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- PDB-5vhv: Pseudomonas fluorescens alkylpurine DNA glycosylase AlkC bound to... -

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Basic information

Entry
Database: PDB / ID: 5vhv
TitlePseudomonas fluorescens alkylpurine DNA glycosylase AlkC bound to DNA containing an oxocarbenium-intermediate analog
Components
  • DNA (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
  • DNA (5'-D(*TP*GP*TP*CP*CP*AP*(NRI)P*GP*TP*CP*T)-3')
  • alkylpurine DNA glycosylase AlkC
KeywordsHYDROLASE/DNA / DNA alkylation repair enzyme / HYDROLASE-DNA complex
Function / homologyDNA alkylation repair enzyme / DNA alkylation repair enzyme / Armadillo-type fold / Chem-9B4 / DNA / DNA (> 10) / DNA alkylation repair protein
Function and homology information
Biological speciesPseudomonas fluorescens (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.799 Å
AuthorsShi, R. / Eichman, B.F.
Funding support United States, 1items
OrganizationGrant numberCountry
National Science Foundation (NSF, United States)1517695 United States
CitationJournal: EMBO J. / Year: 2018
Title: Selective base excision repair of DNA damage by the non-base-flipping DNA glycosylase AlkC.
Authors: Shi, R. / Mullins, E.A. / Shen, X.X. / Lay, K.T. / Yuen, P.K. / David, S.S. / Rokas, A. / Eichman, B.F.
History
DepositionApr 13, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 25, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2017Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name
Revision 1.2Jan 17, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Nov 27, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Oct 4, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: alkylpurine DNA glycosylase AlkC
B: alkylpurine DNA glycosylase AlkC
C: DNA (5'-D(*TP*GP*TP*CP*CP*AP*(NRI)P*GP*TP*CP*T)-3')
D: DNA (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
E: DNA (5'-D(*TP*GP*TP*CP*CP*AP*(NRI)P*GP*TP*CP*T)-3')
F: DNA (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,89315
Polymers94,2246
Non-polymers1,6699
Water22,9691275
1
A: alkylpurine DNA glycosylase AlkC
C: DNA (5'-D(*TP*GP*TP*CP*CP*AP*(NRI)P*GP*TP*CP*T)-3')
D: DNA (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8497
Polymers47,1123
Non-polymers7374
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-36 kcal/mol
Surface area18500 Å2
MethodPISA
2
B: alkylpurine DNA glycosylase AlkC
E: DNA (5'-D(*TP*GP*TP*CP*CP*AP*(NRI)P*GP*TP*CP*T)-3')
F: DNA (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0448
Polymers47,1123
Non-polymers9325
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5330 Å2
ΔGint-39 kcal/mol
Surface area18380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)198.373, 198.373, 60.189
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein alkylpurine DNA glycosylase AlkC


Mass: 40539.543 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas fluorescens (bacteria) / Gene: PFLU_2162 / Production host: Escherichia coli (E. coli) / References: UniProt: C3K795

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DNA chain , 2 types, 4 molecules CEDF

#2: DNA chain DNA (5'-D(*TP*GP*TP*CP*CP*AP*(NRI)P*GP*TP*CP*T)-3')


Mass: 3190.088 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*AP*AP*GP*AP*CP*TP*TP*GP*GP*AP*C)-3')


Mass: 3382.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 5 types, 1284 molecules

#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Chemical ChemComp-9B4 / (2R,5R,13R,16R)-9-(hydroxymethyl)-9-{[(2R)-2-hydroxypropoxy]methyl}-5,13-dimethyl-4,7,11,14-tetraoxaheptadecane-2,16-diol / Pentaerythritol propoxylate (5/4 PO/OH)


Mass: 426.542 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H42O9
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1275 / Source method: isolated from a natural source / Formula: H2O

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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: 3.57 Å3/Da / Density % sol: 65.54 %
Crystal growTemperature: 294.15 K / Method: vapor diffusion, hanging drop / pH: 6.1
Details: 18% pentaerythritol propoxylate, 100 mM MES, pH 6.1

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 12.3.1 / Wavelength: 0.99189 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 30, 2016
RadiationMonochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99189 Å / Relative weight: 1
ReflectionResolution: 1.8→100 Å / Num. obs: 124523 / % possible obs: 99.1 % / Redundancy: 9.7 % / Biso Wilson estimate: 19.75 Å2 / Rmerge(I) obs: 0.092 / Rpim(I) all: 0.031 / Rrim(I) all: 0.097 / Χ2: 1.364 / Net I/σ(I): 14 / Num. measured all: 1208363
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
1.8-1.869.10.49121130.9060.1720.521.32297.1
1.86-1.949.40.377121930.9440.1290.3991.41297.4
1.94-2.039.40.274122330.9690.0940.2911.51898.2
2.03-2.139.40.198123730.9810.0680.2091.63798.9
2.13-2.279.50.146124290.9890.050.1551.69399.6
2.27-2.449.60.117125480.9920.040.1241.51699.8
2.44-2.699.80.094125280.9950.0320.11.4100
2.69-3.0810.10.081125680.9960.0270.0851.174100
3.08-3.8810.30.08126610.9960.0260.0841.191100
3.88-10010.30.063128770.9970.0210.0660.87499.8

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
HKL-2000data reduction
HKL-2000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 5VI0

5vi0


Resolution: 1.799→49.292 Å / SU ML: 0.13 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 15.69 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1638 6250 5.02 %
Rwork0.141 118228 -
obs0.1421 124478 99.05 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 133.83 Å2 / Biso mean: 27.3313 Å2 / Biso min: 7.06 Å2
Refinement stepCycle: final / Resolution: 1.799→49.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5718 870 243 1275 8106
Biso mean--59.68 36.28 -
Num. residues----766
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087070
X-RAY DIFFRACTIONf_angle_d1.0599775
X-RAY DIFFRACTIONf_chiral_restr0.0561083
X-RAY DIFFRACTIONf_plane_restr0.0071075
X-RAY DIFFRACTIONf_dihedral_angle_d17.1774058
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 30

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.7993-1.81970.20242000.17743819401996
1.8197-1.84110.21312000.17193803400397
1.8411-1.86360.21162020.17433852405497
1.8636-1.88720.2142080.1723859406797
1.8872-1.9120.21192020.17383817401998
1.912-1.93820.2062070.1663912411997
1.9382-1.96590.19982050.16133834403998
1.9659-1.99520.20422050.15093891409698
1.9952-2.02640.17972090.14313904411398
2.0264-2.05960.16892060.14583890409699
2.0596-2.09520.17672050.14813939414499
2.0952-2.13320.17442120.13593911412399
2.1332-2.17430.16422050.13493908411399
2.1743-2.21870.15592090.126739694178100
2.2187-2.26690.14252040.128139424146100
2.2669-2.31960.15222090.127439884197100
2.3196-2.37760.17112080.133539324140100
2.3776-2.44190.16772120.130439954207100
2.4419-2.51380.16352050.13239714176100
2.5138-2.59490.15592080.12939564164100
2.5949-2.68770.16612110.135139764187100
2.6877-2.79530.16732110.134740024213100
2.7953-2.92250.15482100.139939644174100
2.9225-3.07650.17612110.14739704181100
3.0765-3.26920.17062120.139740144226100
3.2692-3.52160.14942160.134540214237100
3.5216-3.87580.13742100.128139834193100
3.8758-4.43640.12632160.121240134229100
4.4364-5.58810.142140.131540564270100
5.5881-49.3110.20342180.18654137435599
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)
12.0650.0574-1.21652.1059-1.26373.0333-0.03940.5591-0.3084-0.27680.01490.05690.2594-0.1088-0.0050.17340.0143-0.03170.3326-0.12920.194718.05969.3131-10.1172
21.6675-0.3559-0.35281.04290.34811.00050.08060.1210.1314-0.047-0.025-0.1085-0.07060.0261-0.05550.08080.0024-0.00140.1565-0.00110.139416.005487.04682.2791
31.8866-0.1163-0.62671.91790.31022.30860.09010.02410.17960.1544-0.04770.2701-0.2998-0.2007-0.02550.12570.0170.02960.1737-0.04040.1966-1.86192.404315.7551
41.62460.934-0.70471.4885-0.12820.87670.1824-0.05610.22880.2383-0.07190.2385-0.0965-0.2852-0.1260.17310.00480.06290.2679-0.01580.1496-15.184583.140225.9047
51.6168-0.3157-0.59342.93110.25521.50990.0718-0.07470.02250.0865-0.1001-0.01080.0516-0.16570.0310.1282-0.01890.00670.23270.02070.0775-15.210670.472523.2219
62.8127-0.6544-0.54263.78272.96744.7786-0.2148-0.4491-0.31010.71970.23560.05820.65010.07970.03170.22670.05510.0130.21390.08830.179836.52660.63389.1996
72.2904-0.6196-0.91392.05740.70191.948-0.0626-0.2780.13720.18720.1507-0.0090.08590.063-0.06810.09950.0290.01320.1686-0.02860.141534.896471.86385.8539
81.83620.1136-0.85950.684-0.01520.9960.0478-0.10120.2773-0.0188-0.021-0.0497-0.03350.0619-0.01720.1030.01950.00970.10510.00750.185656.378773.5446-9.438
90.96160.23370.09012.26710.47410.5914-0.00270.15470.0842-0.1870.0351-0.15740.10030.068-0.04510.19430.04550.05430.16010.0120.105468.507752.4351-25.4772
103.07550.8958-0.03041.79170.04110.642-0.01530.1744-0.2211-0.12840.0271-0.1740.19770.0583-0.0230.2330.03980.02570.1285-0.0130.100364.323938.4138-23.0388
117.93070.82321.21730.79910.12761.03920.08020.3649-0.0739-0.0075-0.0407-0.00860.12230.00830.05830.18580.03110.02030.1551-0.00740.091857.851148.1463-26.2828
123.42920.80340.10011.02030.01850.71750.00410.0811-0.1195-0.0672-0.0218-0.01660.1329-0.01630.00230.19670.0280.01070.1244-0.0120.072958.929143.3695-23.6084
131.85221.37350.93381.36810.06894.9250.0648-0.1927-0.21450.024-0.0939-0.1570.20780.1851-0.02920.06170.03860.03180.17850.01220.14241.359671.785512.3981
146.22020.12-0.62372.80080.60851.3563-0.0282-0.0437-0.18190.0292-0.0693-0.0471-0.1032-0.03390.09290.15360.0030.0050.13660.02050.10860.60573.53711.2945
150.32080.780.28553.59990.824.8782-0.1227-0.01340.0798-0.1085-0.09280.1045-0.2023-0.33080.16590.05920.04290.0640.1475-0.01680.108747.79554.8342-13.4897
164.8218-2.7198-0.01743.0220.16540.40620.04970.19890.0361-0.0651-0.15690.1322-0.0207-0.03180.12140.205-0.00650.01610.1457-0.00820.138149.397355.4689-12.1177
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'A' and (resid 5 through 49 )A5 - 49
2X-RAY DIFFRACTION2chain 'A' and (resid 50 through 190 )A50 - 190
3X-RAY DIFFRACTION3chain 'A' and (resid 191 through 233 )A191 - 233
4X-RAY DIFFRACTION4chain 'A' and (resid 234 through 265 )A234 - 265
5X-RAY DIFFRACTION5chain 'A' and (resid 266 through 365 )A266 - 365
6X-RAY DIFFRACTION6chain 'B' and (resid 5 through 28 )B5 - 28
7X-RAY DIFFRACTION7chain 'B' and (resid 29 through 103 )B29 - 103
8X-RAY DIFFRACTION8chain 'B' and (resid 104 through 233 )B104 - 233
9X-RAY DIFFRACTION9chain 'B' and (resid 234 through 265 )B234 - 265
10X-RAY DIFFRACTION10chain 'B' and (resid 266 through 288 )B266 - 288
11X-RAY DIFFRACTION11chain 'B' and (resid 289 through 305 )B289 - 305
12X-RAY DIFFRACTION12chain 'B' and (resid 306 through 365 )B306 - 365
13X-RAY DIFFRACTION13chain 'C' and (resid 1 through 11 )C1 - 11
14X-RAY DIFFRACTION14chain 'D' and (resid 1 through 11 )D1 - 11
15X-RAY DIFFRACTION15chain 'E' and (resid 1 through 11 )E1 - 11
16X-RAY DIFFRACTION16chain 'F' and (resid 1 through 11 )F1 - 11

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