PDB-3tr7: Structure of a uracil-DNA glycosylase (ung) from Coxiella burnetii

ID or keywords:

Entry

Database: PDB / ID: 3tr7

Title

Structure of a uracil-DNA glycosylase (ung) from Coxiella burnetii

Components

Uracil-DNA glycosylase

Keywords

HYDROLASE / DNA metabolism

Function / homology

Function and homology information

base-excision repair, AP site formation via deaminated base removal /

uracil-DNA glycosylase / uracil DNA N-glycosylase activity /

cytoplasm
Similarity search - Function

Biological species

Coxiella burnetii (bacteria)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.1958 Å

Authors

Cheung, J. / Franklin, M.C. / Rudolph, M. / Cassidy, M. / Gary, E. / Burshteyn, F. / Love, J.

Citation

Journal: Proteins / Year: 2015
Title: Structural genomics for drug design against the pathogen Coxiella burnetii.
Authors: Franklin, M.C. / Cheung, J. / Rudolph, M.J. / Burshteyn, F. / Cassidy, M. / Gary, E. / Hillerich, B. / Yao, Z.K. / Carlier, P.R. / Totrov, M. / Love, J.D.

History

Deposition	Sep 9, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 21, 2011	Provider: repository / Type: Initial release
Revision 1.1	Jun 24, 2015	Group: Database references
Revision 1.2	Jan 20, 2016	Group: Database references
Revision 1.3	Nov 8, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3tr7.cif.gz	101.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3tr7.ent.gz	82 KB	Display	PDB format
PDBx/mmJSON format	3tr7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tr/3tr7 ftp://data.pdbj.org/pub/pdb/validation_reports/tr/3tr7	HTTPS FTP

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Related structure data

Related structure data	3tq8C 3tq9C 3tqaC 3tqbC 3tqcC 3tqdC 3tqeC 3tqfC 3tqgC 3tqhC 3tqiC 3tqjC 3tqlC 3tqmC 3tqnC 3tqoC 3tqpC 3tqqC 3tqrC 3tqsC 3tqtC 3tquC 3tqwC 3tqxC 3tqyC 3tqzC 3tr0C 3tr1C 3tr2C 3tr3C 3tr4C 3tr5C 3tr6C 3tr8C 3tr9C 3trbC 3trcC 3trdC 3treC 3trfC 3trgC 3trhC 3triC 3tthC 3ty2C 3uwcC 4f3qC 4f3rC 4nbqC 4ng4C C: citing same article (ref.)
Similar structure data	3zor-d 2zhx-1 1ito-d 6kcw-d 2evo-1 4m7t-d 6ay2-1 1sp4-d 3uav-d 1znc-2 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Uracil-DNA glycosylase

26.1 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	53.175, 54.633, 76.762
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Uracil-DNA glycosylase / / UDG Mass: 26116.473 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_0988, ung / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83CW4, uracil-DNA glycosylase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 197 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Uracil-DNA glycosylase /

/ UDG

Mass: 26116.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Coxiella burnetii (bacteria) / Strain: RSA493 / Gene: CBU_0988, ung / Plasmid: pET / Production host:

Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q83CW4,

uracil-DNA glycosylase

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 197 / 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: 2.13 Å³/Da / Density % sol: 42.38 %
Crystal grow	Temperature: 295 K / Method: sitting drop / pH: 7.5 Details: 30% PEG 1500, pH 7.5, sitting drop, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å

Detector

Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 13, 2011

Radiation

Monochromator: VARIMAX HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.5418 Å / Relative weight: 1

Reflection

Resolution: 2.195→30 Å / Num. all: 11927 / Num. obs: 11784 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4 % / R_merge(I) obs: 0.07 / Χ²: 1.049 / Net I/σ(I): 8.5

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.195-2.24	2.8	0.351	524	1.155	1	91
2.24-2.28	2.9	0.321	566	1.943	1	97.1
2.28-2.32	3.5	0.235	579	0.9	1	99
2.32-2.37	4	0.243	575	0.937	1	99.5
2.37-2.42	4.1	0.207	589	0.893	1	99.5
2.42-2.48	4.1	0.17	588	0.823	1	99.2
2.48-2.54	4.1	0.158	577	0.832	1	99.5
2.54-2.61	4.1	0.169	572	0.777	1	99.1
2.61-2.68	4.2	0.13	589	0.777	1	99.7
2.68-2.77	4.2	0.124	584	0.914	1	98.8
2.77-2.87	4.1	0.109	572	0.854	1	99.5
2.87-2.99	4.3	0.091	586	0.862	1	99.2
2.99-3.12	4.3	0.078	594	0.883	1	99.5
3.12-3.29	4.2	0.066	600	0.901	1	100
3.29-3.49	4.2	0.055	604	1.052	1	99.8
3.49-3.76	4.3	0.056	589	1.339	1	100
3.76-4.14	4.3	0.049	604	1.218	1	100
4.14-4.73	4.2	0.044	615	1.171	1	99.8
4.73-5.96	4.2	0.047	624	1.253	1	99.7
5.96-30	3.8	0.047	653	1.824	1	97

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
PHENIX	1.7.1_743	refinement
PDB_EXTRACT	3.1	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.1958→21.856 Å / Occupancy max: 1 / Occupancy min: 0.37 / FOM work R set: 0.8052 / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 0 / Phase error: 25.18 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2368	558	4.76 %	RANDOM
R_work	0.1889	-	-	-
all	0.1912	11894	-	-
obs	0.1912	11727	98.59 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 31.605 Å² / k_sol: 0.327 e/Å³

Displacement parameters

B_iso max: 89.4 Å² / B_iso mean: 29.5623 Å² / B_iso min: 10.32 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.7357 Å²	0 Å²	-0 Å²
2-	-	3.7165 Å²	-0 Å²
3-	-	-	-1.9808 Å²

Refinement step

Cycle: LAST / Resolution: 2.1958→21.856 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1741	0	0	197	1938

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.002	1813
X-RAY DIFFRACTION	f_angle_d	0.547	2464
X-RAY DIFFRACTION	f_chiral_restr	0.039	261
X-RAY DIFFRACTION	f_plane_restr	0.002	322
X-RAY DIFFRACTION	f_dihedral_angle_d	11.912	673

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.1958-2.4165	0.3402	136	0.2545	2659	2795	96
2.4165-2.7656	0.2645	137	0.214	2766	2903	99
2.7656-3.482	0.2458	136	0.1813	2822	2958	100
3.482-21.8568	0.1953	149	0.1677	2922	3071	100

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	2.487	-0.4812	0.1018	2.1556	-1.6022	4.334	0.0642	0.4137	0.032	-0.4051	-0.1454	-0.1674	0.4741	-0.1823	0.0696	0.2491	0.068	0.0433	0.2463	-0.0077	0.2978	23.5966	12.5176	-6.209
2	0.6478	0.1439	0.3242	0.2583	0.2143	2.6992	0.0224	0.1253	-0.0332	0.0018	-0.066	-0.1673	-0.3656	0.3294	0.0252	0.2092	-0.0013	0.0223	0.2368	0.0121	0.2332	28.2366	27.1195	3.7624
3	1.2766	0.253	-0.5525	0.3456	0.1483	2.2567	0.0382	0.0257	-0.009	0.0118	-0.0259	0.0134	-0.1751	-0.0248	0.0054	0.1937	0.0268	-0.0192	0.1712	0.0023	0.204	19.4327	24.0264	9.7756
4	3.3189	1.2471	-0.1289	3.6259	1.6027	3.5262	-0.1004	0.3524	0.3229	-0.5353	-0.0339	0.4275	-0.2388	-0.2496	0.1406	0.2111	0.0197	-0.0069	0.2584	0.0419	0.2762	7.6977	20.2952	2.6389
5	2.7085	0.301	0.0525	0.7356	-0.6176	3.8	0.0709	0.2351	0.2705	0.3102	0.2467	0.0307	-0.5661	-0.6537	-0.1925	0.2578	0.068	0.0273	0.2908	-0.0212	0.209	8.1589	28.9655	16.2356
6	2.9511	0.297	-0.6305	4.1555	0.4053	2.7313	-0.0135	-0.1284	-0.3248	0.2987	-0.0445	0.2512	0.365	-0.2594	0.0151	0.209	-0.0013	0.0191	0.2423	0.0133	0.2267	13.6733	13.1516	19.1683

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resseq 7:20)	A
2	X-RAY DIFFRACTION	2	chain 'A' and (resseq 21:89)	A
3	X-RAY DIFFRACTION	3	chain 'A' and (resseq 90:167)	A
4	X-RAY DIFFRACTION	4	chain 'A' and (resseq 168:182)	A
5	X-RAY DIFFRACTION	5	chain 'A' and (resseq 183:203)	A
6	X-RAY DIFFRACTION	6	chain 'A' and (resseq 204:225)	A

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