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- PDB-4cis: Structure of MutM in complex with carbocyclic 8-oxo-G containing DNA -

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Basic information

Entry
Database: PDB / ID: 4cis
TitleStructure of MutM in complex with carbocyclic 8-oxo-G containing DNA
Components
  • (DNA) x 2
  • FORMAMIDOPYRIMIDIN DNA GLYCOSYLASE
KeywordsHYDROLASE / BASE EXCISION REPAIR / DNA REPAIR
Function / homology
Function and homology information


oxidized purine nucleobase lesion DNA N-glycosylase activity / DNA-formamidopyrimidine glycosylase / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / nucleotide-excision repair / base-excision repair / damaged DNA binding / zinc ion binding
Similarity search - Function
Formamidopyrimidine-DNA glycosylase / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins ...Formamidopyrimidine-DNA glycosylase / Zinc finger, DNA glycosylase/AP lyase-type / Zinc finger, FPG/IleRS-type / DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site / Zinc finger found in FPG and IleRS / Zinc finger FPG-type signature. / Zinc finger FPG-type profile. / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase H2TH domain / N-terminal domain of MutM-like DNA repair proteins / Formamidopyrimidine-DNA glycosylase N-terminal domain / Formamidopyrimidine-DNA glycosylase N-terminal domain / MutM-like, N-terminal / Formamidopyrimidine-DNA glycosylase, catalytic domain / Formamidopyrimidine-DNA glycosylase catalytic domain profile. / Formamidopyrimidine-DNA glycosylase H2TH domain / DNA glycosylase/AP lyase, H2TH DNA-binding / Helicase, Ruva Protein; domain 3 - #50 / Helicase, Ruva Protein; domain 3 / Ribosomal protein S13-like, H2TH / Alpha-Beta Barrel / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
(R,R)-2,3-BUTANEDIOL / DNA / DNA (> 10) / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsSchneider, S. / Sadeghian, K. / Flaig, D. / Blank, I.D. / Strasser, R. / Stathis, D. / Winnacker, M. / Carell, T. / Ochsenfeld, C.
CitationJournal: Angew. Chem. Int. Ed. Engl. / Year: 2014
Title: Ribose-protonated DNA base excision repair: a combined theoretical and experimental study.
Authors: Sadeghian, K. / Flaig, D. / Blank, I.D. / Schneider, S. / Strasser, R. / Stathis, D. / Winnacker, M. / Carell, T. / Ochsenfeld, C.
History
DepositionDec 15, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 4, 2014Provider: repository / Type: Initial release
Revision 1.1Aug 6, 2014Group: Database references
Revision 1.2Sep 17, 2014Group: Database references
Revision 2.0Mar 7, 2018Group: Atomic model / Database references / Source and taxonomy
Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / citation / entity_src_gen / pdbx_entity_src_syn
Item: _citation.journal_abbrev / _citation.journal_id_ASTM ..._citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain
Revision 2.1Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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 / _struct_conn_type.id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FORMAMIDOPYRIMIDIN DNA GLYCOSYLASE
B: FORMAMIDOPYRIMIDIN DNA GLYCOSYLASE
C: DNA
D: DNA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)73,9187
Polymers73,6974
Non-polymers2213
Water2,432135
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5950 Å2
ΔGint-27.1 kcal/mol
Surface area27820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.063, 112.692, 132.882
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (0.9764, 0.00588, 0.2157), (0.0478, -0.9807, -0.1897), (0.2104, 0.1955, -0.9579)
Vector: 11.61, -31.6, 76.34)

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FORMAMIDOPYRIMIDIN DNA GLYCOSYLASE / FAPY-DNA GLYCOSYLASE / DNA-(APURINIC OR APYRIMIDINIC SITE) LYASE MUTM / FORMAMIDOPYRIMIDIN DNA GLYCOSYLASE


Mass: 32561.838 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Plasmid: PPSG-IBA3 / Production host: Escherichia coli BL21 (bacteria)
References: UniProt: Q031W6, DNA-formamidopyrimidine glycosylase

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DNA chain , 2 types, 2 molecules CD

#2: DNA chain DNA


Mass: 4355.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA


Mass: 4217.750 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Non-polymers , 3 types, 138 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-BU3 / (R,R)-2,3-BUTANEDIOL


Mass: 90.121 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 135 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsCARBOCYCLIC 8-OXO-2'-DEOXY-GUANOSINE-5'-MONOPHOSPHATE (68Z): CARBOCYCLIC RIBOSE
Sequence detailsC-TERMINAL STREP-TAG CONTAINS CARBOCYCLIC 8-OXO GUANINE BASE

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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: 2.65 Å3/Da / Density % sol: 53 % / Description: NONE
Crystal growDetails: 100 MM TRIS PH 7.5, 2 MM SPERMIDINE, 1 MM TCEP, 0.01MM ZNCL2 , 90 MM LISO4, 18% PEG 4000

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1.0763
DetectorType: MARRESEARCH / Detector: CCD / Date: Jul 4, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0763 Å / Relative weight: 1
ReflectionResolution: 2.05→40.93 Å / Num. obs: 41439 / % possible obs: 99.9 % / Observed criterion σ(I): 1.5 / Redundancy: 5.9 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 10.73
Reflection shellResolution: 2.05→2.12 Å / Redundancy: 4.7 % / Rmerge(I) obs: 1.18 / Mean I/σ(I) obs: 1.5 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XC8

1xc8


Resolution: 2.05→40.93 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.927 / SU B: 9.912 / SU ML: 0.136 / Cross valid method: THROUGHOUT / ESU R: 0.227 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.23885 2103 5.1 %RANDOM
Rwork0.21378 ---
obs0.21507 39352 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 30.072 Å2
Baniso -1Baniso -2Baniso -3
1-1.23 Å20 Å20 Å2
2---1.52 Å20 Å2
3---0.29 Å2
Refinement stepCycle: LAST / Resolution: 2.05→40.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4289 569 8 135 5001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0185012
X-RAY DIFFRACTIONr_bond_other_d0.0020.024727
X-RAY DIFFRACTIONr_angle_refined_deg1.8211.8816841
X-RAY DIFFRACTIONr_angle_other_deg1.288310938
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7785526
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.24323.886193
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.25715882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.5981531
X-RAY DIFFRACTIONr_chiral_restr0.1050.2734
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.025092
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021079
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8241.3332116
X-RAY DIFFRACTIONr_mcbond_other0.8231.3332115
X-RAY DIFFRACTIONr_mcangle_it1.1761.9952638
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.231.4782896
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.05→2.103 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.371 137 -
Rwork0.351 2793 -
obs--99.02 %
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)
11.82162.91474.219210.96694.853310.3714-0.03640.07310.030.3053-0.03040.1945-0.19420.23670.06680.0333-0.00880.00580.02540.03160.06590.4798-15.831159.458
22.36020.5322-0.99162.4361-0.82739.02030.0348-0.1866-0.02330.3366-0.0652-0.11240.05750.43180.03040.1449-0.0205-0.01760.0750.00390.08733.06960.952959.455
313.86944.07930.92315.52361.04850.1042-0.1130.75340.1935-0.74510.0908-0.0935-0.05410.04510.02230.1301-0.0222-0.03710.08550.04760.0407-1.27330.714943.5359
41.23851.85890.81618.66841.51432.1520.00140.00760.38290.303-0.02140.479-0.3264-0.17730.020.08860.03670.04450.04780.02170.1538-5.4796-1.141856.148
53.58752.94512.72355.69561.99443.1011-0.13530.12720.19340.32050.1019-0.1482-0.0590.11470.03330.09010.0195-0.03120.02720.02980.08542.8964-3.108954.5563
62.97840.50731.58928.3635.13527.4922-0.07620.1980.02190.26110.0797-0.33-0.00780.2859-0.00350.0458-0.0203-0.00920.06590.04760.07098.4843-2.246451.3889
70.34010.2581-0.50456.2309-0.72680.82660.01880.16290.1763-0.08850.22080.98490.0003-0.3012-0.23970.0430.0106-0.01150.13350.04310.2649-12.2366-9.218351.0907
83.39921.04670.56583.54751.692610.89610.03990.09170.02480.0157-0.18620.93560.1032-0.89950.14620.0668-0.0113-0.00650.0826-0.03660.2761-14.6248-30.437351.2686
92.65750.62631.02094.08571.10381.80760.08950.0949-0.16880.0671-0.06470.06190.2349-0.1037-0.02470.0481-0.00560.00850.0255-0.00240.0207-5.2603-31.835553.773
105.53980.40362.418512.85876.42856.1710.17030.02070.0332-0.5376-0.0105-0.771-0.44050.518-0.15980.1288-0.0206-0.0280.15090.02780.09919.4934-26.405358.26
116.3116-1.3761.57556.8558-3.22858.3511-0.04620.1427-0.08860.0819-0.0786-0.41770.05940.13310.12480.07610.02050.00310.039-0.03210.07436.1731-38.625248.0183
123.1922-1.3552-3.59039.06410.32534.2112-0.0192-0.1327-0.002-0.2208-0.0418-0.07270.0810.17560.06110.10270.0032-0.0360.05380.04070.1087-13.6166-18.788310.5911
131.8241-0.69330.74843.9833-0.67858.61570.12040.16510.0868-0.0611-0.2193-0.2111-0.3140.42030.09890.07890.0067-0.01150.0795-0.01960.1232-10.9791-35.466310.0364
141.296-1.2558-1.28873.70460.85851.3919-0.04610.0871-0.1883-0.2457-0.08110.29640.1666-0.10090.12720.1665-0.0019-0.04710.05910.01450.1029-17.5266-32.942512.57
151.4415-1.5281-0.84126.36952.77529.0152-0.1126-0.1651-0.0910.04850.2478-0.54180.21760.3675-0.13520.1420.03260.00420.04160.0020.1668-2.9203-36.556617.0709
161.0028-1.114-0.27982.74840.12051.1267-0.02940.0517-0.225-0.1006-0.02550.34070.0591-0.21880.05490.1247-0.0195-0.02510.06280.0120.0825-20.1779-28.515315.366
176.0336-2.25510.30933.4635-1.154111.9849-0.06470.03250.1137-0.22220.00820.6769-0.129-1.31890.05650.07460.0324-0.03950.1602-0.00610.2742-30.9417-5.919618.248
182.65650.46450.55483.9817-0.15871.8663-0.0259-0.07090.2029-0.03290.03680.2063-0.1857-0.1594-0.01090.07450.01450.00680.04870.02410.052-22.8389-3.167820.3064
1919.0345-5.9062-6.75462.96373.65265.28120.02870.13850.5292-0.1802-0.0467-0.2674-0.18980.00120.0180.197-0.02650.00190.02250.04330.1927-14.1864-8.58399.3224
200.16141.5912-0.301816.2923-2.99390.5674-0.0517-0.030.01630.25950.1296-0.01460.05310.0298-0.07790.77110.2544-0.14780.7491-0.07940.6796-2.9839-17.698614.598
211.4603-0.10860.75834.52980.81932.16430.00520.01170.05790.13090.0536-0.4694-0.26070.2566-0.05880.09-0.0219-0.01880.06790.02480.1058-9.1733-1.857924.2817
2212.6789-10.2174-2.10488.3788-0.08525.2125-0.5319-0.42140.64250.53180.3826-0.4726-0.3682-0.88710.14930.3956-0.07180.08810.1287-0.16180.3496-17.8937.11727.2252
230.8313-0.4369-1.42715.7483-11.075211.471-0.1541-0.32360.14050.69890.55350.0569-0.2820.3031-0.39950.35910.10520.05410.6034-0.12110.3689-29.7705-11.894535.8602
2421.0474-2.8793-3.52121.1008-2.237411.2533-1.006-1.3276-0.04050.23950.5537-0.0890.0957-1.06580.45230.51790.19190.04960.29380.03690.2351-15.748-24.237535.0671
258.24340.92921.279813.67938.80075.74450.36160.76780.1523-1.64020.0572-0.8066-0.99730.122-0.41890.2954-0.00910.11630.23660.1330.2870.1809-17.574433.019
261.6521-0.0853.88090.0751-0.7713.80120.0738-0.1143-0.1695-0.0204-0.0242-0.03590.21920.0281-0.04960.0972-0.0198-0.0010.06060.02470.0968-4.9553-16.845339.3405
275.69955.81250.80386.3676-1.46912.0995-0.22130.0335-0.2712-0.22680.1577-0.2890.0807-0.59830.06360.12690.06270.03720.07330.02210.148-17.5372-19.575625.3952
281.353-2.9783-6.08716.566813.394227.3906-0.36140.0618-0.07320.92890.01050.15851.8393-0.33340.3510.40410.13010.250.92420.02910.5922-28.9344-21.625238.4681
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 11
2X-RAY DIFFRACTION2A12 - 29
3X-RAY DIFFRACTION3A30 - 37
4X-RAY DIFFRACTION4A38 - 62
5X-RAY DIFFRACTION5A63 - 88
6X-RAY DIFFRACTION6A89 - 111
7X-RAY DIFFRACTION7A112 - 135
8X-RAY DIFFRACTION8A136 - 159
9X-RAY DIFFRACTION9A160 - 215
10X-RAY DIFFRACTION10A216 - 239
11X-RAY DIFFRACTION11A240 - 271
12X-RAY DIFFRACTION12B1 - 11
13X-RAY DIFFRACTION13B12 - 31
14X-RAY DIFFRACTION14B32 - 83
15X-RAY DIFFRACTION15B84 - 97
16X-RAY DIFFRACTION16B98 - 136
17X-RAY DIFFRACTION17B137 - 159
18X-RAY DIFFRACTION18B160 - 203
19X-RAY DIFFRACTION19B204 - 217
20X-RAY DIFFRACTION20B218 - 229
21X-RAY DIFFRACTION21B230 - 266
22X-RAY DIFFRACTION22B267 - 271
23X-RAY DIFFRACTION23C1 - 4
24X-RAY DIFFRACTION24C5 - 10
25X-RAY DIFFRACTION25C11 - 14
26X-RAY DIFFRACTION26D1 - 6
27X-RAY DIFFRACTION27D7 - 10
28X-RAY DIFFRACTION28D11 - 14

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External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

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Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

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