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- PDB-6l6s: The structure of the UdgX mutant H109E crosslinked to single-stra... -

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Basic information

Entry
Database: PDB / ID: 6l6s
TitleThe structure of the UdgX mutant H109E crosslinked to single-stranded DNA
Components
  • DNA (5'-D(P*TP*GP*(ORP)P*AP*GP*GP*CP*AP*TP*GP*C)-3')
  • Phage SPO1 DNA polymerase-related protein
KeywordsDNA BINDING PROTEIN / UdgX / covalent complex / protein-DNA interaction / DNA repair / glycosylase
Function / homology
Function and homology information


uracil DNA N-glycosylase activity / nucleotidyltransferase activity / 4 iron, 4 sulfur cluster binding / DNA repair / metal ion binding
Similarity search - Function
Uracil-DNA glycosylase family 4 / UreE urease accessory protein, C-terminal domain / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / DNA / DNA (> 10) / Type-4 uracil-DNA glycosylase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.0642595849 Å
AuthorsXie, W. / Tu, J. / Zeng, H.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China31870782 China
CitationJournal: DNA Repair (Amst) / Year: 2021
Title: Structural insights into an MsmUdgX mutant capable of both crosslinking and uracil excision capability.
Authors: Jia, Q. / Zeng, H. / Tu, J. / Sun, L. / Cao, W. / Xie, W.
History
DepositionOct 29, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Nov 4, 2020Provider: repository / Type: Initial release
Revision 1.1May 12, 2021Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.journal_id_CSD ..._citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phage SPO1 DNA polymerase-related protein
B: Phage SPO1 DNA polymerase-related protein
C: DNA (5'-D(P*TP*GP*(ORP)P*AP*GP*GP*CP*AP*TP*GP*C)-3')
D: DNA (5'-D(P*TP*GP*(ORP)P*AP*GP*GP*CP*AP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,3136
Polymers54,6094
Non-polymers7032
Water3,585199
1
A: Phage SPO1 DNA polymerase-related protein
C: DNA (5'-D(P*TP*GP*(ORP)P*AP*GP*GP*CP*AP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6563
Polymers27,3052
Non-polymers3521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2200 Å2
ΔGint-28 kcal/mol
Surface area11220 Å2
MethodPISA
2
B: Phage SPO1 DNA polymerase-related protein
D: DNA (5'-D(P*TP*GP*(ORP)P*AP*GP*GP*CP*AP*TP*GP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6563
Polymers27,3052
Non-polymers3521
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2230 Å2
ΔGint-29 kcal/mol
Surface area10200 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.265, 82.348, 122.444
Angle α, β, γ (deg.)90.000, 94.927, 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
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-ID
11
21
12
22

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111DTDTDGDGchain DDD6 - 76 - 7
121DADADCDCchain DDD9 - 169 - 16
231DTDTDGDGchain CCC6 - 76 - 7
241DADADCDCchain CCC9 - 169 - 16
152ALAALATHRTHR(chain A and (resseq 12:13 or (resid 14 and (name...AA12 - 9915 - 102
162ARGARGSERSER(chain A and (resseq 12:13 or (resid 14 and (name...AA106 - 113109 - 116
172THRTHRPHEPHE(chain A and (resseq 12:13 or (resid 14 and (name...AA115 - 152118 - 155
182VALVALTHRTHR(chain A and (resseq 12:13 or (resid 14 and (name...AA154 - 155157 - 158
192HISHISLEULEU(chain A and (resseq 12:13 or (resid 14 and (name...AA157 - 201160 - 204
1102VALVALASPASP(chain A and (resseq 12:13 or (resid 14 and (name...AA203 - 206206 - 209
2112ALAALATHRTHR(chain B and (resseq 12:13 or (resid 14 and (name...BB12 - 9915 - 102
2122ARGARGSERSER(chain B and (resseq 12:13 or (resid 14 and (name...BB106 - 113109 - 116
2132THRTHRPHEPHE(chain B and (resseq 12:13 or (resid 14 and (name...BB115 - 152118 - 155
2142VALVALTHRTHR(chain B and (resseq 12:13 or (resid 14 and (name...BB154 - 155157 - 158
2152HISHISLEULEU(chain B and (resseq 12:13 or (resid 14 and (name...BB157 - 201160 - 204
2162VALVALASPASP(chain B and (resseq 12:13 or (resid 14 and (name...BB203 - 206206 - 209

NCS ensembles :
ID
1
2

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Components

#1: Protein Phage SPO1 DNA polymerase-related protein


Mass: 22474.527 Da / Num. of mol.: 2 / Mutation: H109E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / Gene: MSMEI_0259 / Production host: Escherichia coli (E. coli) / References: UniProt: I7F541, DNA-directed DNA polymerase
#2: DNA chain DNA (5'-D(P*TP*GP*(ORP)P*AP*GP*GP*CP*AP*TP*GP*C)-3')


Mass: 4830.117 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) synthetic construct (others) / Production host: synthetic construct (others)
#3: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Fe4S4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Sequence detailsAUTHORS STATE THAT THE GENEBANK ACCESSION NUMBER IS AWT51284.1. FOR THE PROTEIN.

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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: 1.98 Å3/Da / Density % sol: 37.86 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 2.15 M sodium malonate pH 7.0 and 3.8% MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.997 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Oct 23, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.997 Å / Relative weight: 1
ReflectionResolution: 2.06→50 Å / Num. obs: 26965 / % possible obs: 99.4 % / Redundancy: 6.8 % / Biso Wilson estimate: 22.2292804408 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.05 / Net I/σ(I): 34.2
Reflection shellResolution: 2.07→2.14 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 2675 / CC1/2: 0.914 / % possible all: 99.8

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6IOD

6iod


Resolution: 2.0642595849→40.6638537709 Å / SU ML: 0.26359587024 / Cross valid method: FREE R-VALUE / σ(F): 1.35396944614 / Phase error: 27.4703597128
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.261127931323 1206 4.65152157982 %
Rwork0.209255652371 24721 -
obs0.211757940956 25927 96.0721829029 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 36.0949555326 Å2
Refinement stepCycle: LAST / Resolution: 2.0642595849→40.6638537709 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2862 438 16 200 3516
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0112111426123433
X-RAY DIFFRACTIONf_angle_d1.135417018764743
X-RAY DIFFRACTIONf_chiral_restr0.0581100622235547
X-RAY DIFFRACTIONf_plane_restr0.00823919180425553
X-RAY DIFFRACTIONf_dihedral_angle_d20.3991136631949
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.0643-2.14690.2936459942771080.2477693540892194X-RAY DIFFRACTION77.4562584118
2.1469-2.24460.305758274386930.237399738132680X-RAY DIFFRACTION92.9601072746
2.2446-2.36290.2726065219611290.2391233520972843X-RAY DIFFRACTION99.2983628466
2.3629-2.5110.3068814905981380.2327168624192797X-RAY DIFFRACTION98.3579088472
2.511-2.70480.2936477696921460.242605548542825X-RAY DIFFRACTION99.7649429147
2.7048-2.97690.3045791838741470.2344809292132846X-RAY DIFFRACTION99.8332221481
2.9769-3.40750.2470611352561310.2054649074172847X-RAY DIFFRACTION98.544010589
3.4075-4.29230.2671215537461720.1736523422542819X-RAY DIFFRACTION99.8331108144
4.2923-40.660.2067615759531420.1868048761322870X-RAY DIFFRACTION98.431372549
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)
11.389558015130.8387276616380.180017519061.89922716963-0.2052285169961.640159999720.292921600544-0.493657110675-0.2124269188840.459088298354-0.3783008498-0.238503623417-0.1188813375090.3139442147630.03928717117520.23439836524-0.139707847498-0.04407051180820.2253081388320.07043608636230.18472409879117.9448081332-4.5857182018523.0597598874
21.01132891283-0.4230735366120.6126708496140.4161589126240.1391162607711.015438111290.172103785555-0.228736060334-0.04240180617970.311169004841-0.2196737875340.193015279645-0.0408468940307-0.0299336357679-0.09189022981380.138516845814-0.2695817736770.0896129483359-0.02803264836420.03021148060170.12852210955113.577403723-2.0853291576721.014599704
30.05524142902260.131921575954-0.1013504288410.60291735087-0.1238730318580.2254219733760.140016331689-0.1452942283730.2103949314010.208685400199-0.02780036136290.215467908873-0.1663095908220.0678984010114-7.04770544441E-50.351457945231-0.2259142389680.03445321910780.2243331727910.02858700162540.24171781512420.074918818811.951472705416.9024701296
42.195530103160.673227048290.4100018355962.67829201092-0.4246457507782.183755487470.003232733909970.124668968737-0.395641834665-0.146318319754-0.0901510454447-0.1736064941530.3948030556940.2405632416950.1045146804120.1231714128340.01746369463640.02747630079270.007335450018990.02999112889760.16858595499116.7037030788-8.8477705411710.6196452749
52.757081637560.2869471813080.5458026404915.72528731690.4877681978694.09817923924-0.05485767006640.405174808056-0.0317132449172-0.395964553759-0.0752967979615-0.3243910895270.197258625978-0.1043106913310.05943493612880.136288761418-0.06258503403450.05022697589010.106618130896-0.02186288642360.2246111461148.56197503683-7.625262840359.06643712943
63.0149036883-1.58233564330.06846832093381.27594727772-0.88705802692.80816152182-0.008360592175590.2163643229840.0790323562231-0.2567914280240.0342535162950.6900167850580.00509225180167-0.567289135708-0.03974252621690.136749941871-0.0419945769935-0.04336281206380.226896908685-0.03967378948550.258591132125-1.79908032311-5.9651933117512.0877166241
71.19726883341-0.2612731790620.6005966996551.724314918420.6438338765911.18512707560.0861292517639-0.565867224995-0.0273515964622-0.0474172793103-0.146513210321-0.568868393306-0.1812386812951.019003798320.05624051716430.318518847452-0.1093236236530.05152293684540.7988959666660.1182345184470.330311980048.863032742712.9264262969739.6658559849
83.07916376764-0.7757603484940.9353930445481.968218733821.09972265671.29705375479-0.0344773657578-0.06652558342390.280616799782-0.406471635778-0.0132349187746-0.212700049907-0.4404076512490.3736337061450.06400040302860.356128108954-0.1753912288560.0226322364790.4949534041570.001257427311190.1527442105265.161745043067.7921391765437.814908592
92.64814111231-0.194400476750.08530600907641.15749904269-0.6376053726843.202312034230.195385029323-0.7140526752350.2503147558260.226235630359-0.148729748539-0.152649420886-0.5006181872950.223614316497-0.03129536628860.352225004921-0.102234437320.009057880704760.499180316091-0.03852386429150.227338571438-2.208697325886.7127879145945.5778432693
103.351825158781.74552409792-0.8547423809131.77951071273-2.008591532233.05038322610.2803228435850.1416479148010.6141888570140.003715432050540.0220499410751-0.0534181912122-0.634121782246-0.0698474638335-0.2632376478490.4080630050420.002260536421420.1186530253820.100578358660.03557289093910.33487912487715.66518655569.927596888084.3262673349
112.45578060746-0.914409784229-0.6772951794162.09620225862-0.5586154195824.63656570516-0.141414176856-0.579478183168-0.6721529424650.636488236792-0.08075825022140.1922081339830.980603642955-0.432332767770.207127925330.481302565281-0.181389847561-0.01818373197610.5875968083320.1270322149440.380837286584-6.59668092325-8.0055472191153.1318600709
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 3 through 79 )
2X-RAY DIFFRACTION2chain 'A' and (resid 80 through 101 )
3X-RAY DIFFRACTION3chain 'A' and (resid 102 through 113 )
4X-RAY DIFFRACTION4chain 'A' and (resid 114 through 157 )
5X-RAY DIFFRACTION5chain 'A' and (resid 158 through 186 )
6X-RAY DIFFRACTION6chain 'A' and (resid 187 through 209 )
7X-RAY DIFFRACTION7chain 'B' and (resid 12 through 79 )
8X-RAY DIFFRACTION8chain 'B' and (resid 80 through 96 )
9X-RAY DIFFRACTION9chain 'B' and (resid 97 through 207 )
10X-RAY DIFFRACTION10chain 'C' and (resid 6 through 16 )
11X-RAY DIFFRACTION11chain 'D' and (resid 6 through 16 )

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