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- PDB-6l8o: Crystal structure of the K. lactis Rad5 (Hg-derivative) -

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Basic information

Entry
Database: PDB / ID: 6l8o
TitleCrystal structure of the K. lactis Rad5 (Hg-derivative)
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 / protein metabolic process / 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 / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / Zinc finger, RING-type, conserved site / Zinc finger RING-type signature. ...HIRAN domain / HIRAN domain / HIRAN / SNF2-like, N-terminal domain superfamily / SNF2, N-terminal / SNF2-related domain / Zinc finger, C3HC4 RING-type / Zinc finger, C3HC4 type (RING finger) / 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 / SAD / Resolution: 3.3 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

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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)109,9065
Polymers109,1821
Non-polymers7244
Water0
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-27 kcal/mol
Surface area43050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)187.635, 187.635, 197.544
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Components on special symmetry positions
IDModelComponents
11A-1203-

HG

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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-HG / MERCURY (II) ION / Mercury (element)


Mass: 200.590 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Hg
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
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: 4.6 Å3/Da / Density % sol: 73.24 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7
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: 1.009 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 3, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.009 Å / Relative weight: 1
ReflectionResolution: 3.3→50 Å / Num. obs: 31355 / % possible obs: 100 % / Redundancy: 56.1 % / CC1/2: 1 / Rmerge(I) obs: 0.132 / Net I/σ(I): 39.8
Reflection shellResolution: 3.3→3.36 Å / Redundancy: 50.7 % / Rmerge(I) obs: 3.566 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 1540 / CC1/2: 0.548 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.13_2998: ???)refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 3.3→46.909 Å / SU ML: 0.47 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 23.79
Details: SF FILE CONTAINS FRIEDEL PAIRS UNDER I/F_MINUS AND I/F_PLUS COLUMNS.
RfactorNum. reflection% reflection
Rfree0.2294 1742 5.98 %
Rwork0.1914 --
obs0.1937 31265 99.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 3.3→46.909 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6791 0 11 0 6802
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0026928
X-RAY DIFFRACTIONf_angle_d0.4969346
X-RAY DIFFRACTIONf_dihedral_angle_d9.4474250
X-RAY DIFFRACTIONf_chiral_restr0.0411046
X-RAY DIFFRACTIONf_plane_restr0.0031189
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3003-3.34550.3702970.351993X-RAY DIFFRACTION89
3.3455-3.39330.3621530.31212190X-RAY DIFFRACTION100
3.3933-3.4440.36551520.32382151X-RAY DIFFRACTION100
3.444-3.49780.33761320.33262232X-RAY DIFFRACTION100
3.4978-3.55510.29631520.28842178X-RAY DIFFRACTION100
3.5551-3.61640.26471590.25442190X-RAY DIFFRACTION100
3.6164-3.68210.29621510.24352209X-RAY DIFFRACTION100
3.6821-3.75290.25071110.22382208X-RAY DIFFRACTION100
3.7529-3.82950.30721310.23322201X-RAY DIFFRACTION100
3.8295-3.91270.25531460.20532199X-RAY DIFFRACTION100
3.9127-4.00360.2031190.18642241X-RAY DIFFRACTION100
4.0036-4.10370.18711400.17612150X-RAY DIFFRACTION100
4.1037-4.21460.23251430.17392179X-RAY DIFFRACTION100
4.2146-4.33850.21951470.16162223X-RAY DIFFRACTION100
4.3385-4.47850.18391230.15172222X-RAY DIFFRACTION100
4.4785-4.63840.16221350.14092196X-RAY DIFFRACTION100
4.6384-4.82390.16931430.13412197X-RAY DIFFRACTION100
4.8239-5.04320.17681720.15292174X-RAY DIFFRACTION100
5.0432-5.30880.2021230.16472199X-RAY DIFFRACTION100
5.3088-5.64090.26451520.18642203X-RAY DIFFRACTION100
5.6409-6.07560.25071470.19882199X-RAY DIFFRACTION100
6.0756-6.68540.28641460.2112188X-RAY DIFFRACTION100
6.6854-7.64920.24771590.19042186X-RAY DIFFRACTION100
7.6492-9.62350.17661220.16252214X-RAY DIFFRACTION100
9.6235-46.9090.22371290.19492212X-RAY DIFFRACTION99
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)
17.6835-0.2138-1.31423.4142-0.23362.50630.00680.32821.9154-0.3634-0.1025-0.2029-0.31930.2662-0.09170.9633-0.0157-0.14330.74430.15481.59565.3655120.22284.6913
23.29892.24581.60382.02541.58530.6765-0.06220.8258-1.5704-0.2291-0.45410.660.26040.0008-0.25941.64910.21570.09632.14-0.06962.423453.071497.415490.3951
33.2252-0.38520.50721.60020.12991.94660.3158-0.50280.06240.1061-0.0215-0.17010.04240.1466-0.25820.641-0.02590.06830.90050.00260.729226.763998.88998.3918
45.44022.1605-1.02515.961-1.0972.2291-0.1510.274-0.1992-0.00710.1061-0.12060.2334-0.18160.07530.67310.0893-0.03630.7722-0.00360.630611.270461.553184.6642
53.52132.10851.60656.82533.37665.49270.0482-0.2052-0.024-0.37780.10620.43220.4173-0.4693-0.15470.9906-0.0179-0.00651.15230.25950.99771.300389.422959.2511
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 174:329 )A174 - 329
2X-RAY DIFFRACTION2( CHAIN A AND RESID 330:361 )A330 - 361
3X-RAY DIFFRACTION3( CHAIN A AND ( RESID 362:729 OR RESID 1204:1204 ) )A362 - 729
4X-RAY DIFFRACTION3( CHAIN A AND ( RESID 362:729 OR RESID 1204:1204 ) )A1204
5X-RAY DIFFRACTION4( CHAIN A AND ( RESID 730:795 OR RESID 936:1114 OR RESID 1203:1203 ) )A730 - 795
6X-RAY DIFFRACTION4( CHAIN A AND ( RESID 730:795 OR RESID 936:1114 OR RESID 1203:1203 ) )A936 - 1114
7X-RAY DIFFRACTION4( CHAIN A AND ( RESID 730:795 OR RESID 936:1114 OR RESID 1203:1203 ) )A1203
8X-RAY DIFFRACTION5( CHAIN A AND ( RESID 827:935 OR RESID 1201:1202 ) )A827 - 935
9X-RAY DIFFRACTION5( CHAIN A AND ( RESID 827:935 OR RESID 1201:1202 ) )A1201 - 1202

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