PDB-2zhx: Crystal structure of Uracil-DNA Glycosylase from Mycobacterium tu...

ID or keywords:

Entry

Database: PDB / ID: 2zhx

Title

Crystal structure of Uracil-DNA Glycosylase from Mycobacterium tuberculosis in complex with a proteinaceous inhibitor

Components

Uracil-DNA glycosylase
Uracil-DNA glycosylase inhibitor

Keywords

HYDROLASE/HYDROLASE INHIBITOR / DNA repair / Ung-Ugi complex / Ung-DNA interactions / DNA damage / Glycosidase / Hydrolase / 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 / base-excision repair / cytoplasm
Similarity search - Function

Biological species

Mycobacterium tuberculosis H37Rv (bacteria)

Bacillus phage PBS2 (virus)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 3.1 Å

Authors

Kaushal, P.S. / Talawar, R.K. / Krishna, P.D.V. / Varshney, U. / Vijayan, M.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2008
Title: Unique features of the structure and interactions of mycobacterial uracil-DNA glycosylase: structure of a complex of the Mycobacterium tuberculosis enzyme in comparison with those from other sources
Authors: Kaushal, P.S. / Talawar, R.K. / Krishna, P.D.V. / Varshney, U. / Vijayan, M.

History

Deposition	Feb 11, 2008	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	May 20, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Refinement description / Version format compliance
Revision 1.2	Nov 21, 2018	Group: Advisory / Data collection ...Advisory / Data collection / Derived calculations / Source and taxonomy Category: entity_src_gen / pdbx_distant_solvent_atoms ...entity_src_gen / pdbx_distant_solvent_atoms / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop Item: _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name ..._entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_struct_assembly_prop.biol_id / _pdbx_struct_assembly_prop.value
Revision 1.3	Nov 1, 2023	Group: Data collection / Database references / 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 Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2zhx.cif.gz	413.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	2zhx_validation.pdf.gz	540.5 KB	Display	wwPDB validaton report
Full document	2zhx_full_validation.pdf.gz	603.2 KB	Display
Data in XML	2zhx_validation.xml.gz	86.1 KB	Display
Data in CIF	2zhx_validation.cif.gz	118.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/zh/2zhx ftp://data.pdbj.org/pub/pdb/validation_reports/zh/2zhx	HTTPS FTP

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Related structure data

Related structure data	1udiS 1ughS 1uugS S: Starting model for refinement
Similar structure data	3zor-d 4ws8-d 3ufm-d 3fck-d 4ws5-d 3tr7-d 1z36-d 3wdf-2 1ito-d 1csb-2 Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

1udiS

1ughS

1uugS

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI

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

247 kDa, 14 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Uracil-DNA glycosylase

B: Uracil-DNA glycosylase inhibitor

defined by author&software
35.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

C: Uracil-DNA glycosylase

D: Uracil-DNA glycosylase inhibitor

defined by author&software
35.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

E: Uracil-DNA glycosylase

F: Uracil-DNA glycosylase inhibitor

defined by author&software
35.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

4

G: Uracil-DNA glycosylase

H: Uracil-DNA glycosylase inhibitor

defined by author&software
35.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

5

I: Uracil-DNA glycosylase

J: Uracil-DNA glycosylase inhibitor

defined by author&software
35.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

6

K: Uracil-DNA glycosylase

L: Uracil-DNA glycosylase inhibitor

defined by author&software
35.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

7

M: Uracil-DNA glycosylase

N: Uracil-DNA glycosylase inhibitor

defined by author&software
35.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	201.143, 64.274, 203.677
Angle α, β, γ (deg.)	90.00, 109.72, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	K-237- HOH

#1: Protein	Uracil-DNA glycosylase / UDG Mass: 25813.543 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis H37Rv (bacteria) Strain: H37Rv / Gene: ung, Rv2976c / Plasmid: pRSETb MtuUDG-Ugi / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: P67071, UniProt: P9WFQ9*PLUS, uridine nucleosidase
#2: Protein	Uracil-DNA glycosylase inhibitor Mass: 9482.674 Da / Num. of mol.: 7 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bacillus phage PBS2 (virus) / Gene: ugi, J04434 / Plasmid: pRSETb MtuUDG-Ugi / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P14739
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 519 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.51 Å³/Da / Density % sol: 50.96 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6.2 Details: 10%(w/v) PEG 8000 and 0.2M NaCl in 0.1M phosphate buffer pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 Å
Detector	Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Mar 20, 2006
Radiation	Monochromator: OSMIC MIRROR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 3.1→30 Å / Num. all: 45064 / Num. obs: 43788 / % possible obs: 97.2 % / Observed criterion σ(F): 1 / Redundancy: 2.8 % / R_sym value: 0.149 / Net I/σ(I): 8.2
Reflection shell	Resolution: 3.1→3.21 Å / Mean I/σ(I) obs: 2.4 / R_sym value: 0.421 / % possible all: 91.8

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
HKL-2000		data collection
DENZO		data reduction
SCALEPACK		data scaling
PHASES		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UGH, 1UUG and 1UDI

1ugh

1uug

1udi

Resolution: 3.1→30 Å / Cor.coef. F_o:F_c: 0.906 / Cor.coef. F_o:F_c free: 0.867 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.56 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.27638	2228	5.1 %	RANDOM
R_work	0.23367	-	-	-
obs	0.23581	41560	97.17 %	-
all	-	45064	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 58.364 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.91 Å²	0 Å²	-3.05 Å²
2-	-	6.61 Å²	0 Å²
3-	-	-	-5.75 Å²

Refinement step

Cycle: LAST / Resolution: 3.1→30 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	16321	0	0	519	16840

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	16729
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.435	1.975	22884
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.003	5	2133
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	39.33	23.382	692
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.961	15	2522
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.063	15	135
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	2577
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	12964
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.263	0.2	8901
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.321	0.2	11354
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.177	0.2	748
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.249	0.2	56
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.175	0.2	8
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	8.302	1.5	10779
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	10.906	2	17338
X-RAY DIFFRACTION	r_scbond_it	1.1	3	5950
X-RAY DIFFRACTION	r_scangle_it	1.936	4.5	5546
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 3.1→3.18 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.367	174	-
R_work	0.339	2775	-
obs	-	-	90.63 %

Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

ID	L11 (°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)
1	0.9925	-0.4226	0.0107	0.2633	-0.2796	0.9071	-0.0096	0.0871	-0.0559	-0.0206	0.0195	-0.004	0.1649	-0.0936	-0.0099	-0.0134	-0.0828	-0.0129	0.0038	0.015	-0.0531	-23.583	0.9041	53.1279
2	2.3664	0.1125	-0.7812	0.3691	0.7911	2.144	0.0521	-0.0238	0.2305	-0.0066	-0.1084	-0.0837	-0.0001	-0.085	0.0563	-0.1051	-0.0329	-0.0609	-0.0824	-0.0111	0.0176	-31.2711	18.5975	66.273
3	0.5378	-0.2183	0.2707	0.6011	0.217	0.5655	-0.0487	0.0189	0.0944	0.0001	0.08	0.089	0.0463	0.125	-0.0312	-0.0335	-0.0431	0.0026	-0.0653	0.0001	-0.0184	-65.1423	-3.1656	56.2806
4	2.1315	0.2088	0.2784	1.0271	-0.3195	0.821	-0.0234	0.0375	0.1845	-0.1053	0.053	0.0814	0.1159	-0.04	-0.0296	-0.0122	-0.0103	-0.0339	-0.1529	0.0776	0.0412	-86.8118	3.2486	50.916
5	0.4962	-0.1098	0.0423	0.4256	-0.4618	1.0307	-0.0524	0.0272	-0.0266	0.0571	0.0141	-0.0806	-0.0347	-0.1124	0.0382	-0.0416	0.0142	-0.0145	-0.0677	0.0073	-0.0442	-3.4459	4.1175	79.7288
6	3.48	-1.0243	1.3697	1.6471	0.1033	1.1343	0.1062	0.1029	0.1494	-0.1895	-0.1105	-0.4171	0.2352	0.0988	0.0043	-0.0235	0.0117	0.0621	-0.1309	0.0593	-0.0072	14.7333	-10.2043	81.9117
7	1.5321	0.3777	-0.1912	0.7739	0.3649	1.744	0.0418	-0.0597	-0.0398	-0.0024	-0.0435	-0.0287	0.3429	0.2187	0.0016	0.0079	0.0398	-0.0339	-0.0868	-0.0184	-0.0669	-59.2672	-16.6753	86.5779
8	3.5138	0.1988	-0.4395	0.0174	-0.1714	3.5656	-0.0559	-0.3432	-0.1878	-0.4694	-0.2193	0.0583	0.3618	0.9016	0.2752	-0.1417	0.1955	0.0557	0.2091	-0.001	-0.1741	-39.384	-15.2721	75.2154
9	1.318	-0.1515	-0.1506	0.167	-0.4556	1.9012	0.0562	0.2143	-0.1259	0.0147	-0.0004	0.0371	0.2719	0.042	-0.0558	0.005	-0.0125	-0.0473	-0.1105	-0.0257	-0.0654	-76.4335	-22.7656	31.7758
10	3.3835	0.2609	-0.3967	0.948	1.5309	2.6743	-0.3562	0.2694	-0.4523	0.1524	0.0712	-0.025	0.8801	0.4314	0.285	0.3105	0.1959	-0.0353	-0.1935	-0.1255	-0.1232	-63.4516	-40.3317	24.1033
11	0.8654	0.1837	-0.3602	0.1622	-0.5299	2.2157	-0.0678	0.2784	0.0083	0.1149	-0.0744	0.0062	0.0842	0.1375	0.1422	-0.0833	-0.0941	-0.0419	0.1459	0.0571	-0.1323	-10.9381	8.1009	23.0032
12	3.3423	-1.6467	-1.4402	2.634	-1.2414	2.7088	0.0292	0.0908	-0.2828	0.057	-0.0741	-0.2107	0.5427	0.0312	0.0448	0.0212	-0.0614	-0.0156	-0.0572	-0.0877	-0.1692	-6.7341	-14.049	27.8256
13	1.5227	-0.4629	0.8062	1.3673	-0.2863	2.5343	-0.0004	-0.5113	-0.1208	-0.0029	-0.0657	-0.0511	-0.1558	-0.7647	0.0661	-0.1662	-0.0205	-0.0399	0.3679	-0.0127	-0.2161	-33.4266	16.4133	-0.4213
14	1.3169	-0.5383	-0.6823	4.4668	-1.7879	3.353	-0.3739	-0.3016	0.5038	0.2403	-0.1632	-0.043	-1.0169	-0.289	0.5371	0.0861	0.0852	-0.2639	0.1813	-0.2812	-0.3516	-25.7426	35.7354	9.2392

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 227
2	X-RAY DIFFRACTION	2	B	3 - 84
3	X-RAY DIFFRACTION	3	C	3 - 227
4	X-RAY DIFFRACTION	4	D	3 - 84
5	X-RAY DIFFRACTION	5	E	4 - 227
6	X-RAY DIFFRACTION	6	F	3 - 84
7	X-RAY DIFFRACTION	7	G	3 - 227
8	X-RAY DIFFRACTION	8	H	3 - 84
9	X-RAY DIFFRACTION	9	I	3 - 227
10	X-RAY DIFFRACTION	10	J	3 - 84
11	X-RAY DIFFRACTION	11	K	3 - 227
12	X-RAY DIFFRACTION	12	L	3 - 84
13	X-RAY DIFFRACTION	13	M	3 - 227
14	X-RAY DIFFRACTION	14	N	3 - 84

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