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- PDB-8ioo: Crystal structure of Deinococcus radiodurans RecJ-like protein in... -

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Basic information

Entry
Database: PDB / ID: 8ioo
TitleCrystal structure of Deinococcus radiodurans RecJ-like protein in complex with Mg2+
ComponentsRecJ-like protein
KeywordsHYDROLASE / RNase / nuclease
Function / homology: / DDH domain / DHH family, N-terminal domain / DHH phosphoesterase superfamily / DHHA1 domain / DHHA1 domain / nucleic acid binding / metal ion binding / Uncharacterized protein
Function and homology information
Biological speciesDeinococcus radiodurans (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsCheng, K.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32100017 China
National Natural Science Foundation of China (NSFC)32270043 China
CitationJournal: Nucleic Acids Res. / Year: 2024
Title: Structural and functional investigation of the DHH/DHHA1 family proteins in Deinococcus radiodurans.
Authors: Wang, Y. / Hao, W. / Guo, Z. / Sun, Y. / Wu, Y. / Sun, Y. / Gao, T. / Luo, Y. / Jin, L. / Yang, J. / Cheng, K.
History
DepositionMar 13, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 20, 2024Provider: repository / Type: Initial release
Revision 1.1Jun 12, 2024Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jul 17, 2024Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: RecJ-like protein
B: RecJ-like protein
C: RecJ-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)107,88014
Polymers107,2543
Non-polymers62611
Water7,927440
1
A: RecJ-like protein
B: RecJ-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,98410
Polymers71,5022
Non-polymers4818
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4640 Å2
ΔGint-103 kcal/mol
Surface area27320 Å2
MethodPISA
2
C: RecJ-like protein
hetero molecules

C: RecJ-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,7928
Polymers71,5022
Non-polymers2896
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_556-x,y,-z+11
Buried area4820 Å2
ΔGint-117 kcal/mol
Surface area27160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)152.897, 124.842, 80.917
Angle α, β, γ (deg.)90.000, 92.720, 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 RecJ-like protein


Mass: 35751.203 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Deinococcus radiodurans (radioresistant)
Gene: DR_0826 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9RW43
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 440 / 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: 3.72 Å3/Da / Density % sol: 66.9 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop
Details: 1.4 M MgSO4, 0.08 M MES (pH 6.5), 15% (v/v) glycerol

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2→42.04 Å / Num. obs: 106336 / % possible obs: 99.5 % / Redundancy: 2.9 % / Biso Wilson estimate: 36.92 Å2 / Rmerge(I) obs: 0.054 / Net I/σ(I): 8.7
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.358 / Num. unique obs: 7618

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
DIALSdata reduction
DIALSdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.04 Å / SU ML: 0.2444 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 28.3723
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2438 5046 4.96 %
Rwork0.2276 96759 -
obs0.2284 101805 99.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 51.73 Å2
Refinement stepCycle: LAST / Resolution: 2→42.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7295 0 31 440 7766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00957458
X-RAY DIFFRACTIONf_angle_d1.244610174
X-RAY DIFFRACTIONf_chiral_restr0.07911157
X-RAY DIFFRACTIONf_plane_restr0.01581361
X-RAY DIFFRACTIONf_dihedral_angle_d16.02162678
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.020.36921820.34783223X-RAY DIFFRACTION98.72
2.02-2.050.31511570.33073176X-RAY DIFFRACTION98.9
2.05-2.070.34021350.31533238X-RAY DIFFRACTION98.71
2.07-2.10.31761700.31373167X-RAY DIFFRACTION98.96
2.1-2.130.3661550.30323243X-RAY DIFFRACTION99.36
2.13-2.150.28971670.28413174X-RAY DIFFRACTION99.52
2.15-2.190.29511690.27843232X-RAY DIFFRACTION99.62
2.19-2.220.2841640.26923180X-RAY DIFFRACTION99.58
2.22-2.250.28591870.26553227X-RAY DIFFRACTION99.33
2.25-2.290.28551600.25713204X-RAY DIFFRACTION99.44
2.29-2.330.25891550.25653208X-RAY DIFFRACTION99.44
2.33-2.370.26961870.25723191X-RAY DIFFRACTION99.62
2.37-2.420.26091580.26643233X-RAY DIFFRACTION99.68
2.42-2.470.29531890.27423230X-RAY DIFFRACTION99.77
2.47-2.520.31581650.26733229X-RAY DIFFRACTION99.85
2.52-2.580.2531520.25863213X-RAY DIFFRACTION99.91
2.58-2.640.2161680.25263235X-RAY DIFFRACTION99.91
2.64-2.710.2771920.24943206X-RAY DIFFRACTION99.91
2.71-2.790.28161820.24293224X-RAY DIFFRACTION99.82
2.79-2.880.2781580.24223264X-RAY DIFFRACTION99.94
2.88-2.990.26441640.25313229X-RAY DIFFRACTION99.82
2.99-3.110.25011740.24213215X-RAY DIFFRACTION99.76
3.11-3.250.25091420.23123256X-RAY DIFFRACTION99.91
3.25-3.420.23841680.22183233X-RAY DIFFRACTION99.68
3.42-3.630.2241610.19693250X-RAY DIFFRACTION99.85
3.63-3.910.22941880.20533239X-RAY DIFFRACTION99.85
3.91-4.310.19431670.18463245X-RAY DIFFRACTION99.74
4.31-4.930.20621830.18423238X-RAY DIFFRACTION99.97
4.93-6.210.2431540.21513290X-RAY DIFFRACTION99.91
6.21-42.040.21071930.20573267X-RAY DIFFRACTION99.28

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