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- PDB-5loi: Crystal structure of Myceliophthora thermophila Rad26 (residues 3... -

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Basic information

Entry
Database: PDB / ID: 5loi
TitleCrystal structure of Myceliophthora thermophila Rad26 (residues 373-841)
ComponentsRad26
KeywordsSIGNALING PROTEIN / Rad26 (ATRIP) / Rad3 (ATR) / DNA-damage response (DDR) / kinase signaling
Function / homologyRad26-like, helical repeats / : / : / Rad26-like, helical repeats / Rad26-like, C-terminal domain / Rad26-like, N-terminal domain / DNA repair protein Rad26
Function and homology information
Biological speciesMyceliophthora thermophila ATCC 42464 (fungus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 3.153 Å
AuthorsAndersen, K.R.
CitationJournal: J. Biol. Chem. / Year: 2017
Title: Insights into Rad3 kinase recruitment from the crystal structure of the DNA damage checkpoint protein Rad26.
Authors: Andersen, K.R.
History
DepositionAug 9, 2016Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 2017Provider: repository / Type: Initial release
Revision 1.1Apr 5, 2017Group: Database references
Revision 1.2May 31, 2017Group: Database references
Revision 1.3Nov 13, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Rad26


Theoretical massNumber of molelcules
Total (without water)51,6981
Polymers51,6981
Non-polymers00
Water00
1
A: Rad26

A: Rad26


Theoretical massNumber of molelcules
Total (without water)103,3972
Polymers103,3972
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area3860 Å2
ΔGint-25 kcal/mol
Surface area37470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)210.783, 210.783, 104.766
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number97
Space group name H-MI422

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Components

#1: Protein Rad26


Mass: 51698.379 Da / Num. of mol.: 1 / Fragment: UNP residues 373-841
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Myceliophthora thermophila ATCC 42464 (fungus)
Gene: MYCTH_2305697 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): LOBSTR / References: UniProt: G2QDY6
Has protein modificationY

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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: 5.63 Å3/Da / Density % sol: 78.14 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: 0.1M BIS-TRIS pH 6.5 10% (w/v) PEG 10K 0.2M Potassium sodium tartrate

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 14, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.15→105.4 Å / Num. all: 540544 / Num. obs: 20640 / % possible obs: 99.4 % / Redundancy: 26.2 % / CC1/2: 0.999 / Rmerge(I) obs: 0.123 / Rpim(I) all: 0.025 / Net I/σ(I): 23
Reflection shellResolution: 3.15→3.27 Å / Redundancy: 26.8 % / Rmerge(I) obs: 4.781 / Mean I/σ(I) obs: 0.8 / Num. unique obs: 1932 / CC1/2: 0.612 / Rpim(I) all: 0.937 / % possible all: 95.07

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Processing

Software
NameVersionClassification
PHENIX(dev_2614: ???)refinement
PDB_EXTRACT3.2data extraction
XDSdata reduction
SHELXCDphasing
RefinementMethod to determine structure: SAD / Resolution: 3.153→105.391 Å / SU ML: 0.51 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.5 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2351 3764 9.73 %
Rwork0.2074 --
obs0.2101 20526 99.4 %
all-38691 -
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3.153→105.391 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3013 0 0 0 3013
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093081
X-RAY DIFFRACTIONf_angle_d1.014205
X-RAY DIFFRACTIONf_dihedral_angle_d6.4151872
X-RAY DIFFRACTIONf_chiral_restr0.06504
X-RAY DIFFRACTIONf_plane_restr0.007535
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)
11.55580.17770.63120.82340.82030.5287-1.91220.6138-0.2741-1.95421.4221-0.66650.47730.0442-0.00042.50450.21260.09682.0408-0.04161.7606166.9086147.73387.5051
21.1378-1.6201-1.08654.83480.44374.40010.0297-0.1258-0.54320.3304-0.04030.06451.12920.06540.00111.46110.34190.08851.4007-0.03671.3347149.019155.112910.926
31.2591-1.3476-1.08893.97990.77314.93710.1645-0.0683-0.3677-0.0408-0.0762-0.39150.29880.6152-0.00131.19460.16230.09851.38080.19981.4314149.7931170.803712.8191
42.42580.25442.1452.37340.35834.08380.39080.79660.34120.0948-0.03550.0081-0.2718-0.04310.00191.08750.16260.16061.14820.18281.3476142.0975181.895813.936
52.81-0.53383.2797.9986-0.3024.07630.24750.36640.574-0.43630.0122-0.1489-0.69810.10730.00081.30510.0350.21531.39950.26811.3432142.0067194.77035.1388
61.65680.22960.0864.04280.1182.5724-0.49680.2218-0.0901-1.29120.2247-0.14520.33710.05780.00161.87930.05550.05131.2970.25991.4395140.3512203.5664-3.9614
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 374 through 408 )
2X-RAY DIFFRACTION2chain 'A' and (resid 409 through 496 )
3X-RAY DIFFRACTION3chain 'A' and (resid 497 through 587 )
4X-RAY DIFFRACTION4chain 'A' and (resid 588 through 658 )
5X-RAY DIFFRACTION5chain 'A' and (resid 659 through 790 )
6X-RAY DIFFRACTION6chain 'A' and (resid 791 through 832 )

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