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- PDB-1ee8: CRYSTAL STRUCTURE OF MUTM (FPG) PROTEIN FROM THERMUS THERMOPHILUS HB8 -

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Basic information

Entry
Database: PDB / ID: 1ee8
TitleCRYSTAL STRUCTURE OF MUTM (FPG) PROTEIN FROM THERMUS THERMOPHILUS HB8
ComponentsMUTM (FPG) PROTEIN
KeywordsDNA BINDING PROTEIN / BETA SANDWICH / ZINC FINGER / HELIX TWO-TURNS HELIX / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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
Formamidopyrimidine-DNA glycosylase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.9 Å
AuthorsSugahara, M. / Mikawa, T. / Kumasaka, T. / Yamamoto, M. / Kato, R. / Fukuyama, K. / Inoue, Y. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
Citation
Journal: EMBO J. / Year: 2000
Title: Crystal structure of a repair enzyme of oxidatively damaged DNA, MutM (Fpg), from an extreme thermophile, Thermus thermophilus HB8.
Authors: Sugahara, M. / Mikawa, T. / Kumasaka, T. / Yamamoto, M. / Kato, R. / Fukuyama, K. / Inoue, Y. / Kuramitsu, S.
#1: Journal: Nucleic Acids Res. / Year: 1998
Title: Termostable Repair Enzyme for Oxidative DNA Damage from Extremely Thermophilic Bacterium, Thermus Thermophilus HB8
Authors: Mikawa, T. / Kato, R. / Sugahara, M. / Kuramitsu, S.
#2: Journal: J.BIOCHEM.(TOKYO) / Year: 2000
Title: Crystallization and Preliminary X-ray Crystallographic Studies of Thermus Thermophilus HB8 MutM Protein Involved in Repairs Oxidative DNA Damage
Authors: Sugahara, M. / Mikawa, T. / Kato, R. / Kumasaka, T. / Yamamoto, M. / Fukuyama, K. / Inoue, Y. / kuramitsu, S.
History
DepositionJan 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 31, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
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_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.pdbx_dist_value / _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_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_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: MUTM (FPG) PROTEIN
B: MUTM (FPG) PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,7974
Polymers59,6672
Non-polymers1312
Water5,260292
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)44.421, 61.289, 98.342
Angle α, β, γ (deg.)90.00, 91.71, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein MUTM (FPG) PROTEIN


Mass: 29833.305 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: PET3A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: O50606
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 292 / 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: 2.24 Å3/Da / Density % sol: 45.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9.8
Details: PEG MME 2000, 2-mercaptoethanol, CHES, pH 9.8, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Crystal grow
*PLUS
Details: Sugahara, M., (2000) J. Biochem., 127, 9.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL45XU / Wavelength: 1.5418
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 37892 / Num. obs: 37892 / % possible obs: 0.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 25.65 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 29.1
Reflection shellResolution: 1.9→1.93 Å / Redundancy: 3.96 % / Rmerge(I) obs: 0.91 / Num. unique all: 1730 / % possible all: 0.821
Reflection
*PLUS
% possible obs: 90 % / Num. measured all: 402397 / Rmerge(I) obs: 0.07
Reflection shell
*PLUS
% possible obs: 82.1 % / Num. unique obs: 1729 / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 3.2

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Processing

Software
NameVersionClassification
SOLVEphasing
CNS0.9refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→50 Å / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2
RfactorNum. reflection% reflectionSelection details
Rfree0.258 3654 10 %RANDOM
Rwork0.214 ---
obs-36536 --
Refinement stepCycle: LAST / Resolution: 1.9→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4208 0 2 292 4502
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Highest resolution: 1.9 Å / Lowest resolution: 50 Å / σ(F): 2 / % reflection Rfree: 10 % / Rfactor obs: 0.214
Solvent computation
*PLUS
Displacement parameters
*PLUS
Biso mean: 30.82 Å2
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.35
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.37
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scangle_it

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