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- PDB-4lzb: Uracil binding pocket in Vaccinia virus uracil DNA glycosylase -

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Basic information

Entry
Database: PDB / ID: 4lzb
TitleUracil binding pocket in Vaccinia virus uracil DNA glycosylase
ComponentsUracil-DNA glycosylase
KeywordsHYDROLASE / alpha/beta DNA glycosylase fold / viral processivity factor / DNA binding component / DNA repair / A20
Function / homology
Function and homology information


uracil-DNA glycosylase / uracil DNA N-glycosylase activity / DNA repair / DNA binding
Similarity search - Function
Uracil-DNA glycosylase, active site / Uracil-DNA glycosylase signature. / Uracil-DNA Glycosylase, subunit E / Uracil-DNA glycosylase-like domain / Uracil-DNA glycosylase-like domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
: / URACIL / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesVaccinia virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.03 Å
AuthorsSchormann, N. / Chattopadhyay, D.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2013
Title: Structure of the uracil complex of Vaccinia virus uracil DNA glycosylase.
Authors: Schormann, N. / Banerjee, S. / Ricciardi, R. / Chattopadhyay, D.
History
DepositionJul 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 11, 2013Provider: repository / Type: Initial release
Revision 1.1Feb 5, 2014Group: Database references
Revision 1.2Sep 20, 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 / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / 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_asym_id / _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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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
B: Uracil-DNA glycosylase
C: Uracil-DNA glycosylase
D: Uracil-DNA glycosylase
E: Uracil-DNA glycosylase
F: Uracil-DNA glycosylase
G: Uracil-DNA glycosylase
H: Uracil-DNA glycosylase
I: Uracil-DNA glycosylase
J: Uracil-DNA glycosylase
K: Uracil-DNA glycosylase
L: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)331,04474
Polymers327,03712
Non-polymers4,00762
Water29,1301617
1
A: Uracil-DNA glycosylase
F: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,32015
Polymers54,5062
Non-polymers81313
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Uracil-DNA glycosylase
E: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,62521
Polymers54,5062
Non-polymers1,11919
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Uracil-DNA glycosylase
K: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9028
Polymers54,5062
Non-polymers3966
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Uracil-DNA glycosylase
H: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,12111
Polymers54,5062
Non-polymers6159
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
G: Uracil-DNA glycosylase
J: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,16012
Polymers54,5062
Non-polymers65410
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
I: Uracil-DNA glycosylase
L: Uracil-DNA glycosylase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)54,9177
Polymers54,5062
Non-polymers4105
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)93.470, 114.045, 302.516
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D
51E
61F
71G
81H
91I
101J
111K
121L

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: TYR / End label comp-ID: TYR / Refine code: 6 / Auth seq-ID: 1 - 218 / Label seq-ID: 21 - 238

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD
5EE
6FF
7GG
8HH
9II
10JJ
11KK
12LL

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Components

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Protein , 1 types, 12 molecules ABCDEFGHIJKL

#1: Protein
Uracil-DNA glycosylase / UDG


Mass: 27253.119 Da / Num. of mol.: 12 / Mutation: D17N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vaccinia virus / Strain: VACV-WR-109 / Gene: ACAM3000_MVA_101, D4, MVA101R, UNG / Plasmid: PET15b / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta(DE3)pLysS / References: UniProt: Q91UM2, uracil-DNA glycosylase

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Non-polymers , 6 types, 1679 molecules

#2: Chemical
ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#3: Chemical
ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: K
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 16 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical
ChemComp-URA / URACIL


Mass: 112.087 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C4H4N2O2
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1617 / 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: 2.47 Å3/Da / Density % sol: 50.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 10% PEG8000, 10% DMSO, 0.1 M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 1.77 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Mar 13, 2013 / Details: mirrors
RadiationMonochromator: Kohzu HLD8-24 Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.77 Å / Relative weight: 1
ReflectionResolution: 2.03→49.64 Å / Num. all: 198586 / Num. obs: 198856 / % possible obs: 95.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 17 % / Rmerge(I) obs: 0.13 / Rsym value: 0.13 / Net I/σ(I): 25.9
Reflection shellResolution: 2.03→2.14 Å / Redundancy: 10.2 % / Rmerge(I) obs: 0.584 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.584 / % possible all: 88.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.7.0032refinement
PDB_EXTRACT3.11data extraction
RAPDdata collection
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4DOF CHAIN A

4dof


Resolution: 2.03→49.64 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.917 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.792 / SU ML: 0.132 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / ESU R: 0.221 / ESU R Free: 0.181 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24607 10025 5.1 %RANDOM
Rwork0.21288 ---
obs0.21455 188435 94.93 %-
all-198460 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 31.91 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å2-0 Å2-0 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 2.03→49.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms21115 0 224 1617 22956
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01922182
X-RAY DIFFRACTIONr_bond_other_d0.0010.0221036
X-RAY DIFFRACTIONr_angle_refined_deg1.0491.95830168
X-RAY DIFFRACTIONr_angle_other_deg0.737348551
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.72152657
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.92624.202978
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12153766
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5311591
X-RAY DIFFRACTIONr_chiral_restr0.0620.23312
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02124713
X-RAY DIFFRACTIONr_gen_planes_other0.0010.025132
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0913.12210574
X-RAY DIFFRACTIONr_mcbond_other1.0913.12210573
X-RAY DIFFRACTIONr_mcangle_it1.8464.67313246
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0683.2511608
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 3124 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDTypeRms dev position (Å)Weight position
1ALOOSE POSITIONAL0.585
2BLOOSE POSITIONAL0.675
3CLOOSE POSITIONAL0.595
4DLOOSE POSITIONAL0.615
5ELOOSE POSITIONAL0.595
6FLOOSE POSITIONAL0.635
7GLOOSE POSITIONAL0.65
8HLOOSE POSITIONAL0.565
9ILOOSE POSITIONAL0.655
10JLOOSE POSITIONAL0.615
11KLOOSE POSITIONAL0.725
12LLOOSE POSITIONAL0.625
1ALOOSE THERMAL9.6310
2BLOOSE THERMAL10.0410
3CLOOSE THERMAL4.3710
4DLOOSE THERMAL4.6710
5ELOOSE THERMAL8.1510
6FLOOSE THERMAL7.1610
7GLOOSE THERMAL4.6210
8HLOOSE THERMAL4.1110
9ILOOSE THERMAL5.3410
10JLOOSE THERMAL8.5310
11KLOOSE THERMAL12.0510
12LLOOSE THERMAL10.0210
LS refinement shellResolution: 2.029→2.082 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.305 704 -
Rwork0.266 12574 -
obs--86.81 %

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