNA helicase activity / DNA repair / DNA binding / ATP binding / cytosol
UvrD-like helicase, ATP-binding domain / UvrD-like helicase C-terminal domain / UvrD-like helicase C-terminal domain / P-loop containing nucleoside triphosphate hydrolase / DNA helicase, UvrD/REP type / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
DNA helicase / DNA helicase IV
Biological speciesBacillus subtilis (bacteria)
MethodX-RAY DIFFRACTION / SAD / Resolution: 2 Å
AuthorsMurakami, K.S. / Chon, U.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)GM131860 United States
Validation Report
SummaryFull reportAbout validation report
History
DepositionFeb 12, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 13, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA helicase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3762
Polymers21,2811
Non-polymers951
Water1,964109
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
γ
α
β
Length a, b, c (Å)106.963, 38.813, 44.427
Angle α, β, γ (deg.)90.000, 101.448, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11A-1004-

HOH

21A-1009-

HOH

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Components

#1: Protein DNA helicase / Helicase


Mass: 21281.357 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus subtilis (bacteria) / Gene: B4417_3167 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A164TSE8, UniProt: O32215*PLUS, DNA helicase
#2: Chemical ChemComp-PO4 / PHOSPHATE ION / Phosphate


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.12 Å3/Da / Density % sol: 42.08 %
Crystal growTemperature: 300 K / Method: vapor diffusion / pH: 6.2
Details: 0.1M Na/K phosphate, pH 6.2, 0.2 M NaCl, 50 % PEG200

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5414 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: May 2, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5414 Å / Relative weight: 1
ReflectionResolution: 2→24.73 Å / Num. obs: 11905 / % possible obs: 96.7 % / Redundancy: 20 % / Biso Wilson estimate: 21.97 Å2 / CC1/2: 0.991 / CC star: 0.998 / Rmerge(I) obs: 0.044 / Net I/σ(I): 60.1
Reflection shellResolution: 2→2.03 Å / Rmerge(I) obs: 0.206 / Num. unique obs: 463 / CC1/2: 0.991 / CC star: 0.998 / % possible all: 72

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIX1.17.1_3660phasing
PHENIX1.17.1_3660model building
RefinementMethod to determine structure: SAD / Resolution: 2→24.73 Å / SU ML: 0.18 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.615
RfactorNum. reflection% reflection
Rfree0.2015 1174 10.01 %
Rwork0.1723 --
Obs0.1752 11730 95.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 25.23 Å2
Refinement stepCycle: LAST / Resolution: 2→24.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1268 0 5 109 1382
Refine LS restraints
Refinement-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00721299
X-RAY DIFFRACTIONf_angle_d0.80211755
X-RAY DIFFRACTIONf_chiral_restr0.0538197
X-RAY DIFFRACTIONf_plane_restr0.0048223
X-RAY DIFFRACTIONf_dihedral_angle_d20.061172
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefinement-ID% reflection obs (%)
2-2.090.23331180.17231047X-RAY DIFFRACTION76.04
2.09-2.20.22561460.1611304X-RAY DIFFRACTION94.96
2.2-2.340.23081480.16471353X-RAY DIFFRACTION98.17
2.34-2.520.19451480.18181329X-RAY DIFFRACTION97.17
2.52-2.770.1971500.17951356X-RAY DIFFRACTION97.54
2.77-3.170.22721530.18721350X-RAY DIFFRACTION97.28
3.17-3.990.17051520.16181382X-RAY DIFFRACTION100
3.99-24.730.19731590.17271435X-RAY DIFFRACTION99.81

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