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- PDB-7ykm: Structure of DciA DUF721 domain from Deinococcus radiodurans -

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Basic information

Entry
Database: PDB / ID: 7ykm
TitleStructure of DciA DUF721 domain from Deinococcus radiodurans
ComponentsDciA DUF721 domain
KeywordsREPLICATION / putative DnaB helicase loader
Function / homologyProtein of unknown function DUF721/UPF0232 / Dna[CI] antecedent, DciA / DUF721 domain-containing protein
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.5 Å
AuthorsCheng, K.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100017 China
CitationJournal: To Be Published
Title: Structure of DciA DUF721 domain from Deinococcus radiodurans
Authors: Cheng, K.
History
DepositionJul 22, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Aug 2, 2023Provider: repository / Type: Initial release
Revision 1.1May 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: DciA DUF721 domain


Theoretical massNumber of molelcules
Total (without water)11,6511
Polymers11,6511
Non-polymers00
Water97354
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)92.593, 37.438, 86.285
Angle α, β, γ (deg.)90.000, 164.339, 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

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Components

#1: Protein DciA DUF721 domain


Mass: 11650.569 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_1088 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RVE1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / Source method: isolated from a natural source / Formula: H2O

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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: 1.73 Å3/Da / Density % sol: 29.01 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5
Details: 2.0 M Ammonium nitrate, 0.1 M Sodium acetate trihydrate pH 5.0, 200 mM NaCl

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9762 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Nov 20, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 1.5→34.34 Å / Num. obs: 12543 / % possible obs: 96.7 % / Redundancy: 3.1 % / Biso Wilson estimate: 23.66 Å2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 8.9
Reflection shellResolution: 1.5→1.53 Å / Rmerge(I) obs: 0.441 / Num. unique obs: 541

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
xia2data reduction
xia2data scaling
PHASERphasing
RefinementResolution: 1.5→24.7671680257 Å / SU ML: 0.111679141259 / Cross valid method: FREE R-VALUE / σ(F): 1.38631587379 / Phase error: 24.1848672742
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.21522758015 625 4.98285896516 %
Rwork0.192616725639 11918 -
obs0.193799119145 12543 97.1421933086 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.6558283239 Å2
Refinement stepCycle: LAST / Resolution: 1.5→24.7671680257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms635 0 0 54 689
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00726345883143648
X-RAY DIFFRACTIONf_angle_d1.00059929944874
X-RAY DIFFRACTIONf_chiral_restr0.073934010711996
X-RAY DIFFRACTIONf_plane_restr0.00613853579053114
X-RAY DIFFRACTIONf_dihedral_angle_d19.5611972386239
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.65060.2538879192541360.2063294628162865X-RAY DIFFRACTION93.8398999375
1.6506-1.88940.213214388931520.1969420115032961X-RAY DIFFRACTION97.1294851794
1.8894-2.38020.2128781885221650.1918926214733003X-RAY DIFFRACTION98.3545482769
2.3802-24.760.2106424120671720.1889575629883089X-RAY DIFFRACTION99.1788321168
Refinement TLS params.Method: refined / Origin x: -17.71268691 Å / Origin y: -4.30015817704 Å / Origin z: 1.70654909409 Å
111213212223313233
T0.11380824537 Å20.0196873477562 Å2-0.0192152843113 Å2-0.138702362546 Å2-0.00164752298832 Å2--0.0576016904097 Å2
L1.24232011106 °20.678787979241 °2-0.0562626074701 °2-3.16297317986 °2-1.04165793061 °2--2.33601196307 °2
S0.0202868793244 Å °-0.059829796602 Å °0.0158161934841 Å °-0.00625656020844 Å °-0.0793778289575 Å °-0.13896022459 Å °0.0307633254325 Å °0.109625093607 Å °0.0307015082402 Å °
Refinement TLS groupSelection details: all

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