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- PDB-6l8n: Crystal structure of the K. lactis Rad5 -

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Basic information

Entry
Database: PDB / ID: 6l8n
TitleCrystal structure of the K. lactis Rad5
ComponentsDNA repair protein RAD5
KeywordsDNA BINDING PROTEIN / DNA damage tolerance / Helicase / Snf2 family
Function / homology
Function and homology information


hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides / ATP-dependent chromatin remodeler activity / helicase activity / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / DNA repair / DNA binding / zinc ion binding / ATP binding / nucleus / cytoplasm
Similarity search - Function
HIRAN domain / HIRAN domain / HIRAN / : / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain ...HIRAN domain / HIRAN domain / HIRAN / : / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / : / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. / Ring finger / Helicase conserved C-terminal domain / Zinc finger RING-type profile. / Zinc finger, RING-type / helicase superfamily c-terminal domain / Superfamilies 1 and 2 helicase C-terminal domain profile. / Superfamilies 1 and 2 helicase ATP-binding type-1 domain profile. / DEAD-like helicases superfamily / Helicase, C-terminal / Helicase superfamily 1/2, ATP-binding domain / Zinc finger, RING/FYVE/PHD-type / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
DNA repair protein RAD5
Similarity search - Component
Biological speciesKluyveromyces lactis NRRL Y-1140 (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.6 Å
AuthorsShen, M. / Xiang, S.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31870769 China
CitationJournal: Nat Commun / Year: 2021
Title: Structural basis for the multi-activity factor Rad5 in replication stress tolerance.
Authors: Shen, M. / Dhingra, N. / Wang, Q. / Cheng, C. / Zhu, S. / Tian, X. / Yu, J. / Gong, X. / Li, X. / Zhang, H. / Xu, X. / Zhai, L. / Xie, M. / Gao, Y. / Deng, H. / He, Y. / Niu, H. / Zhao, X. / Xiang, S.
History
DepositionNov 6, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 20, 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.pdbx_database_id_DOI / _citation.title / _citation.year
Revision 1.2Jan 27, 2021Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed
Revision 1.3Mar 27, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Apr 3, 2024Group: Refinement description / Category: pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: DNA repair protein RAD5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)109,3133
Polymers109,1821
Non-polymers1312
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10 Å2
ΔGint-2 kcal/mol
Surface area42430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)188.539, 188.539, 198.231
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein DNA repair protein RAD5


Mass: 109182.031 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Kluyveromyces lactis NRRL Y-1140 (yeast)
Strain: NRRL Y-1140 / Gene: RAD5, KLLA0F17479g / Production host: Escherichia coli (E. coli)
References: UniProt: Q6CJM4, Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
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: 4.66 Å3/Da / Density % sol: 73.59 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES pH 7.5, 0.9M Ammonium citrate tribasic pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jul 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 3.6→50 Å / Num. obs: 24712 / % possible obs: 99 % / Redundancy: 6.9 % / CC1/2: 0.997 / Rmerge(I) obs: 0.076 / Net I/σ(I): 30.88
Reflection shellResolution: 3.6→3.66 Å / Redundancy: 7.2 % / Rmerge(I) obs: 1.406 / Mean I/σ(I) obs: 1.525 / Num. unique obs: 1226 / CC1/2: 0.524 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Hg-soaked crystal structure of KlRad5

Resolution: 3.6→45.856 Å / SU ML: 0.46 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 25.89
RfactorNum. reflection% reflection
Rfree0.2394 1459 5.97 %
Rwork0.2041 --
obs0.2062 24440 99.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.6→45.856 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6566 0 2 0 6568
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026691
X-RAY DIFFRACTIONf_angle_d0.4069025
X-RAY DIFFRACTIONf_dihedral_angle_d8.6534105
X-RAY DIFFRACTIONf_chiral_restr0.0391015
X-RAY DIFFRACTIONf_plane_restr0.0031144
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.6-3.72860.33841480.30362247X-RAY DIFFRACTION100
3.7286-3.87780.36171360.27982266X-RAY DIFFRACTION100
3.8778-4.05420.28121340.24352278X-RAY DIFFRACTION100
4.0542-4.26780.25251380.19612294X-RAY DIFFRACTION100
4.2678-4.5350.22041300.17362296X-RAY DIFFRACTION100
4.535-4.88480.18951570.14962290X-RAY DIFFRACTION100
4.8848-5.37570.21271520.1762294X-RAY DIFFRACTION100
5.3757-6.1520.27431640.20262284X-RAY DIFFRACTION99
6.152-7.74480.27671600.23842335X-RAY DIFFRACTION99
7.7448-45.8560.2081400.19822397X-RAY DIFFRACTION95
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)
15.90831.0035-2.07243.2534-1.81264.9653-0.27010.12551.1496-0.7547-0.0937-0.8491-0.45910.83730.21151.8477-0.2307-0.12581.67060.04572.603566.1075119.713485.2031
23.7495-0.07441.52621.85890.54220.97120.3176-0.04390.0194-0.0809-0.0314-0.10520.00740.0331-0.35321.17660.00830.12091.3977-0.01241.126626.906699.37698.4501
36.01512.6663-1.22915.5733-0.47091.6704-0.07640.05910.12990.29430.02220.03110.1217-0.3745-0.07431.20840.0248-0.05421.6170.14291.233711.225861.92484.6905
44.98340.70561.04777.08271.39386.0340.2631-1.49570.45291.0514-0.4137-0.66230.142-0.5121-0.24291.15060.0091-0.03991.41060.32881.49481.315789.73259.5606
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 174:335 )A174 - 335
2X-RAY DIFFRACTION2( CHAIN A AND RESID 360:729 )A360 - 729
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 730:795 OR RESID 936:1114 ) )A730 - 795
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 730:795 OR RESID 936:1114 ) )A936 - 1114
5X-RAY DIFFRACTION4( CHAIN A AND ( RESID 827:935 OR RESID 1201:1202 ) )A827 - 935
6X-RAY DIFFRACTION4( CHAIN A AND ( RESID 827:935 OR RESID 1201:1202 ) )A1201 - 1202

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