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- PDB-3cxm: Leishmania naiffi uracil-DNA glycosylase in complex with 5-bromouracil -

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Basic information

Entry
Database: PDB / ID: 3cxm
TitleLeishmania naiffi uracil-DNA glycosylase in complex with 5-bromouracil
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / base excision repair / BER / DNA damage repair / Leishmania / MSGPP / SGPP / glycosylase / 5-bromouracil / Structural Genomics / Structural Genomics of Pathogenic Protozoa Consortium / DNA repair / Glycosidase / PSI-2 / Protein Structure Initiative
Function / homology
Function and homology information


base-excision repair, AP site formation via deaminated base removal / uracil-DNA glycosylase / uracil DNA N-glycosylase activity / mitochondrion / nucleus
Similarity search - Function
Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like / Uracil DNA glycosylase superfamily / Uracil-DNA glycosylase-like domain superfamily ...Uracil-DNA glycosylase family 1 / Uracil DNA glycosylase superfamily / UreE urease accessory protein, C-terminal domain / Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / 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
BROMIDE ION / URACIL / 5-bromopyrimidine-2,4(1H,3H)-dione / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesLeishmania naiffi (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.5 Å
AuthorsLarson, E.T. / Merritt, E.A. / Structural Genomics of Pathogenic Protozoa Consortium (SGPP)
CitationJournal: To be Published
Title: Structures of Leishmania naiffi uracil-DNA glycosylase in complex with several ligands identified with fragment cocktail crystallography.
Authors: Larson, E.T. / Merritt, E.A.
History
DepositionApr 24, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 6, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 / _struct_ref_seq_dif.details / _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: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7615
Polymers30,2861
Non-polymers4754
Water4,324240
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)75.320, 75.320, 105.703
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Uracil-DNA glycosylase


Mass: 30285.660 Da / Num. of mol.: 1 / Fragment: Residues 129-373
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania naiffi (eukaryote) / Gene: similar to LbrM18_V2.0540 / Plasmid: AVA0421 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: D0VWU0*PLUS, Hydrolases; Glycosylases; Hydrolysing N-glycosyl compounds

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Non-polymers , 5 types, 244 molecules

#2: Chemical ChemComp-BR / BROMIDE ION


Mass: 79.904 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Br
#3: Chemical ChemComp-URB / 5-bromopyrimidine-2,4(1H,3H)-dione / 5-bromouracil


Mass: 190.983 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H3BrN2O2
#4: Chemical ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H4N2O2
#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.: 240 / Source method: isolated from a natural source / Formula: H2O

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Details

Sequence details1. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) ...1. THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT THE UNIPROT KNOWLEDGEBASE DATABASE (UNIPROTKB) AT THE TIME OF DEPOSITION. 2. THE GENE USED IN THIS STUDY WAS CLONED FROM L. NAIFFI GENOMIC DNA USING PRIMERS DESIGNED FOR RESIDUES 129 TO 373 OF THE AVAILABLE L. BRAZILIENSIS SEQUENCE (UNIPROT ID A4H9F6_LEIBR). ACCORDINGLY, THE NUMBERING OF THE L. NAIFFI PROTEIN USED HERE FOLLOWS THAT OF THE L. BRAZILIENSIS HOMOLOG DESPITE THE LACK OF KNOWLEDGE OF THE FULL-LENGTH L. NAIFFI SEQUENCE.

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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: 2.86 Å3/Da / Density % sol: 56.96 %
Description: 1. The Blu-ice software package was used for data collection. The reference is: McPhillips T.M., McPhillips S.E., Chiu H.J., Cohen A.E., Deacon A.M., Ellis P.J., Garman E., Gonzalez A., ...Description: 1. The Blu-ice software package was used for data collection. The reference is: McPhillips T.M., McPhillips S.E., Chiu H.J., Cohen A.E., Deacon A.M., Ellis P.J., Garman E., Gonzalez A., Sauter N.K., Phizackerley R.P., Soltis S.M., Kuhn P., Blu-Ice and the Distributed Control System: software for data acquisition and instrument control at macromolecular crystallography beamlines. J.Synchrotron Radiat. 2002 Nov 1, 9(Pt 6):401-6. Epub 2002 Nov 1. PMID: 12409628. 2. The TLS motion determination server (http://skuld.bmsc.washington.edu/~tlsmd/) was used for selection of the TLS groups used in refinement. The reference is: Painter J. and Merritt E.A., TLSMD web server for the generation of multi-group TLS models. J.Appl.Cryst. 2006 Feb, 39(Pt 1):109-111. Epub 2006 Jan 12.
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 1.3 M Potassium phosphate dibasic, 0.1 M Sodium acetate pH 4.5, 5 mM DTT, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91724 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Mar 28, 2007 / Details: Mirrors
RadiationMonochromator: Double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91724 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 52821 / % possible obs: 97.2 % / Redundancy: 10.2 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.045 / Χ2: 0.978 / Net I/σ(I): 14.3
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.62 / Mean I/σ(I) obs: 1.5 / Num. unique all: 4325 / Χ2: 0.979 / % possible all: 79.9

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation2.5 Å37.66 Å
Translation2.5 Å37.66 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefmac_5.4.0066refinement
PDB_EXTRACT3.005data extraction
Blu-Icedata collection
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 1EUI

1eui


Resolution: 1.5→37.66 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.977 / WRfactor Rfree: 0.155 / WRfactor Rwork: 0.133 / SU B: 2.276 / SU ML: 0.042 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.05 / ESU R Free: 0.053 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY. 2. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.16 2693 5.1 %RANDOM
Rwork0.138 ---
obs0.139 52760 97.21 %-
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: 15.353 Å2
Baniso -1Baniso -2Baniso -3
1-0.34 Å20.17 Å20 Å2
2--0.34 Å20 Å2
3----0.52 Å2
Refinement stepCycle: LAST / Resolution: 1.5→37.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1933 0 24 240 2197
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0212108
X-RAY DIFFRACTIONr_bond_other_d0.0010.021471
X-RAY DIFFRACTIONr_angle_refined_deg1.6231.9412883
X-RAY DIFFRACTIONr_angle_other_deg0.9743.0013571
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9265267
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.47522.981104
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.75215347
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4011518
X-RAY DIFFRACTIONr_chiral_restr0.1030.2301
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0212374
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02456
X-RAY DIFFRACTIONr_mcbond_it2.03341257
X-RAY DIFFRACTIONr_mcbond_other0.6824495
X-RAY DIFFRACTIONr_mcangle_it3.25962038
X-RAY DIFFRACTIONr_scbond_it4.4066851
X-RAY DIFFRACTIONr_scangle_it7.07310832
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.5-1.5390.2881620.2562932402976.793
1.539-1.5810.2522020.2353291387490.165
1.581-1.6270.2411850.2143442379595.573
1.627-1.6770.2451610.1893510369399.404
1.677-1.7320.2181690.1723372354499.915
1.732-1.7920.1831790.1613301348299.943
1.792-1.860.1771790.1453124330499.97
1.86-1.9360.1521630.1423072323699.969
1.936-2.0220.1491600.13629043064100
2.022-2.120.1681600.13627782938100
2.12-2.2340.141360.12426692805100
2.234-2.3690.1681300.1232520265199.962
2.369-2.5320.1541180.13223672485100
2.532-2.7340.1571370.13621952332100
2.734-2.9930.1591190.13520232142100
2.993-3.3440.133940.1318501944100
3.344-3.8560.157640.11316431707100
3.856-4.710.122880.10813761464100
4.71-6.610.151560.13910781134100
6.61-37.6620.152310.15962065399.694
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)
11.51430.20290.35550.56960.0691.3557-0.09960.03060.16950.02880.09530.0117-0.2577-0.09630.00430.11510.0346-0.01320.1250.0049-0.0036-43.33926.95311.055
28.1473-0.17750.31265.246-4.20613.33270.0222-0.3076-0.10820.19410.28070.278-0.1079-0.9143-0.30290.08650.03610.02030.22710.03530.0076-50.34718.12223.678
31.84341.0354-1.09541.4602-1.61723.7375-0.07890.05950.01250.10470.1255-0.0131-0.1957-0.2218-0.04660.120.0261-0.00290.0812-0.0169-0.0117-36.95725.41722.095
41.33271.1562-1.19881.3649-0.76881.75780.0423-0.1542-0.07060.1346-0.0866-0.1063-0.17220.1940.04420.1558-0.0115-0.01480.16430.00610.0489-27.85722.42124.733
53.44280.3415-0.44871.30610.51591.0744-0.0008-0.6369-0.56710.104-0.1107-0.26180.08590.25520.11150.0626-0.0476-0.01510.1630.10520.0631-13.50420.86327.72
60.70910.5547-0.03150.9279-0.00610.9895-0.04470.081-0.0551-0.0520.0329-0.0813-0.09150.07280.01180.1460.00320.00020.1392-0.0090.0358-31.70120.80115.832
73.9182-0.30760.58620.9275-0.89333.2095-0.03620.3374-0.9702-0.13290.0088-0.0540.1250.19580.02730.0937-0.02140.07640.0453-0.09640.244-21.56313.97911.14
82.10690.6033-0.38151.5813-0.15531.5327-0.0625-0.0252-0.3009-0.1262-0.1282-0.21610.02490.060.19070.1164-0.03990.01860.15680.01680.1142-12.83224.21916.423
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA130 - 16625 - 61
2X-RAY DIFFRACTION2AA167 - 17462 - 69
3X-RAY DIFFRACTION3AA175 - 19570 - 90
4X-RAY DIFFRACTION4AA196 - 22691 - 121
5X-RAY DIFFRACTION5AA227 - 250122 - 145
6X-RAY DIFFRACTION6AA251 - 302146 - 197
7X-RAY DIFFRACTION7AA303 - 338198 - 233
8X-RAY DIFFRACTION8AA339 - 371234 - 266

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