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- PDB-4lyl: Crystal structure of uracil-DNA glycosylase from cod (Gadus morhu... -

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Basic information

Entry
Database: PDB / ID: 4lyl
TitleCrystal structure of uracil-DNA glycosylase from cod (Gadus morhua) in complex with the proteinaceous inhibitor UGI
Components
  • Uracil-DNA glycosylase
  • Uracil-DNA glycosylase inhibitor
KeywordsHYDROLASE/HYDROLASE INHIBITOR / ALPHA/BETA FOLD / HYDROLYSIS / INTRACELLULAR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
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
Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / 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 ...Bacteriophage PBS2, uracil-glycosylase inhibitor / Bacteriophage PBS2, uracil-glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase inhibitor / 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 / Nuclear Transport Factor 2; Chain: A, / Roll / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uracil-DNA glycosylase inhibitor / Uracil-DNA glycosylase
Similarity search - Component
Biological speciesGadus morhua (Atlantic cod)
Bacillus phage PBS2 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsAssefa, N.G. / Niiranen, L.M.K. / Johnson, K.A. / Leiros, H.-K.S. / Smalas, A.O. / Willassen, N.P. / Moe, E.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structural and biophysical analysis of interactions between cod and human uracil-DNA N-glycosylase (UNG) and UNG inhibitor (Ugi).
Authors: Assefa, N.G. / Niiranen, L. / Johnson, K.A. / Leiros, H.K. / Smalas, A.O. / Willassen, N.P. / Moe, E.
History
DepositionJul 31, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 13, 2014Provider: repository / Type: Initial release
Revision 1.1Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase inhibitor
C: Uracil-DNA glycosylase
D: Uracil-DNA glycosylase inhibitor
E: Uracil-DNA glycosylase
F: Uracil-DNA glycosylase inhibitor
G: Uracil-DNA glycosylase
H: Uracil-DNA glycosylase inhibitor
I: Uracil-DNA glycosylase
J: Uracil-DNA glycosylase inhibitor
K: Uracil-DNA glycosylase
L: Uracil-DNA glycosylase inhibitor
M: Uracil-DNA glycosylase
N: Uracil-DNA glycosylase inhibitor
O: Uracil-DNA glycosylase
P: Uracil-DNA glycosylase inhibitor


Theoretical massNumber of molelcules
Total (without water)278,16516
Polymers278,16516
Non-polymers00
Water26,7161483
1
A: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase inhibitor


Theoretical massNumber of molelcules
Total (without water)34,7712
Polymers34,7712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2080 Å2
ΔGint-10 kcal/mol
Surface area13350 Å2
MethodPISA
2
C: Uracil-DNA glycosylase
D: Uracil-DNA glycosylase inhibitor


Theoretical massNumber of molelcules
Total (without water)34,7712
Polymers34,7712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2140 Å2
ΔGint-8 kcal/mol
Surface area13510 Å2
MethodPISA
3
E: Uracil-DNA glycosylase
F: Uracil-DNA glycosylase inhibitor


Theoretical massNumber of molelcules
Total (without water)34,7712
Polymers34,7712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-11 kcal/mol
Surface area13470 Å2
MethodPISA
4
G: Uracil-DNA glycosylase
H: Uracil-DNA glycosylase inhibitor


Theoretical massNumber of molelcules
Total (without water)34,7712
Polymers34,7712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-9 kcal/mol
Surface area13440 Å2
MethodPISA
5
I: Uracil-DNA glycosylase
J: Uracil-DNA glycosylase inhibitor


Theoretical massNumber of molelcules
Total (without water)34,7712
Polymers34,7712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2090 Å2
ΔGint-11 kcal/mol
Surface area13560 Å2
MethodPISA
6
K: Uracil-DNA glycosylase
L: Uracil-DNA glycosylase inhibitor


Theoretical massNumber of molelcules
Total (without water)34,7712
Polymers34,7712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2100 Å2
ΔGint-11 kcal/mol
Surface area13340 Å2
MethodPISA
7
M: Uracil-DNA glycosylase
N: Uracil-DNA glycosylase inhibitor


Theoretical massNumber of molelcules
Total (without water)34,7712
Polymers34,7712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2120 Å2
ΔGint-10 kcal/mol
Surface area13440 Å2
MethodPISA
8
O: Uracil-DNA glycosylase
P: Uracil-DNA glycosylase inhibitor


Theoretical massNumber of molelcules
Total (without water)34,7712
Polymers34,7712
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2130 Å2
ΔGint-11 kcal/mol
Surface area13500 Å2
MethodPISA
9
A: Uracil-DNA glycosylase
B: Uracil-DNA glycosylase inhibitor
O: Uracil-DNA glycosylase
P: Uracil-DNA glycosylase inhibitor


Theoretical massNumber of molelcules
Total (without water)69,5414
Polymers69,5414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-30 kcal/mol
Surface area25770 Å2
MethodPISA
10
C: Uracil-DNA glycosylase
D: Uracil-DNA glycosylase inhibitor
M: Uracil-DNA glycosylase
N: Uracil-DNA glycosylase inhibitor


Theoretical massNumber of molelcules
Total (without water)69,5414
Polymers69,5414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5350 Å2
ΔGint-27 kcal/mol
Surface area25860 Å2
MethodPISA
11
E: Uracil-DNA glycosylase
F: Uracil-DNA glycosylase inhibitor
K: Uracil-DNA glycosylase
L: Uracil-DNA glycosylase inhibitor


Theoretical massNumber of molelcules
Total (without water)69,5414
Polymers69,5414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-30 kcal/mol
Surface area25720 Å2
MethodPISA
12
G: Uracil-DNA glycosylase
H: Uracil-DNA glycosylase inhibitor
I: Uracil-DNA glycosylase
J: Uracil-DNA glycosylase inhibitor


Theoretical massNumber of molelcules
Total (without water)69,5414
Polymers69,5414
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5310 Å2
ΔGint-30 kcal/mol
Surface area25890 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.210, 86.920, 175.370
Angle α, β, γ (deg.)90.000, 90.350, 90.000
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21C
31E
41G
51I
61K
71M
81O
12B
22D
32F
42H
52J
62L
72N
82P

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1113A-10 - 999
2113C-10 - 999
3113E-10 - 999
4113G-10 - 999
5113I-10 - 999
6113K-10 - 999
7113M-10 - 999
8113O-10 - 999
1123B-10 - 999
2123D-10 - 999
3123F-10 - 999
4123H-10 - 999
5123J-10 - 999
6123L-10 - 999
7123N-10 - 999
8123P-10 - 999

NCS ensembles :
ID
1
2

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Components

#1: Protein
Uracil-DNA glycosylase


Mass: 25287.910 Da / Num. of mol.: 8 / Fragment: Catalytic domain (UNP residues 82-301)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Gadus morhua (Atlantic cod) / Gene: ung1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9I983, uridine nucleosidase
#2: Protein
Uracil-DNA glycosylase inhibitor


Mass: 9482.674 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus phage PBS2 (virus) / Gene: UGI / Production host: Escherichia coli (E. coli) / References: UniProt: P14739
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1483 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.69 Å3/Da / Density % sol: 54.29 %
Crystal growMethod: vapor diffusion, hanging drop / pH: 7.4
Details: 17% PEG 4000, 4% PEG 550 MME, 0.27M LITHIUM SULFATE, 0.01M SODIUM BROMIDE, 0.1M TRIS-HCL, PH 7.4, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 277.0K

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.763
11-h,-k,l20.237
ReflectionResolution: 1.94→175 Å / Num. obs: 199006 / % possible obs: 91.2 % / Redundancy: 2.94 % / Biso Wilson estimate: 29.86 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 10.76
Reflection shellResolution: 1.94→2.04 Å / Redundancy: 3.16 % / Rmerge(I) obs: 0.413 / Mean I/σ(I) obs: 3.29 / % possible all: 86.6

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.93→29.48 Å / Cor.coef. Fo:Fc: 0.915 / Cor.coef. Fo:Fc free: 0.879 / WRfactor Rfree: 0.2843 / WRfactor Rwork: 0.2394 / FOM work R set: 0.6763 / SU B: 4.915 / SU ML: 0.15 / SU R Cruickshank DPI: 0.0457 / SU Rfree: 0.0407 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.046 / ESU R Free: 0.041 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: REFINED INDIVIDUALLY. DUE TO TWINNING THE APPARENT RESOLUTION IS HIGHER THAN THAT FROM THE DATA.
RfactorNum. reflection% reflectionSelection details
Rfree0.2834 10083 5.1 %RANDOM
Rwork0.2369 188922 --
obs0.2393 199005 89.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.63 Å2 / Biso mean: 25.036 Å2 / Biso min: 7.64 Å2
Baniso -1Baniso -2Baniso -3
1-13.15 Å20 Å2-4.31 Å2
2--5.65 Å2-0 Å2
3----18.79 Å2
Refinement stepCycle: LAST / Resolution: 1.93→29.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms19472 0 0 1483 20955
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.01920051
X-RAY DIFFRACTIONr_bond_other_d0.0050.0218986
X-RAY DIFFRACTIONr_angle_refined_deg1.6681.94927243
X-RAY DIFFRACTIONr_angle_other_deg0.866343865
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.42752440
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.88424.592932
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.69153423
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5051588
X-RAY DIFFRACTIONr_chiral_restr0.1030.22944
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.02122562
X-RAY DIFFRACTIONr_gen_planes_other0.0010.024554
X-RAY DIFFRACTIONr_mcbond_it2.1932.3889760
X-RAY DIFFRACTIONr_mcbond_other2.1922.3879759
X-RAY DIFFRACTIONr_mcangle_it2.9973.57112176
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-IDDom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
11A892tight positional0.220.05
12C892tight positional0.240.05
13E892tight positional0.250.05
14G892tight positional0.230.05
15I892tight positional0.20.05
16K892tight positional0.240.05
17M892tight positional0.20.05
18O892tight positional0.240.05
21B326tight positional0.260.05
22D326tight positional0.260.05
23F326tight positional0.270.05
24H326tight positional0.290.05
25J326tight positional0.320.05
26L326tight positional0.340.05
27N326tight positional0.340.05
28P326tight positional0.290.05
11A891loose positional0.625
12C891loose positional0.645
13E891loose positional0.575
14G891loose positional0.565
15I891loose positional0.645
16K891loose positional0.555
17M891loose positional0.565
18O891loose positional0.555
21B309loose positional0.915
22D309loose positional0.835
23F309loose positional0.775
24H309loose positional0.895
25J309loose positional0.845
26L309loose positional0.875
27N309loose positional0.835
28P309loose positional0.745
11A892tight thermal2.430.5
12C892tight thermal2.260.5
13E892tight thermal2.60.5
14G892tight thermal3.280.5
15I892tight thermal2.440.5
16K892tight thermal2.710.5
17M892tight thermal3.10.5
18O892tight thermal2.210.5
21B326tight thermal4.870.5
22D326tight thermal3.620.5
23F326tight thermal2.30.5
24H326tight thermal2.30.5
25J326tight thermal3.750.5
26L326tight thermal2.090.5
27N326tight thermal4.060.5
28P326tight thermal1.850.5
11A891loose thermal2.8510
12C891loose thermal2.810
13E891loose thermal2.8210
14G891loose thermal3.4110
15I891loose thermal2.9110
16K891loose thermal2.9510
17M891loose thermal3.310
18O891loose thermal2.7210
21B309loose thermal4.7310
22D309loose thermal3.8910
23F309loose thermal2.8810
24H309loose thermal2.6510
25J309loose thermal3.5810
26L309loose thermal2.3510
27N309loose thermal4.1510
28P309loose thermal2.1710
LS refinement shellResolution: 1.93→1.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.33 535 -
Rwork0.262 9048 -
all-9583 -
obs--58.83 %

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