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- PDB-2xzf: CRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS ... -

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Basic information

Entry
Database: PDB / ID: 2xzf
TitleCRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND AN OXIDIZED PYRIMIDINE CONTAINING DNA AT 293K
Components
  • 5'-D(*CP*TP*CP*TP*TP*TP*VETP*TP*TP*TP*CP*TP*CP*GP)-3'
  • 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*GP*CP)-3'
  • FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASEDNA-formamidopyrimidine glycosylase
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX
Function / homology
Function and homology information


DNA-formamidopyrimidine glycosylase / oxidized purine nucleobase lesion DNA N-glycosylase activity / class I DNA-(apurinic or apyrimidinic site) endonuclease activity / DNA-(apurinic or apyrimidinic site) lyase / 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
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: 1.799 Å
AuthorsLeBihan, Y.V. / Izquierdo, M.A. / Coste, F. / Culard, F. / Gehrke, T.H. / Essalhi, K. / Aller, P. / Carrel, T. / Castaing, B.
CitationJournal: Nucleic Acids Res. / Year: 2011
Title: 5-Hydroxy-5-Methylhydantoin DNA Lesion, a Molecular Trap for DNA Glycosylases
Authors: Le Bihan, Y.V. / Izquierdo, M.A. / Coste, F. / Aller, P. / Culard, F. / Gehrke, T.H. / Essalhi, K. / Carrel, T. / Castaing, B.
History
DepositionNov 25, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 5, 2011Provider: repository / Type: Initial release
Revision 1.1Dec 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: FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE
B: 5'-D(*CP*TP*CP*TP*TP*TP*VETP*TP*TP*TP*CP*TP*CP*GP)-3'
C: 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*GP*CP)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8105
Polymers39,6533
Non-polymers1582
Water8,809489
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-20.1 kcal/mol
Surface area16000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.569, 91.569, 142.777
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11A-2073-

HOH

21A-2123-

HOH

31A-2280-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE / DNA-formamidopyrimidine glycosylase / FAPY-DNA GLYCOSYLASE


Mass: 31116.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) LACTOCOCCUS LACTIS SUBSP. CREMORIS (lactic acid bacteria)
Plasmid: PMAL-C / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P42371, DNA-formamidopyrimidine glycosylase

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DNA chain , 2 types, 2 molecules BC

#2: DNA chain 5'-D(*CP*TP*CP*TP*TP*TP*VETP*TP*TP*TP*CP*TP*CP*GP)-3'


Mass: 4180.727 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*AP*GP*CP)-3'


Mass: 4355.883 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 491 molecules

#4: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 489 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer details(5-HYDROXY-5-METHYLHYDANTOIN-2-HYDROXYCYCLOPENTYL)METHYL 5'-PHOSPHATE (VET): DNA LINKING

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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: 3.5 Å3/Da / Density % sol: 65 % / Description: NONE
Crystal growpH: 7.6 / Details: HEPES, SODIUM CITRATE, PH 7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97935
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 21, 2006 / Details: BENT CYLINDRICAL MIRROR
RadiationMonochromator: SINGLE CRYSTAL, SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97935 Å / Relative weight: 1
ReflectionResolution: 1.8→48 Å / Num. obs: 56390 / % possible obs: 99.1 % / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 22.61 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 25.3
Reflection shellResolution: 1.8→1.9 Å / Redundancy: 9 % / Rmerge(I) obs: 0.51 / Mean I/σ(I) obs: 4.5 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XC8

1xc8


Resolution: 1.799→47.96 Å / SU ML: 0.21 / σ(F): 1.37 / Phase error: 16.78 / Stereochemistry target values: ML / Details: RESIDUES 219-223 OF CHAIN A ARE DISORDERED
RfactorNum. reflection% reflection
Rfree0.1911 2858 5.1 %
Rwork0.1595 --
obs0.1611 56346 98.89 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 48.194 Å2 / ksol: 0.379 e/Å3
Displacement parametersBiso mean: 27.2 Å2
Baniso -1Baniso -2Baniso -3
1--0.0507 Å20 Å20 Å2
2---0.0507 Å20 Å2
3---0.1014 Å2
Refinement stepCycle: LAST / Resolution: 1.799→47.96 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2120 566 7 489 3182
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082817
X-RAY DIFFRACTIONf_angle_d1.2543913
X-RAY DIFFRACTIONf_dihedral_angle_d18.3891121
X-RAY DIFFRACTIONf_chiral_restr0.08440
X-RAY DIFFRACTIONf_plane_restr0.006399
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7992-1.86350.27572850.25085036X-RAY DIFFRACTION95
1.8635-1.93810.2132690.19355248X-RAY DIFFRACTION99
1.9381-2.02640.20332820.16155297X-RAY DIFFRACTION99
2.0264-2.13320.18552800.15875283X-RAY DIFFRACTION99
2.1332-2.26680.1722790.14965299X-RAY DIFFRACTION99
2.2668-2.44190.20873080.1575314X-RAY DIFFRACTION99
2.4419-2.68760.20122880.16975372X-RAY DIFFRACTION99
2.6876-3.07640.21912780.18195417X-RAY DIFFRACTION100
3.0764-3.87570.1932630.15185501X-RAY DIFFRACTION100
3.8757-47.97740.15783260.1385721X-RAY DIFFRACTION100
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)
10.2523-0.37030.30451.16410.22881.0529-0.05550.11990.1173-0.2206-0.09780.2632-0.0595-0.17390.09570.12140.0037-0.01780.14210.01070.1744-0.1585-4.7871-17.2313
20.41180.33610.01311.15750.1390.6019-0.0103-0.20090.19870.07170.1017-0.1721-0.16740.1905-0.09790.1265-0.00610.02010.2113-0.02770.183215.4064-4.9991-8.32
30.2888-0.2206-0.46591.19440.22511.14650.0091-0.03460.1835-0.13940.1013-0.3888-0.10790.3292-0.10840.1358-0.05540.02870.2014-0.02780.259918.6776-1.7687-13.8904
40.2852-0.66350.07281.2933-0.1040.4-0.04560.01740.058-0.12070.0282-0.1155-0.06520.09050.00620.1191-0.04380.0130.17540.00830.122511.3613-7.544-18.5893
50.1153-0.09780.22461.48130.5750.7767-0.0379-0.08030.0320.21930.06120.13350.0735-0.15740.00320.17750.00410.03530.1793-0.01040.15057.4535-5.9624-1.5833
61.1844-0.01260.09550.3826-0.09410.5340.00250.06820.1547-0.01730.0636-0.0823-0.0780.0289-0.05480.1218-0.01140.02950.1460.0010.136112.9356-8.7358-14.1437
70.99520.57710.1370.90420.29641.6103-0.25140.1033-0.0084-0.07590.1763-0.0196-0.24490.26640.06780.1708-0.0288-0.01870.18380.02830.14263.2706-11.8253-31.2479
80.975-0.0117-0.18955.99811.24660.4949-0.25010.3403-0.0522-0.58850.2876-0.62830.13570.294-0.08290.2089-0.05940.03960.2215-0.03520.1378-2.4574-21.0362-39.2356
90.93330.6705-0.1710.8043-0.0790.908-0.0790.0329-0.0914-0.07510.04110.04610.128-0.22550.03340.1058-0.0261-0.00230.1686-0.00770.1483-8.3292-21.4441-29.6752
100.90290.2961-0.04520.75630.90871.7122-0.1658-0.31530.52690.1398-0.11240.2581-0.3233-0.12690.24610.16560.0038-0.01680.2672-0.03430.2549-8.1244-6.4804-19.7482
110.57571.3210.95093.37441.73772.2535-0.0468-0.45450.49950.5089-0.06040.4852-0.14580.49680.05280.1826-0.01230.02150.464-0.14460.3197-12.2948-7.6066-13.773
120.81260.58930.39430.91430.26711.45710.2081-0.28870.01360.1678-0.23220.10770.2398-0.53460.05660.1123-0.0910.01760.2761-0.02130.1626-17.5586-24.7132-19.5674
131.84770.2741-1.553.6116-2.91776.7477-0.3315-0.1993-0.4629-0.4716-0.2430.3091.36840.99990.66250.40390.06160.12790.36380.14160.3033-3.6068-34.054-0.9014
140.95020.2993-0.92620.6958-0.28461.29-0.04460.0627-0.1742-0.02920.0446-0.19410.3507-0.0911-0.07060.1688-0.02070.01560.2150.01150.19241.6949-21.8035-15.3276
154.9119-0.85720.42219.67963.55337.93630.3150.0113-0.41170.2665-0.3417-1.80341.06220.1765-0.110.36790.0915-0.01010.3171-0.06510.44611.9566-36.4047-20.5713
167.56843.3774-4.93238.269-5.5294.92090.68570.8022-0.58181.0307-0.1815-0.0854-0.801-0.6586-0.37910.38650.03470.02130.3786-0.06960.23353.3646-35.3738-19.5274
170.4270.95891.6643.37334.87577.41640.395-0.0538-0.00840.63010.1742-0.4141.3791-0.3137-0.49140.3485-0.0167-0.0640.1850.0260.18247.6101-26.3962-6.8349
188.28396.4126-2.40235.0819-2.22741.32820.2772-0.85170.90030.4039-0.18661.37480.1425-0.052-0.16440.3667-0.1280.14230.40610.07740.5066-7.866-29.17872.4581
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:13)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 14:37)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 38:54)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 55:75)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 76:96)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 97:127)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 128:139)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 140:153)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 154:205)
10X-RAY DIFFRACTION10(CHAIN A AND RESID 206:225)
11X-RAY DIFFRACTION11(CHAIN A AND RESID 226:235)
12X-RAY DIFFRACTION12(CHAIN A AND RESID 236:271)
13X-RAY DIFFRACTION13(CHAIN B AND RESID 1:5)
14X-RAY DIFFRACTION14(CHAIN B AND RESID 6:10)
15X-RAY DIFFRACTION15(CHAIN B AND RESID 11:14)
16X-RAY DIFFRACTION16(CHAIN C AND RESID 15:18)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 19:22)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 23:28)

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