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

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Basic information

Entry
Database: PDB / ID: 2xzu
TitleCRYSTAL STRUCTURE OF A COMPLEX BETWEEN THE WILD-TYPE LACTOCOCCUS LACTIS FPG (MUTM) AND AN OXIDIZED PYRIMIDINE CONTAINING DNA AT 310K
Components
  • 5'-D(*CP*TP*CP*TP*TP*TP*VETP*TP*TP*TP*CP*TP*CP*G)-3'
  • 5'-D(GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*G*A)-3'
  • FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE
KeywordsHYDROLASE/DNA / HYDROLASE-DNA COMPLEX / LYASE
Function / homology
Function and homology information


DNA-formamidopyrimidine glycosylase / 8-oxo-7,8-dihydroguanine 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. / Formamidopyrimidine-DNA glycosylase H2TH domain / MutM-like, N-terminal / 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. / Formamidopyrimidine-DNA glycosylase H2TH domain / MutM-like, N-terminal / 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 (lactic acid bacteria)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.82 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 29, 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 / 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 / _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
Revision 1.2Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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*G)-3'
C: 5'-D(GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*G*A)-3'
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8105
Polymers39,6533
Non-polymers1582
Water8,791488
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4150 Å2
ΔGint-18.4 kcal/mol
Surface area15820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.739, 91.739, 143.236
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-2081-

HOH

21A-2129-

HOH

31A-2279-

HOH

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Components

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Protein , 1 types, 1 molecules A

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


Mass: 31116.217 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CHAIN A RESIDUE P 1 COVALENTLY LINKED TO CHAIN B RESIDUE VET 7
Source: (gene. exp.) LACTOCOCCUS LACTIS (lactic acid bacteria)
Strain: SUBSP CREMORIS / Plasmid: PFLAG / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P42371, DNA-formamidopyrimidine glycosylase, DNA-(apurinic or apyrimidinic site) lyase

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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*G)-3'


Mass: 4180.727 Da / Num. of mol.: 1 / Source method: obtained synthetically
Details: CHAIN B RESIDUE VET 7 COVALENTLY LINKED TO CHAIN A RESIDUE P 1
Source: (synth.) SYNTHETIC CONSTRUCT (others)
#3: DNA chain 5'-D(GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*G*A)-3'


Mass: 4355.884 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others)

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Non-polymers , 3 types, 490 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


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


Mass: 18.015 Da / Num. of mol.: 488 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY
Nonpolymer details(5-METHYLHYDANTOIN-2-HYDROXYCYCLOPENTYL)METHYL 5'-PHOSPHATE (VET): VET IS COVALENTLY ATTACHED TO ...(5-METHYLHYDANTOIN-2-HYDROXYCYCLOPENTYL)METHYL 5'-PHOSPHATE (VET): VET IS COVALENTLY ATTACHED TO THE CATALYTIC N-TERMINAL PROLINE OF FPG.

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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: 1.82→48.06 Å / Num. obs: 55526 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 22.49 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.4
Reflection shellResolution: 1.82→1.92 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.1 / % possible all: 99.9

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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: 1.82→48.079 Å / SU ML: 0.2 / σ(F): 1.35 / Phase error: 16.57 / Stereochemistry target values: ML / Details: RESIDUES A 219 TO A 223 ARE DISORDERED.
RfactorNum. reflection% reflection
Rfree0.1887 2814 5.1 %
Rwork0.157 --
obs0.1587 55438 99.93 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 46.162 Å2 / ksol: 0.363 e/Å3
Displacement parametersBiso mean: 27.296 Å2
Baniso -1Baniso -2Baniso -3
1-1.8066 Å20 Å20 Å2
2--1.8066 Å20 Å2
3----3.6132 Å2
Refinement stepCycle: LAST / Resolution: 1.82→48.079 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 565 7 488 3187
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0222843
X-RAY DIFFRACTIONf_angle_d2.1083949
X-RAY DIFFRACTIONf_dihedral_angle_d18.7541140
X-RAY DIFFRACTIONf_chiral_restr0.155444
X-RAY DIFFRACTIONf_plane_restr0.011404
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.82-1.88510.28372700.25745180X-RAY DIFFRACTION100
1.8851-1.96060.25432830.19925172X-RAY DIFFRACTION100
1.9606-2.04980.222810.17715193X-RAY DIFFRACTION100
2.0498-2.15780.19762910.16385162X-RAY DIFFRACTION100
2.1578-2.2930.17662630.155243X-RAY DIFFRACTION100
2.293-2.47010.20082810.15015227X-RAY DIFFRACTION100
2.4701-2.71860.18642990.16085219X-RAY DIFFRACTION100
2.7186-3.1120.21032640.17315298X-RAY DIFFRACTION100
3.112-3.92050.17912860.14675335X-RAY DIFFRACTION100
3.9205-48.09560.15322960.13365595X-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)
10.43520.2290.50411.04250.27911.1946-0.00910.1154-0.04980.04520.0691-0.03850.0450.113-0.05610.08390.0081-0.00420.1489-0.00060.14639.62044.9722-24.1426
20.17930.19140.26951.01920.12371.32470.03360.0769-0.17040.0830.0497-0.33390.0570.393-0.09120.10770.0416-0.02350.2226-0.02440.253218.64061.8087-21.9156
30.24680.6136-0.08051.3608-0.25990.5941-0.0097-0.0008-0.05980.04920.0129-0.20660.05990.12470.01970.09770.0409-0.01650.17160.00190.128311.3847.6237-17.1605
40.1919-0.0274-0.27981.8711.27151.16630.00350.0898-0.0529-0.3236-0.03680.1661-0.2762-0.15380.04920.19880.0065-0.03770.1932-0.00950.14725.81925.0139-34.8456
50.7382-0.19-0.37910.92930.11870.48490.0014-0.0196-0.0988-0.01750.039-0.0280.070.0806-0.03250.0969-0.011-0.02120.15120.00350.136910.8819.6828-19.8347
60.3843-0.7903-0.02834.2132-0.22740.3115-0.1772-0.12510.03330.68260.1131-0.23830.07770.15990.01220.20710.0579-0.00740.19210.01060.1614-2.135818.27933.8699
71.0793-0.6148-0.7280.8255-0.32291.78890.04130.09980.07980.0803-0.07390.0341-0.1847-0.18680.02260.11130.02140.00980.1220.00530.1456-5.635921.3854-9.3661
82.7149-2.26060.36221.9063-0.25864.1698-0.1441-0.07050.45340.18650.07830.2483-0.5955-0.58470.01660.18330.09540.01650.15840.01740.1499-11.125428.7458-4.1449
91.4105-1.0574-0.50271.70140.1440.257-0.0973-0.0839-0.21650.32970.06440.14160.1941-0.3069-0.01110.13050.03150.03390.22220.01560.1523-10.957517.37220.4188
102.747-0.8237-0.50630.57130.5060.853-0.15960.3631-0.5981-0.2525-0.18410.28780.2845-0.33760.27270.12060.00040.01590.2064-0.02430.2198-8.0976.4665-15.4614
110.6412-0.93020.16353.99631.1070.8234-0.13870.6725-0.2336-0.69090.07890.5970.02330.45440.04020.1570.0048-0.01320.5017-0.14620.2579-12.2617.6846-21.9567
120.7582-0.5607-0.26111.01190.60172.14180.23480.29970.0231-0.1831-0.27660.1288-0.3207-0.60480.00690.10890.1184-0.01450.2795-0.00020.1575-17.418824.8709-16.1645
133.7221.1031-1.22316.0578-3.60582.26830.08260.21930.2910.8764-0.06680.3426-0.90880.44050.12450.33120.0181-0.04950.35880.10150.2886-3.447834.2353-34.7433
141.7851-0.51311.15771.0156-0.39492.29760.0146-0.10620.1271-0.00220.0585-0.2219-0.3409-0.1266-0.09830.15090.0224-0.00320.1629-0.00310.17722.031822.0481-20.2486
155.66151.2122-1.49296.66851.69684.51740.52340.27520.0025-0.3042-0.3708-2.2826-0.84650.2416-0.19290.3594-0.11690.02730.2576-0.01420.487812.17536.5804-15.1717
161.0704-0.60940.85342.755-2.23715.9920.3762-0.1266-0.69340.11030.00570.09790.221-0.664-0.35810.3835-0.0222-0.11780.2282-0.02580.25544.964435.4116-12.4146
171.5109-1.8028-2.19622.92323.07333.42640.40960.19390.2471-0.57950.1759-0.4606-1.5605-0.3731-0.5240.38880.00220.0730.19350.01980.22727.740726.5454-28.8611
180.7889-1.6038-1.90188.46243.29085.0678-0.1591.1543-0.7652-0.4846-0.27661.7030.4893-0.54060.15540.22980.0584-0.15790.41420.02870.4627-5.922125.7716-36.9365
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(CHAIN A AND RESID 1:37)
2X-RAY DIFFRACTION2(CHAIN A AND RESID 38:54)
3X-RAY DIFFRACTION3(CHAIN A AND RESID 55:75)
4X-RAY DIFFRACTION4(CHAIN A AND RESID 76:90)
5X-RAY DIFFRACTION5(CHAIN A AND RESID 91:137)
6X-RAY DIFFRACTION6(CHAIN A AND RESID 138:151)
7X-RAY DIFFRACTION7(CHAIN A AND RESID 152:181)
8X-RAY DIFFRACTION8(CHAIN A AND RESID 182:191)
9X-RAY DIFFRACTION9(CHAIN A AND RESID 192:205)
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 15:20)
17X-RAY DIFFRACTION17(CHAIN C AND RESID 21:24)
18X-RAY DIFFRACTION18(CHAIN C AND RESID 25:28)

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