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- PDB-8ir4: Crystal structure of the SLF1 BRCT domain in complex with a Rad18... -

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Basic information

Entry
Database: PDB / ID: 8ir4
TitleCrystal structure of the SLF1 BRCT domain in complex with a Rad18 peptide containing pS442
Components
  • SER-ASP-SER-CYS-ASN-SER-SEP-SER-SER-ASP-ILE-ILE-ARG-ASP-LEU-LEU-GLU
  • SMC5-SMC6 complex localization factor protein 1
KeywordsGENE REGULATION / SLF1 / BRCT
Function / homologyISOPROPYL ALCOHOL / Uncharacterized protein
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.62 Å
AuthorsXiang, S. / Huang, W. / Qiu, F.
Funding support China, 2items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)32071205 China
National Natural Science Foundation of China (NSFC)31870769 China
CitationJournal: J.Biol.Chem. / Year: 2023
Title: Structural insights into Rad18 targeting by the SLF1 BRCT domains.
Authors: Huang, W. / Qiu, F. / Zheng, L. / Shi, M. / Shen, M. / Zhao, X. / Xiang, S.
History
DepositionMar 17, 2023Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Nov 15, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: SMC5-SMC6 complex localization factor protein 1
B: SMC5-SMC6 complex localization factor protein 1
C: SER-ASP-SER-CYS-ASN-SER-SEP-SER-SER-ASP-ILE-ILE-ARG-ASP-LEU-LEU-GLU
D: SER-ASP-SER-CYS-ASN-SER-SEP-SER-SER-ASP-ILE-ILE-ARG-ASP-LEU-LEU-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,24913
Polymers51,9144
Non-polymers3359
Water9,890549
1
A: SMC5-SMC6 complex localization factor protein 1
C: SER-ASP-SER-CYS-ASN-SER-SEP-SER-SER-ASP-ILE-ILE-ARG-ASP-LEU-LEU-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1367
Polymers25,9572
Non-polymers1805
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2340 Å2
ΔGint-40 kcal/mol
Surface area11980 Å2
MethodPISA
2
B: SMC5-SMC6 complex localization factor protein 1
D: SER-ASP-SER-CYS-ASN-SER-SEP-SER-SER-ASP-ILE-ILE-ARG-ASP-LEU-LEU-GLU
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,1126
Polymers25,9572
Non-polymers1554
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2160 Å2
ΔGint-33 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.421, 76.098, 141.371
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein / Protein/peptide , 2 types, 4 molecules ABCD

#1: Protein SMC5-SMC6 complex localization factor protein 1 / Ankyrin repeat domain-containing protein 32 / BRCT domain-containing protein 1 / Smc5/6 localization factor 1


Mass: 24034.965 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: SLF1, ANKRD32, BRCTD1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9BQI6
#2: Protein/peptide SER-ASP-SER-CYS-ASN-SER-SEP-SER-SER-ASP-ILE-ILE-ARG-ASP-LEU-LEU-GLU


Mass: 1921.909 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human)

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Non-polymers , 4 types, 558 molecules

#3: Chemical ChemComp-IPA / ISOPROPYL ALCOHOL / 2-PROPANOL


Mass: 60.095 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O / Comment: alkaloid*YM
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 549 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.09 Å3/Da / Density % sol: 41.26 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / Details: 0.3M MgCl2, 0.1M BIS-TRIS pH6.5, 22% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL02U1 / Wavelength: 0.9792 Å
DetectorType: DECTRIS EIGER2 S 9M / Detector: PIXEL / Date: Dec 18, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 1.62→35.34 Å / Num. obs: 55039 / % possible obs: 98 % / Redundancy: 6.7 % / CC1/2: 0.997 / Rmerge(I) obs: 0.093 / Net I/σ(I): 14.8
Reflection shellResolution: 1.62→1.71 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.715 / Num. unique obs: 7782 / CC1/2: 0.741 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(1.20.1_4487: ???)refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.62→29.6 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.43 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.213 2828 5.14 %
Rwork0.181 --
obs0.182 54968 97.6 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.62→29.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3426 0 15 549 3990
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.004
X-RAY DIFFRACTIONf_angle_d0.777
X-RAY DIFFRACTIONf_dihedral_angle_d6.408467
X-RAY DIFFRACTIONf_chiral_restr0.047516
X-RAY DIFFRACTIONf_plane_restr0.009582
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.62-1.650.27341310.24942485X-RAY DIFFRACTION96
1.65-1.680.25411380.22312507X-RAY DIFFRACTION95
1.68-1.710.2711570.21042556X-RAY DIFFRACTION98
1.71-1.750.24391580.21662539X-RAY DIFFRACTION97
1.75-1.780.22911320.20152569X-RAY DIFFRACTION98
1.78-1.830.24421400.20242572X-RAY DIFFRACTION97
1.83-1.870.24121460.20262575X-RAY DIFFRACTION98
1.87-1.920.24941260.20282579X-RAY DIFFRACTION97
1.92-1.980.26151410.19252595X-RAY DIFFRACTION99
1.98-2.040.20541620.19332573X-RAY DIFFRACTION97
2.04-2.120.2181300.18292640X-RAY DIFFRACTION98
2.12-2.20.21421400.1762601X-RAY DIFFRACTION99
2.2-2.30.19651310.18152640X-RAY DIFFRACTION98
2.3-2.420.19921160.17312593X-RAY DIFFRACTION97
2.42-2.570.19921510.18292618X-RAY DIFFRACTION99
2.57-2.770.23441460.18812664X-RAY DIFFRACTION99
2.77-3.050.20241530.18992676X-RAY DIFFRACTION99
3.05-3.490.20951200.16552688X-RAY DIFFRACTION98
3.49-4.40.16551540.14722710X-RAY DIFFRACTION99
4.4-29.60.23051560.17872760X-RAY DIFFRACTION96
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)
12.20770.27550.41683.02050.3572.65060.1566-0.04610.0844-0.47630.0416-0.1298-0.0092-0.2136-0.09370.14680.01240.01640.1020.02620.104111.3232-1.7863-25.4051
24.4436-1.5005-1.57754.30841.16233.155-0.16470.2261-0.0275-0.2450.2931-0.2203-0.05770.5136-0.08980.1477-0.01720.04950.20950.00180.146315.46472.3815-34.2434
30.1721-0.16230.21190.6148-0.5510.44310.0326-0.04020.0303-0.1225-0.0151-0.08570.09190.02830.04660.15160.00210.00160.1319-0.00520.134711.2848-6.3309-22.7369
41.0854-0.1755-0.42262.4883-0.38760.37690.05420.1387-0.0481-0.2933-0.03650.18530.1691-0.0549-0.00990.2246-0.0051-0.04130.2203-0.01050.15721.7018-7.297-32.0071
51.6192-0.6729-0.80821.66531.08773.1107-0.0801-0.0972-0.1366-0.02790.08890.2540.18-0.0526-0.04210.1583-0.0344-0.03780.1710.04070.1794-0.6558-15.4415-19.4023
61.8334-0.87190.64041.0828-0.34930.8692-0.10080.08890.14410.05020.0093-0.24590.00830.3845-0.00910.19460.0107-0.01460.25250.03770.155516.1881-17.9773-8.411
71.0406-0.2370.58250.8346-1.07451.6981-0.0452-0.26560.05510.1437-0.0358-0.1897-0.24240.07940.11030.1687-0.0076-0.0250.22130.01350.170517.43-13.4874-6.7121
81.79840.0717-0.37931.91220.3082.9616-0.0289-0.052-0.18040.0040.1295-0.30260.5485-0.112-0.03030.24840.0068-0.0020.2110.02210.221218.3869-29.1742-2.7555
91.2979-1.30311.27551.8708-1.32882.89060.0022-0.2138-0.3037-0.09550.13570.20470.3730.0792-0.10090.2133-0.0156-0.00560.19150.02530.1679.6214-24.7823-14.7888
102.0888-0.1938-0.07192.1293-0.20492.1685-0.0419-0.1427-0.04930.20150.15940.0220.0037-0.0655-0.08510.14160.00720.00890.15670.0090.125519.5123-27.0087-43.2729
111.0118-0.0782-0.13851.2296-0.25450.5690.0272-0.0075-0.01210.0925-0.00630.0284-0.0644-0.0196-0.00790.11560.00910.01110.1393-0.010.119117.1884-22.6179-49.6205
120.2354-0.4197-0.07952.9160.3011.1153-0.0385-0.36760.29560.55010.08680.3114-0.393-0.07720.06250.25640.04530.05260.2035-0.05060.2469.6026-7.5491-47.6581
131.5637-0.23260.03881.51580.96053.56360.01310.11080.0982-0.0359-0.05050.073-0.2043-0.16190.04350.12680.01420.01440.16020.01650.155712.6543-11.797-60.1559
140.91970.7575-0.07122.27050.8491.0376-0.16220.50720.0153-0.19930.1744-0.35360.00010.2502-0.11870.1091-0.01650.03610.25550.02690.21931.181-10.838-65.4186
150.9773-0.1096-0.50480.75010.27961.77250.19980.13840.1899-0.0801-0.0063-0.2884-0.04420.1809-0.14210.1206-0.00740.0620.24250.01990.24634.9084-11.9885-64.0174
162.73981.14180.30870.8272-0.58371.41380.3631-0.05571.2959-0.12850.2836-0.8183-0.72030.4126-0.00910.5958-0.23960.39560.33960.04171.197338.11572.532-66.8386
172.8764-0.6345-1.37953.45310.032.87390.0256-0.07470.223-0.01890.1142-0.0161-0.3948-0.0194-0.14460.21690.00660.02540.1407-0.00840.239422.0376-3.654-59.5744
182.64940.92221.5013.19450.17832.304-0.24060.33980.1252-0.5228-0.0913-0.87890.35640.60720.17710.20830.03060.05930.31510.0560.35523.2574-9.8722-27.7228
198.0773-5.7051-5.87894.50344.73164.9888-0.05970.3048-0.0060.1423-0.3956-0.86110.28910.20140.1760.45090.08120.02860.31030.01750.337322.5362-21.9124-21.1661
200.2326-0.1094-0.48580.05920.24271.02050.0334-0.3719-0.21440.8426-0.007-0.8021-0.42350.09210.03370.26-0.0387-0.11820.26210.01060.388829.9237-15.7563-42.6137
213.156-0.42861.30923.0611-1.16984.2766-0.1051-0.5210.50410.5333-0.2648-1.0464-1.03250.13370.27840.3995-0.0467-0.12860.23640.01320.553931.7023-5.1558-49.5475
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN 'A' AND (RESID 6 THROUGH 16 )
2X-RAY DIFFRACTION2CHAIN 'A' AND (RESID 17 THROUGH 29 )
3X-RAY DIFFRACTION3CHAIN 'A' AND (RESID 30 THROUGH 69 )
4X-RAY DIFFRACTION4CHAIN 'A' AND (RESID 70 THROUGH 101 )
5X-RAY DIFFRACTION5CHAIN 'A' AND (RESID 102 THROUGH 118 )
6X-RAY DIFFRACTION6CHAIN 'A' AND (RESID 119 THROUGH 139 )
7X-RAY DIFFRACTION7CHAIN 'A' AND (RESID 140 THROUGH 158 )
8X-RAY DIFFRACTION8CHAIN 'A' AND (RESID 159 THROUGH 185 )
9X-RAY DIFFRACTION9CHAIN 'A' AND (RESID 186 THROUGH 201 )
10X-RAY DIFFRACTION10CHAIN 'B' AND (RESID 5 THROUGH 29 )
11X-RAY DIFFRACTION11CHAIN 'B' AND (RESID 30 THROUGH 88 )
12X-RAY DIFFRACTION12CHAIN 'B' AND (RESID 89 THROUGH 101 )
13X-RAY DIFFRACTION13CHAIN 'B' AND (RESID 102 THROUGH 118 )
14X-RAY DIFFRACTION14CHAIN 'B' AND (RESID 119 THROUGH 136 )
15X-RAY DIFFRACTION15CHAIN 'B' AND (RESID 137 THROUGH 169 )
16X-RAY DIFFRACTION16CHAIN 'B' AND (RESID 170 THROUGH 188 )
17X-RAY DIFFRACTION17CHAIN 'B' AND (RESID 189 THROUGH 201 )
18X-RAY DIFFRACTION18CHAIN 'C' AND (RESID 437 THROUGH 445 )
19X-RAY DIFFRACTION19CHAIN 'C' AND (RESID 446 THROUGH 452 )
20X-RAY DIFFRACTION20CHAIN 'D' AND (RESID 438 THROUGH 445 )
21X-RAY DIFFRACTION21CHAIN 'D' AND (RESID 446 THROUGH 451 )

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