[English] 日本語
Yorodumi
- PDB-6rp7: The crystal structure of a complex between the LlFpg protein, a T... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 6rp7
TitleThe crystal structure of a complex between the LlFpg protein, a THF-DNA and an inhibitor
Components
  • DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3')
  • DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')
  • Formamidopyrimidine-DNA glycosylase
KeywordsHYDROLASE / DNA glycosylase complex / inhibitor
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 / 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
6,7-dimethyl-2-sulfanylidene-1~{H}-pteridin-4-one / DNA / DNA (> 10) / Formamidopyrimidine-DNA glycosylase / Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesLactococcus lactis subsp. cremoris (lactic acid bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsCoste, F. / Goffinont, S. / Castaing, B.
CitationJournal: Int J Mol Sci / Year: 2020
Title: Thiopurine Derivative-Induced Fpg/Nei DNA Glycosylase Inhibition: Structural, Dynamic and Functional Insights.
Authors: Rieux, C. / Goffinont, S. / Coste, F. / Tber, Z. / Cros, J. / Roy, V. / Guerin, M. / Gaudon, V. / Bourg, S. / Biela, A. / Aucagne, V. / Agrofoglio, L. / Garnier, N. / Castaing, B.
History
DepositionMay 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 15, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id
Revision 1.2Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Formamidopyrimidine-DNA glycosylase
D: DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3')
E: DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8275
Polymers39,5273
Non-polymers3002
Water3,189177
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-21 kcal/mol
Surface area15630 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.669, 91.669, 141.043
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

-
Components

-
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
Source: (gene. exp.) Lactococcus lactis subsp. cremoris (lactic acid bacteria)
Gene: mutM, fpg, NCDO763_0992 / Production host: Escherichia coli (E. coli)
References: UniProt: A0A165FVI1, UniProt: P42371*PLUS, DNA-formamidopyrimidine glycosylase, DNA-(apurinic or apyrimidinic site) lyase

-
DNA chain , 2 types, 2 molecules DE

#2: DNA chain DNA (5'-D(*CP*TP*CP*TP*TP*TP*(3DR)P*TP*TP*TP*CP*TP*CP*G)-3')


Mass: 4054.614 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#3: DNA chain DNA (5'-D(*GP*CP*GP*AP*GP*AP*AP*AP*CP*AP*AP*AP*GP*A)-3')


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

-
Non-polymers , 3 types, 179 molecules

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


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Chemical ChemComp-KD8 / 6,7-dimethyl-2-sulfanylidene-1~{H}-pteridin-4-one


Mass: 208.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8N4OS / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 177 / Source method: isolated from a natural source / Formula: H2O

-
Details

Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 3.8 Å3/Da / Density % sol: 67.63 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: HEPES, CITRATE

-
Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.97857 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97857 Å / Relative weight: 1
ReflectionResolution: 2→47.72 Å / Num. obs: 41266 / % possible obs: 99.8 % / Redundancy: 5.8 % / CC1/2: 0.998 / Rmerge(I) obs: 0.064 / Net I/σ(I): 13.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.8 % / Num. unique obs: 5925 / % possible all: 99.9

-
Phasing

PhasingMethod: molecular replacement

-
Processing

Software
NameVersionClassificationNB
XDSdata reduction
SCALAdata scaling
PHASERphasing
PHENIX1.14_3260refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1PM5

1pm5


Resolution: 2→45.834 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 0.12 / Phase error: 19.45 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1855 3827 4.94 %
Rwork0.1658 73639 -
obs0.1668 77466 99.84 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 131.43 Å2 / Biso mean: 52.5569 Å2 / Biso min: 29.43 Å2
Refinement stepCycle: final / Resolution: 2→45.834 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2105 557 20 177 2859
Biso mean--51.76 53.72 -
Num. residues----295
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 27

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2-2.02530.28631490.300727362885100
2.0253-2.0520.30721580.288327252883100
2.052-2.08010.29541370.274827202857100
2.0801-2.10980.27351280.263227232851100
2.1098-2.14130.24211540.240327362890100
2.1413-2.17470.27461440.231427402884100
2.1747-2.21040.21561290.215527232852100
2.2104-2.24850.21481570.198827372894100
2.2485-2.28940.23381490.194927022851100
2.2894-2.33340.22451710.195626982869100
2.3334-2.38110.18831570.178126972854100
2.3811-2.43280.20981470.165327612908100
2.4328-2.48940.17661570.176627262883100
2.4894-2.55170.20461250.181327322857100
2.5517-2.62070.25751350.198227542889100
2.6207-2.69780.2431630.212927162879100
2.6978-2.78480.22351170.203927372854100
2.7848-2.88430.28881310.201727362867100
2.8843-2.99980.23261630.202327142877100
2.9998-3.13630.2151190.188627312850100
3.1363-3.30160.16461400.17427582898100
3.3016-3.50840.20111330.149427232856100
3.5084-3.77920.18581140.143427352849100
3.7792-4.15930.13521640.13592697286199
4.1593-4.76060.12931490.116527202869100
4.7606-5.99570.15681170.13082733285099
5.9957-45.84650.13741200.15512729284999
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)
14.06730.25791.45993.271-0.68692.9279-0.1934-0.23650.2702-0.31640.15840.6984-0.2479-0.89540.06310.47290.0212-0.04770.497-0.02410.4752-30.79043.347211.479
28.15154.4227-5.90198.1927-2.58984.4302-0.43420.29690.5194-0.09290.24280.06421.1135-0.98750.31890.48160.1416-0.0130.8601-0.09840.5251-33.63076.020619.3993
33.6855.48040.92959.69822.88832.5227-0.00550.4896-1.0171-1.11660.12820.08540.7055-0.6145-0.13140.708-0.0684-0.15880.5553-0.10150.5972-25.1976-1.8942-0.2161
48.61131.3023-2.03382.80650.14563.69790.1271-0.209-0.63820.006-0.14-0.36850.25490.14320.03620.38180.04130.00350.32220.07760.5199-3.33090.511416.5139
53.21710.4624-0.76162.6615-0.84622.51240.2132-0.13650.28760.0239-0.201-0.2887-0.35630.22430.00250.4343-0.01780.0240.2741-0.02170.3651-4.398415.840413.7876
65.5850.2691-4.76621.7943-1.50348.5458-0.07640.7357-0.1662-0.27180.0845-0.08860.3601-0.3568-0.02360.40640.0201-0.00080.3244-0.05330.3693-7.54285.55462.7691
71.37960.479-0.47251.3709-0.42912.2160.153-0.1326-0.05660.1165-0.1273-0.167-0.20260.0932-0.02430.36770.0094-0.00020.2992-0.02160.3702-9.51449.90617.6741
82.62520.5138-0.80923.55551.19478.03630.0942-0.2462-0.15670.2318-0.23030.12040.389-0.58350.14890.3336-0.0914-0.02510.34720.02420.3873-23.0465-6.094330.546
95.35744.0153-4.85185.0297-3.58244.6087-0.1247-0.9566-0.50440.2982-0.3436-0.58030.48871.09390.40810.4824-0.0074-0.06960.35940.09570.4999-12.4918-10.314330.7261
106.50996.22371.31748.50861.5240.2813-0.51950.4211-1.143-0.74710.3358-1.09160.65010.15050.2210.73440.02070.09240.462-0.05920.7082-9.6279-10.942513.2261
116.9126-4.3753-5.33512.91613.53364.2725-0.5956-0.4916-1.6754-0.51840.20110.95510.9971-0.15270.30190.6534-0.13270.0510.4698-0.00380.6801-25.4566-19.977916.868
124.59381.6435-1.515.2343-4.4534.03360.14150.05-0.6290.644-0.48520.0070.07960.07870.27090.5824-0.15290.01240.4506-0.05390.545-27.4726-14.56922.5884
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1chain 'D' and (resid 1 through 14 )D1 - 14
2X-RAY DIFFRACTION2chain 'E' and (resid 15 through 22 )E15 - 22
3X-RAY DIFFRACTION3chain 'E' and (resid 23 through 28 )E23 - 28
4X-RAY DIFFRACTION4chain 'A' and (resid 1 through 16 )A1 - 16
5X-RAY DIFFRACTION5chain 'A' and (resid 17 through 72 )A17 - 72
6X-RAY DIFFRACTION6chain 'A' and (resid 73 through 91 )A73 - 91
7X-RAY DIFFRACTION7chain 'A' and (resid 92 through 141 )A92 - 141
8X-RAY DIFFRACTION8chain 'A' and (resid 142 through 193 )A142 - 193
9X-RAY DIFFRACTION9chain 'A' and (resid 194 through 213 )A194 - 213
10X-RAY DIFFRACTION10chain 'A' and (resid 214 through 239 )A214 - 239
11X-RAY DIFFRACTION11chain 'A' and (resid 240 through 257 )A240 - 257
12X-RAY DIFFRACTION12chain 'A' and (resid 258 through 271 )A258 - 271

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

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

-
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

Read more