PDB-2r6f: Crystal Structure of Bacillus stearothermophilus UvrA

ID or keywords:

Entry

Database: PDB / ID: 2r6f

Title

Crystal Structure of Bacillus stearothermophilus UvrA

Components

Excinuclease ABC subunit A

Keywords

HYDROLASE / UvrA / nucleotide excision repair / DNA repair / ABC ATPase / ATP-binding cassette / DNA damage / DNA excision / DNA-binding / Excision nuclease / Metal-binding / Nucleotide-binding / SOS response

Function / homology

Function and homology information

excinuclease ABC activity / excinuclease repair complex / SOS response / nucleotide-excision repair / ATP hydrolysis activity / DNA binding / zinc ion binding / ATP binding / cytoplasm
Similarity search - Function

Biological species

Geobacillus stearothermophilus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 3.2 Å

Authors

Inuzuka, Y. / Pakotiprapha, D. / Bowman, B.R. / Jeruzalmi, D. / Verdine, G.L.

Citation

Journal: Mol.Cell / Year: 2008
Title: Crystal Structure of Bacillus stearothermophilus UvrA Provides Insight into ATP-Modulated Dimerization, UvrB Interaction, and DNA Binding.
Authors: Pakotiprapha, D. / Inuzuka, Y. / Bowman, B.R. / Moolenaar, G.F. / Goosen, N. / Jeruzalmi, D. / Verdine, G.L.

History

Deposition	Sep 5, 2007	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 8, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Source and taxonomy / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.3	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_ncs_dom_lim / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 999

The sequence of this protein is not available at UNP database at the time of processing. Residues - ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	2r6f.cif.gz	712.4 KB	Display	PDBx/mmCIF format
PDB format	pdb2r6f.ent.gz	590.6 KB	Display	PDB format
PDBx/mmJSON format	2r6f.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/r6/2r6f ftp://data.pdbj.org/pub/pdb/validation_reports/r6/2r6f	HTTPS FTP

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Related structure data

Similar structure data	7850 2e76-1 10730 4pv1-1 1q90-1 6049 4h13-1 6pwx-d 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
Related items in Molecule of the Month	#123 - Mar 2010 P-glycoprotein similarity (4) #215 - Nov 2017 Aspartate Transcarbamoylase similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #192 - Dec 2015 Vancomycin similarity (1) #95 - Nov 2007 Multidrug Resistance Transporters similarity (4) #187 - Jul 2015 New Delhi Metallo-β-Lactamase similarity (1)

Deposited unit

A: Excinuclease ABC subunit A

B: Excinuclease ABC subunit A

hetero molecules

220 kDa, 2 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)	102.713, 94.720, 130.481
Angle α, β, γ (deg.)	90.000, 108.800, 90.000
Int Tables number	4
Space group name H-M	P12₁1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Refine code: 5

Dom-ID	Component-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	1	MSE	MSE	ARG	ARG	A	A	1 - 117	21 - 137
2	1	1	MSE	MSE	ARG	ARG	B	B	1 - 117	21 - 137
3	2	1	SER	SER	VAL	VAL	A	A	256 - 286	276 - 306
4	2	1	SER	SER	VAL	VAL	B	B	256 - 286	276 - 306
5	3	1	MSE	MSE	ALA	ALA	A	A	399 - 949	419 - 969
6	3	1	MSE	MSE	ALA	ALA	B	B	399 - 949	419 - 969
1	1	2	PRO	PRO	LEU	LEU	A	A	118 - 151	138 - 171
2	1	2	PRO	PRO	LEU	LEU	B	B	118 - 151	138 - 171
3	2	2	ASP	ASP	ASP	ASP	A	A	205 - 229	225 - 249
4	2	2	ASP	ASP	ASP	ASP	B	B	205 - 229	225 - 249
5	3	2	LYS	LYS	PHE	PHE	A	A	247 - 255	267 - 275
6	3	2	LYS	LYS	PHE	PHE	B	B	247 - 255	267 - 275
1	1	3	ASP	ASP	PRO	PRO	A	A	287 - 309	307 - 329
2	1	3	ASP	ASP	PRO	PRO	B	B	287 - 309	307 - 329
3	2	3	TYR	TYR	LEU	LEU	A	A	314 - 318	334 - 338
4	2	3	TYR	TYR	LEU	LEU	B	B	314 - 318	334 - 338
5	3	3	ARG	ARG	TYR	TYR	A	A	324 - 398	344 - 418
6	3	3	ARG	ARG	TYR	TYR	B	B	324 - 398	344 - 418

NCS ensembles :

ID
1
2
3

#1: Protein	Excinuclease ABC subunit A Mass: 108784.602 Da / Num. of mol.: 2 / Fragment: UvrA Source method: isolated from a genetically manipulated source Source: (gene. exp.) Geobacillus stearothermophilus (bacteria) Strain: 10 / Gene: uvrA / Plasmid: pET28 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5KVB6*PLUS
#2: Chemical	ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₁₀H₁₅N₅O₁₀P₂ / Comment: ADP, energy-carrying molecule*YM
#3: Chemical	ChemComp-ZN / ZINC ION Mass: 65.409 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Zn
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.76 Å³/Da / Density % sol: 55.46 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 13%PEG2000MME, 50 mM Na-HEPES pH 7.0, 500 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2	100	1
1,2		1

Diffraction source

Source	Site	Beamline	ID	Wavelength (Å)
SYNCHROTRON	APS	24-ID-C	1	0.97925, 0.97941, 0.96403
SYNCHROTRON	APS	24-ID-C	2	1.28281

Radiation

ID	Protocol	Monochromatic (M) / Laue (L)	Scattering type	Wavelength-ID
1	MAD	M	x-ray	1
2	SINGLE WAVELENGTH	M	x-ray	2

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97925	1
2	0.97941	1
3	0.96403	1
4	1.28281	1

Reflection

Redundancy: 6.9 % / Av σ(I) over netI: 13.4 / Number: 266945 / R_merge(I) obs: 0.079 / Χ²: 1.02 / D res high: 3.2 Å / D res low: 50 Å / Num. obs: 38657 / % possible obs: 98.3

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.89	50	99.3	1	0.055	1.024	7.1
5.47	6.89	100	1	0.079	1.025	7.1
4.78	5.47	100	1	0.077	1.027	7.3
4.34	4.78	100	1	0.067	1.002	7.3
4.03	4.34	100	1	0.077	1.003	7.3
3.79	4.03	100	1	0.105	1.018	7.4
3.6	3.79	100	1	0.134	1.018	7.3
3.45	3.6	99.9	1	0.186	1.022	7.1
3.31	3.45	98.2	1	0.261	1.031	6
3.2	3.31	85.9	1	0.305	1.019	4.9

Reflection

Resolution: 3.2→50 Å / Num. obs: 38657 / % possible obs: 98.3 % / Redundancy: 6.9 % / R_merge(I) obs: 0.079 / Χ²: 1.019 / Net I/σ(I): 13.4

Reflection shell

Resolution: 3.2→3.31 Å / Redundancy: 4.9 % / R_merge(I) obs: 0.305 / Num. unique all: 3362 / Χ²: 1.019 / % possible all: 85.9

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Phasing

Phasing	Method: MAD

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
REFMAC		refinement
PDB_EXTRACT	3	data extraction
ADSC	Quantum	data collection
HKL-2000		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 3.2→50 Å / Cor.coef. F_o:F_c: 0.908 / Cor.coef. F_o:F_c free: 0.888 / SU B: 59.032 / SU ML: 0.486 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.617
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. The data were collected from 2 crystals. One crystal was used for Se MAD, and the other one for Zn SAD. The Se MAD data was used for ...

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.292	3880	10 %	RANDOM
R_work	0.253	-	-	-
obs	0.257	34862	98.51 %	-

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: 68.793 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-4.56 Å²	0 Å²	2.36 Å²
2-	-	3.03 Å²	0 Å²
3-	-	-	3.05 Å²

Refinement step

Cycle: LAST / Resolution: 3.2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13868	0	114	4	13986

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.007	0.022	14228
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	9844
X-RAY DIFFRACTION	r_angle_refined_deg	1.247	1.993	19261
X-RAY DIFFRACTION	r_angle_other_deg	0.87	3	23962
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.24	5	1772
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	24.383	23.598	642
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.071	15	2511
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	10.925	15	126
X-RAY DIFFRACTION	r_chiral_restr	0.069	0.2	2166
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	15758
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2816
X-RAY DIFFRACTION	r_nbd_refined	0.201	0.2	3530
X-RAY DIFFRACTION	r_nbd_other	0.18	0.2	10655
X-RAY DIFFRACTION	r_nbtor_refined	0.169	0.2	7069
X-RAY DIFFRACTION	r_nbtor_other	0.08	0.2	7148
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	272
X-RAY DIFFRACTION	r_xyhbond_nbd_other	0.169	0.2	2
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.128	0.2	16
X-RAY DIFFRACTION	r_symmetry_vdw_other	0.18	0.2	94
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.197	0.2	2
X-RAY DIFFRACTION	r_mcbond_it	0.329	1.5	11191
X-RAY DIFFRACTION	r_mcbond_other	0.031	1.5	3628
X-RAY DIFFRACTION	r_mcangle_it	0.364	2	14212
X-RAY DIFFRACTION	r_scbond_it	0.422	3	6036
X-RAY DIFFRACTION	r_scangle_it	0.699	4.5	5049

Refine LS restraints NCS

Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	4095	MEDIUM POSITIONAL	0.27	0.5
1	1	5116	LOOSE POSITIONAL	0.36	5
1	1	4095	MEDIUM THERMAL	0.75	2
1	1	5116	LOOSE THERMAL	0.8	10
2	3	401	MEDIUM POSITIONAL	0.17	0.5
2	3	508	LOOSE POSITIONAL	0.3	5
2	3	401	MEDIUM THERMAL	0.13	2
2	3	508	LOOSE THERMAL	0.14	10
3	5	603	MEDIUM POSITIONAL	0.2	0.5
3	5	893	LOOSE POSITIONAL	0.3	5
3	5	603	MEDIUM THERMAL	0.13	2
3	5	893	LOOSE THERMAL	0.11	10

LS refinement shell

Resolution: 3.2→3.284 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.368	256	-
R_work	0.338	2172	-
all	-	2428	-
obs	-	-	83.61 %

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	2.5211	0.1624	0.0578	2.0941	-0.1611	1.1308	0.1344	0.0424	0.0415	0.1447	-0.1369	-0.0461	-0.0346	0.0897	0.0025	-0.1945	-0.0434	0.0144	-0.2036	-0.1061	-0.3628	47.6592	15.069	24.2715
2	2.5418	0.7188	0.0269	2.8011	0.6631	1.2486	0.222	-0.1165	0.122	0.1334	-0.4007	0.4936	-0.0463	-0.3965	0.1786	-0.1508	0.0418	-0.0196	0.0188	-0.0813	-0.0581	11.1944	49.2698	23.3983
3	16.9653	-1.7694	2.5102	2.9193	-0.5533	0.4025	0.1302	0.2724	-1.0262	0.0843	-0.0212	0.2549	-0.1977	-0.0598	-0.109	0.062	0.0641	-0.027	0.3452	-0.0093	0.4236	-11.6142	-2.4702	32.2518
4	11.824	-2.3753	-0.2107	0.4772	0.0423	0.0038	-0.124	0.3393	-0.8198	-0.7355	0.2515	-0.3148	0.0477	0.6711	-0.1275	0.5116	-0.0814	0.2591	0.5319	-0.1996	1.3057	72.3835	65.9044	29.0911
5	7.3027	0.9021	1.1911	7.4569	-2.1711	10.3377	-0.1463	-0.7026	-1.2386	0.931	-0.0208	-1.0159	0.5023	0.1466	0.1671	0.6494	0.0114	0.0121	0.4156	0.1916	0.3197	45.5916	-6.5832	60.9701
6	6.1914	-3.7778	-2.3961	10.9468	1.849	5.586	-0.3093	0.6481	-0.4834	-0.1711	0.0282	0.52	0.5928	-0.3196	0.2811	0.4426	-0.0356	0.0417	0.4875	0.1324	0.0031	10.7051	68.2578	60.5656

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	1 - 117	21 - 137
2	X-RAY DIFFRACTION	1	A	A	256 - 286	276 - 306
3	X-RAY DIFFRACTION	1	A	A	399 - 949	419 - 969
4	X-RAY DIFFRACTION	2	B	B	1 - 117	21 - 137
5	X-RAY DIFFRACTION	2	B	B	256 - 286	276 - 306
6	X-RAY DIFFRACTION	2	B	B	399 - 949	419 - 969
7	X-RAY DIFFRACTION	3	A	A	118 - 153	138 - 173
8	X-RAY DIFFRACTION	3	A	A	200 - 255	220 - 275
9	X-RAY DIFFRACTION	4	B	B	118 - 151	138 - 171
10	X-RAY DIFFRACTION	4	B	B	205 - 229	225 - 249
11	X-RAY DIFFRACTION	5	A	A	287 - 309	307 - 329
12	X-RAY DIFFRACTION	5	A	A	314 - 318	334 - 338
13	X-RAY DIFFRACTION	5	A	A	324 - 398	344 - 418
14	X-RAY DIFFRACTION	6	B	B	287 - 398	307 - 418

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