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- PDB-4uob: Crystal structure of Deinococcus radiodurans Endonuclease III-3 -

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Basic information

Entry
Database: PDB / ID: 4uob
TitleCrystal structure of Deinococcus radiodurans Endonuclease III-3
ComponentsENDONUCLEASE III-3
KeywordsLYASE / ENDONUCLEASE III / FES CLUSTER / BASE EXCISION REPAIR / DNA GLYCOSYLASE / DEINOCOCCUS RADIODURANS
Function / homology
Function and homology information


base-excision repair / 4 iron, 4 sulfur cluster binding / endonuclease activity / metal ion binding
Similarity search - Function
Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / Endonuclease III; domain 1 ...Endonuclease III-like, iron-sulphur cluster loop motif / FES / Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal) / Endonuclease Iii, domain 2 / Hypothetical protein; domain 2 / HhH-GPD superfamily base excision DNA repair protein / Helix-hairpin-helix, base-excision DNA repair, C-terminal / HhH-GPD domain / endonuclease III / Endonuclease III; domain 1 / DNA glycosylase / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / : / IRON/SULFUR CLUSTER / Endonuclease III, putative
Similarity search - Component
Biological speciesDEINOCOCCUS RADIODURANS (radioresistant)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.31 Å
AuthorsSarre, A. / Okvist, M. / Klar, T. / Hall, D. / Smalas, A.O. / McSweeney, S. / Timmins, J. / Moe, E.
CitationJournal: J.Struct.Biol. / Year: 2015
Title: Structural and Functional Characterization of Two Unusual Endonuclease III Enzymes from Deinococcus Radiodurans.
Authors: Sarre, A. / Okvist, M. / Klar, T. / Hall, D.R. / Smalas, A.O. / Mcsweeney, S. / Timmins, J. / Moe, E.
History
DepositionJun 2, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 10, 2015Provider: repository / Type: Initial release
Revision 1.1Jul 29, 2015Group: Database references
Revision 1.2Aug 12, 2015Group: Database references
Revision 1.3May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _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.ptnr1_symmetry / _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.ptnr2_symmetry / _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: ENDONUCLEASE III-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,3209
Polymers31,4811
Non-polymers8398
Water7,963442
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)91.240, 40.510, 72.150
Angle α, β, γ (deg.)90.00, 102.34, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-2124-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein ENDONUCLEASE III-3


Mass: 31480.668 Da / Num. of mol.: 1 / Fragment: RESIDUES 76-338
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) DEINOCOCCUS RADIODURANS (radioresistant)
Strain: R1 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): PLYSS
References: UniProt: Q9RVU4, DNA-(apurinic or apyrimidinic site) lyase

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Non-polymers , 5 types, 450 molecules

#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-CO / COBALT (II) ION


Mass: 58.933 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Co
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H3O2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 442 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence detailsOUR CLONE IS N-TERMINALLY TRUNCATED - WE DELETED THE FIRST 75 AMINO ACIDS AND ADDED AN N-TERMINAL ...OUR CLONE IS N-TERMINALLY TRUNCATED - WE DELETED THE FIRST 75 AMINO ACIDS AND ADDED AN N-TERMINAL HIS-TAG AND TEV CLEAVAGE SITE.

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

CrystalDensity Matthews: 2.07 Å3/Da / Density % sol: 44.5 % / Description: NONE
Crystal growpH: 6.5
Details: 0.1M MES PH6.5, 1.4M AMMONIUM SULPHATE AND 0.01M COBALT (II) CHLORIDE HEXAHYDRATE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.07812, 1.735
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.078121
21.7351
ReflectionResolution: 1.31→50 Å / Num. obs: 61009 / % possible obs: 98.2 % / Observed criterion σ(I): 2 / Redundancy: 6.8 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 17.4
Reflection shellResolution: 1.31→1.34 Å / Redundancy: 1.87 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.1 / % possible all: 90.2

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE: 1.9_1692)refinement
XDSdata reduction
XSCALEdata scaling
Auto-Rickshawphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 1.31→41.932 Å / SU ML: 0.11 / σ(F): 1.99 / Phase error: 14.7 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1593 3081 5.1 %
Rwork0.1335 --
obs0.1348 60998 98.18 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.31→41.932 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1915 0 35 442 2392
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012071
X-RAY DIFFRACTIONf_angle_d1.2572835
X-RAY DIFFRACTIONf_dihedral_angle_d14.268789
X-RAY DIFFRACTIONf_chiral_restr0.069290
X-RAY DIFFRACTIONf_plane_restr0.007377
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.31-1.33050.27051140.23082283X-RAY DIFFRACTION87
1.3305-1.35230.25031490.20272594X-RAY DIFFRACTION96
1.3523-1.37560.19561100.1832575X-RAY DIFFRACTION97
1.3756-1.40060.20611580.15452623X-RAY DIFFRACTION98
1.4006-1.42760.19881440.15232660X-RAY DIFFRACTION99
1.4276-1.45670.18561310.14272591X-RAY DIFFRACTION99
1.4567-1.48840.21261420.142638X-RAY DIFFRACTION99
1.4884-1.5230.14411410.11922642X-RAY DIFFRACTION99
1.523-1.56110.14641460.11532680X-RAY DIFFRACTION99
1.5611-1.60330.15241440.1122603X-RAY DIFFRACTION99
1.6033-1.65050.14991410.1132664X-RAY DIFFRACTION99
1.6505-1.70380.12981450.11062640X-RAY DIFFRACTION100
1.7038-1.76470.14571570.11482690X-RAY DIFFRACTION100
1.7647-1.83530.15471390.12112644X-RAY DIFFRACTION100
1.8353-1.91880.1961410.17382605X-RAY DIFFRACTION96
1.9188-2.020.16471340.14352625X-RAY DIFFRACTION98
2.02-2.14660.13971430.12482663X-RAY DIFFRACTION100
2.1466-2.31230.18551260.1522570X-RAY DIFFRACTION95
2.3123-2.54490.15191460.12872693X-RAY DIFFRACTION100
2.5449-2.91310.15231470.13422717X-RAY DIFFRACTION100
2.9131-3.66990.15291420.12782708X-RAY DIFFRACTION100
3.6699-41.95330.14061410.12222809X-RAY DIFFRACTION100

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