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- PDB-1vk2: Crystal structure of Uracil-DNA glycosylase (TM0511) from Thermot... -

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Basic information

Entry
Database: PDB / ID: 1vk2
TitleCrystal structure of Uracil-DNA glycosylase (TM0511) from Thermotoga maritima at 1.90 A resolution
ComponentsUracil-DNA glycosylase TM0511
KeywordsHYDROLASE / TM0511 / URACIL-DNA GLYCOSYLASE / STRUCTURAL GENOMICS / JCSG / PSI / Protein Structure Initiative / Joint Center for Structural Genomics
Function / homology
Function and homology information


uracil-DNA glycosylase / uracil DNA N-glycosylase activity / 4 iron, 4 sulfur cluster binding / DNA repair / metal ion binding
Similarity search - Function
Uracil-DNA glycosylase family 4 / : / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
IRON/SULFUR CLUSTER / Unknown ligand / Type-4 uracil-DNA glycosylase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.9 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: To be published
Title: Crystal structure of Uracil-DNA glycosylase (TM0511) from Thermotoga maritima at 1.90 A resolution
Authors: Joint Center for Structural Genomics (JCSG)
History
DepositionApr 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 4, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_conn_type / struct_ref_seq_dif / 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_atom_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_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_conn_type.id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 600HETEROGEN AN UNIDENTIFIED ENTITY AT THE ACTIVE SITE IS MODELED AS A UNL, UNKNOWN LIGAND, RESIDUE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Uracil-DNA glycosylase TM0511
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,4873
Polymers23,1351
Non-polymers3522
Water2,054114
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.049, 61.049, 127.500
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Uracil-DNA glycosylase TM0511


Mass: 23135.275 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Gene: TM0511 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9WYY1, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds
#2: Chemical ChemComp-SF4 / IRON/SULFUR CLUSTER


Mass: 351.640 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Fe4S4
#3: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 114 / 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: 2.65 Å3/Da / Density % sol: 53.13 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 8.5
Details: TRIS pH 8.5, 8% PEG-8000, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K. cryo condition: 25% PEG-200.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.2.1 / Wavelength: 1.0000, 0.9796, 0.9794
DetectorType: ADSC / Detector: CCD / Date: Mar 3, 2004
RadiationMonochromator: Double Crystal Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.97961
30.97941
ReflectionResolution: 1.9→50 Å / Num. obs: 19816 / % possible obs: 99.97 % / Redundancy: 7.87 % / Biso Wilson estimate: 37.82 Å2 / Rsym value: 0.068 / Net I/σ(I): 25.15
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 6.13 % / Mean I/σ(I) obs: 2.03 / Num. unique all: 1938 / Rsym value: 0.841 / % possible all: 99.95

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
autoSHARPphasing
REFMAC5.1.24refinement
RefinementMethod to determine structure: MAD / Resolution: 1.9→44.09 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.958 / SU B: 2.88 / SU ML: 0.081 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.124 / ESU R Free: 0.117
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS AN FE4S4 LIGAND IS COVALENTLY BOUND TO CYS18A, CYS21A, CYS89A and CYS105A OF THE PROTEIN. AN UNIDENTIFIED ENTITY AT THE ACTIVE SITE IS MODELED AS UNL RESIDUE.
RfactorNum. reflection% reflectionSelection details
Rfree0.20573 1013 5.1 %RANDOM
Rwork0.17743 ---
obs0.17886 18702 99.96 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.426 Å2
Baniso -1Baniso -2Baniso -3
1-1.31 Å20 Å20 Å2
2--1.31 Å20 Å2
3----2.62 Å2
Refinement stepCycle: LAST / Resolution: 1.9→44.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1479 0 11 114 1604
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0211516
X-RAY DIFFRACTIONr_bond_other_d0.0020.021427
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.9832061
X-RAY DIFFRACTIONr_angle_other_deg0.86733303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6935189
X-RAY DIFFRACTIONr_chiral_restr0.0910.2235
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021667
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02300
X-RAY DIFFRACTIONr_nbd_refined0.2080.2318
X-RAY DIFFRACTIONr_nbd_other0.2390.21682
X-RAY DIFFRACTIONr_nbtor_other0.0840.2924
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1460.282
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0440.22
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3530.231
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0950.24
X-RAY DIFFRACTIONr_mcbond_it2.0393946
X-RAY DIFFRACTIONr_mcangle_it3.69151539
X-RAY DIFFRACTIONr_scbond_it6.4198570
X-RAY DIFFRACTIONr_scangle_it9.48311510
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 72 5.12 %
Rwork0.258 1334 -
Refinement TLS params.Method: refined / Origin x: 52.708 Å / Origin y: 21.5221 Å / Origin z: 73.6181 Å
111213212223313233
T0.0066 Å2-0.0035 Å20.0035 Å2-0.0575 Å2-0.0075 Å2--0.0393 Å2
L1.7978 °2-0.3729 °2-0.9715 °2-1.7406 °20.0869 °2--2.3389 °2
S0.1389 Å °0.1117 Å °-0.0024 Å °-0.061 Å °-0.097 Å °0.1638 Å °-0.1049 Å °-0.142 Å °-0.0419 Å °
Refinement TLS groupSelection: ALL

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