PDB-8gm6: Structure of apurinic/apyrimidinic DNA lyase TK0353 from Thermoco...

ID or keywords:

Entry

Database: PDB / ID: 8gm6

Title

Structure of apurinic/apyrimidinic DNA lyase TK0353 from Thermococcus kodakarensis (Selenomethionine)

Components

TK0353

Keywords

LYASE / apurinic/apyrimidinic DNA lyase DNA binding protein

Function / homology

Uncharacterized protein

Function and homology information

Biological species

Thermococcus kodakarensis (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.98 Å

Authors

Eckenroth, B.E. / Gardner, A.F. / Doublie, S.

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Cancer Institute (NIH/NCI)	P01-CA098993	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	R50-CA233185	United States

Citation

Journal: J.Biol.Chem. / Year: 2023
Title: Thermococcus kodakarensis TK0353 is a novel AP lyase with a new fold.
Authors: Caffrey, P.J. / Eckenroth, B.E. / Burkhart, B.W. / Zatopek, K.M. / McClung, C.M. / Santangelo, T.J. / Doublie, S. / Gardner, A.F.

History

Deposition	Mar 24, 2023	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 6, 2023	Provider: repository / Type: Initial release
Revision 1.1	Dec 13, 2023	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Dec 27, 2023	Group: Database references / Category: citation / Item: _citation.journal_volume
Revision 1.3	Oct 30, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Summary document	8gm6_validation.pdf.gz	456.5 KB	Display	wwPDB validaton report
Full document	8gm6_full_validation.pdf.gz	461.2 KB	Display
Data in XML	8gm6_validation.xml.gz	15.6 KB	Display
Data in CIF	8gm6_validation.cif.gz	21.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/gm/8gm6 ftp://data.pdbj.org/pub/pdb/validation_reports/gm/8gm6	HTTPS FTP

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Related structure data

Related structure data	8gm7C 8syjC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: TK0353

B: TK0353

hetero molecules

39.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: TK0353

hetero molecules

defined by author
Evidence: light scattering, 25 angstrom radius determined by dynamic light scattering equivalent to the monomeric species.
19.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: TK0353

hetero molecules

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

Unit cell

Length a, b, c (Å)	99.542, 99.542, 159.507
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	178
Space group name H-M	P6₁22
Space group name Hall	P6₁2(x,y,z+5/12)
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/6 #3: y,-x+y,z+5/6 #4: -y,x-y,z+1/3 #5: -x+y,-x,z+2/3 #6: x-y,-y,-z #7: -x,-x+y,-z+2/3 #8: -x,-y,z+1/2 #9: y,x,-z+1/3 #10: -y,-x,-z+5/6 #11: -x+y,y,-z+1/2 #12: x,x-y,-z+1/6

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 2 through 5 or (resid 6...
d_2	ens_1	(chain "B" and (resid 2 through 22 or resid 24...

NCS domain segments:

Ens-ID: ens_1

Dom-ID	Component-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
d_1	1	TYR	TYR	PHE	PHE	A	A	2 - 22	2 - 22
d_1	2	PHE	PHE	PHE	PHE	A	A	24 - 31	24 - 31
d_1	3	TYR	TYR	GLY	GLY	A	A	33 - 36	33 - 36
d_1	4	ILE	ILE	LEU	LEU	A	A	38 - 39	38 - 39
d_1	5	TYR	TYR	SER	SER	A	A	41 - 42	41 - 42
d_1	6	LYS	LYS	GLU	GLU	A	A	44 - 57	44 - 57
d_1	7	THR	THR	GLY	GLY	A	A	59 - 60	59 - 60
d_1	8	PRO	PRO	ASN	ASN	A	A	62 - 77	62 - 77
d_1	9	VAL	VAL	LYS	LYS	A	A	79 - 81	79 - 81
d_1	10	LEU	LEU	ARG	ARG	A	A	83 - 158	83 - 158
d_1	11	GLU	GLU	GLU	GLU	A	A	160 - 167	160 - 167
d_2	1	TYR	TYR	PHE	PHE	B	B	2 - 22	2 - 22
d_2	2	PHE	PHE	PHE	PHE	B	B	24 - 31	24 - 31
d_2	3	TYR	TYR	GLY	GLY	B	B	33 - 36	33 - 36
d_2	4	ILE	ILE	LEU	LEU	B	B	38 - 39	38 - 39
d_2	5	TYR	TYR	SER	SER	B	B	41 - 42	41 - 42
d_2	6	LYS	LYS	GLU	GLU	B	B	44 - 57	44 - 57
d_2	7	THR	THR	GLY	GLY	B	B	59 - 60	59 - 60
d_2	8	PRO	PRO	ASN	ASN	B	B	62 - 77	62 - 77
d_2	9	VAL	VAL	LYS	LYS	B	B	79 - 81	79 - 81
d_2	10	LEU	LEU	ARG	ARG	B	B	83 - 158	83 - 158
d_2	11	GLU	GLU	GLU	GLU	B	B	160 - 167	160 - 167

NCS oper: (Code: givenMatrix: (-0.980924933597, 0.0476049927212, -0.188467608136), (-0.106029362387, 0.681584705922, 0.72401661788), (0.162923445091, 0.730189053138, -0.663535905372)Vector: -28. ...

#1: Protein	TK0353 Mass: 19784.605 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK0353 / Production host: Escherichia coli (E. coli) / Strain (production host): T7 Express / References: UniProt: Q5JCX2
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N
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: 2.88 Å³/Da / Density % sol: 57.33 % / Description: small hexagonal
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 2.5 M (NH4)2SO4 with 0.1 M Tris pH 8.0 mixed 1:1 with Protein at 20 mg/ml in 10 mM Tris pH 7.5, 100 mM NaCl, 10% glycerol and 1 mM DTT. Cryoprotection by addition of 1.5 M Li2SO4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9794 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 16, 2000
Radiation	Monochromator: Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.98→43.1 Å / Num. obs: 61936 / % possible obs: 100 % / Redundancy: 17.6 % / B_iso Wilson estimate: 38.78 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.19 / R_pim(I) all: 0.046 / R_rim(I) all: 0.195 / Net I/σ(I): 12.6
Reflection shell	Resolution: 1.98→2.02 Å / Redundancy: 16.3 % / R_merge(I) obs: 4.63 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 3685 / CC_1/2: 0.471 / R_pim(I) all: 1.18 / R_rim(I) all: 4.78 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
MOSFLM	7.4.0	data reduction
Aimless	0.7.3	data scaling
CRANK2	2.0.227	phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.98→43.1 Å / SU ML: 0.2696 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 28.0841
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2333	6236	10.07 %
R_work	0.1985	55700	-
obs	0.2021	61936	99.98 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 61.93 Å²

Refinement step

Cycle: LAST / Resolution: 1.98→43.1 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2638	0	16	125	2779

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0093	2739
X-RAY DIFFRACTION	f_angle_d	0.9948	3706
X-RAY DIFFRACTION	f_chiral_restr	0.0579	406
X-RAY DIFFRACTION	f_plane_restr	0.0086	480
X-RAY DIFFRACTION	f_dihedral_angle_d	13.4567	1051

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.784288418023 Å

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.98-2	0.3623	219	0.375	1834	X-RAY DIFFRACTION	99.85
2-2.02	0.3545	214	0.3631	1851	X-RAY DIFFRACTION	99.95
2.02-2.05	0.3671	177	0.3479	1884	X-RAY DIFFRACTION	100
2.05-2.07	0.3903	185	0.3338	1898	X-RAY DIFFRACTION	100
2.07-2.1	0.3613	205	0.328	1849	X-RAY DIFFRACTION	100
2.1-2.13	0.3161	221	0.3256	1832	X-RAY DIFFRACTION	100
2.13-2.16	0.3454	222	0.3182	1869	X-RAY DIFFRACTION	100
2.16-2.19	0.3314	187	0.3005	1851	X-RAY DIFFRACTION	99.9
2.19-2.23	0.3247	196	0.2811	1872	X-RAY DIFFRACTION	100
2.23-2.26	0.32	196	0.2885	1889	X-RAY DIFFRACTION	100
2.26-2.3	0.282	181	0.2762	1880	X-RAY DIFFRACTION	100
2.3-2.34	0.3292	162	0.2555	1868	X-RAY DIFFRACTION	100
2.34-2.39	0.29	184	0.2489	1890	X-RAY DIFFRACTION	100
2.39-2.44	0.356	201	0.2405	1882	X-RAY DIFFRACTION	100
2.44-2.49	0.31	234	0.2525	1827	X-RAY DIFFRACTION	100
2.49-2.55	0.2639	202	0.2326	1862	X-RAY DIFFRACTION	100
2.55-2.61	0.2552	211	0.224	1868	X-RAY DIFFRACTION	100
2.61-2.68	0.2594	184	0.2264	1859	X-RAY DIFFRACTION	100
2.68-2.76	0.2956	217	0.2286	1854	X-RAY DIFFRACTION	99.95
2.76-2.85	0.2769	229	0.2279	1840	X-RAY DIFFRACTION	100
2.85-2.95	0.2762	223	0.231	1820	X-RAY DIFFRACTION	100
2.95-3.07	0.2708	211	0.2188	1854	X-RAY DIFFRACTION	99.95
3.07-3.21	0.2333	207	0.2233	1874	X-RAY DIFFRACTION	100
3.21-3.38	0.2348	244	0.1854	1817	X-RAY DIFFRACTION	100
3.38-3.59	0.2235	235	0.1672	1837	X-RAY DIFFRACTION	100
3.59-3.87	0.1924	242	0.1589	1819	X-RAY DIFFRACTION	99.95
3.87-4.26	0.2129	219	0.138	1837	X-RAY DIFFRACTION	100
4.26-4.87	0.1531	210	0.124	1852	X-RAY DIFFRACTION	100
4.87-6.13	0.1665	186	0.1623	1892	X-RAY DIFFRACTION	100
6.14-43.1	0.1838	232	0.167	1839	X-RAY DIFFRACTION	99.9

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	4.11105142065	-2.34367633491	-2.60870963135	2.24324957785	0.381068968548	4.70751724303	-0.150208082307	0.588583571312	-0.397774420679	-1.06346942156	-0.0410013649577	0.877028080022	0.888583541017	0.115623920367	0.0230063138254	0.717398193129	-0.0187968475667	-0.213779885789	0.647018374571	-0.204091970461	0.830719374886	-32.8815760691	32.3161574722	-9.86263973947
2	6.42174827742	-1.1961438618	1.43915380997	5.1486554841	-2.14610967447	4.27891286767	0.184519658439	0.178803452214	-1.25307296958	-0.504810953171	-0.0260708815771	0.569667676386	0.813312904053	0.313507882506	-0.107580099828	0.38032922461	0.0195861060919	-0.00356482367727	0.482954681872	0.0918910367628	0.598384054877	-27.5145833397	31.8430568811	-1.7908966811
3	0.55783525215	-0.203198126651	-0.295930231478	0.586959387964	-0.529563630371	0.954678455175	-0.298305278661	-0.113590870542	-0.609754394931	0.37838906203	0.691431359263	0.771428051306	-0.305592158796	-0.510260223009	0.30140304936	0.906984051875	0.155424705237	0.471341537035	0.896776067605	0.509558344694	1.0619898914	-33.3024780828	30.679991719	5.83235215033
4	3.62318834574	-0.0498172997985	-0.693819680622	1.83190645428	1.66630248109	2.72684367717	-0.510907938889	-0.326119520084	-0.545203852136	1.48959162251	0.291466710391	0.778849320248	0.0835697705799	0.311575239457	0.153884889865	0.49686036606	0.0071824252882	0.10962215715	0.612198431777	0.156386288051	0.468838946726	-24.3322122154	41.1803355423	7.35812457951
5	4.39047730324	-0.694163175018	0.380601694672	3.53585733359	0.576887523769	3.44419043982	-0.293222565933	0.0802139389724	0.306037101259	-0.236363095771	0.188665400459	0.0826826551658	-0.106409794724	0.342887535647	0.0916994251471	0.236828810697	-0.0675267764301	-0.0324479723927	0.497151372359	0.125099390098	0.338929611094	-25.3597386107	47.6820306702	-4.96270285645
6	2.82508854358	-0.242404491923	-1.07410819911	4.87564651785	0.748216743504	3.7563934014	0.0134143868283	0.22281369254	0.425455796925	-0.713662330372	0.210246804221	0.0237374612443	-0.55683031488	0.0614130891441	-0.13435930441	0.414370495498	-0.104587644902	0.00838441859638	0.549731819223	0.163640455689	0.35677012111	-23.9113733038	53.224390434	-8.62835217241
7	6.18876639308	-1.68600997928	-0.740613831342	4.80198030787	1.18618505372	2.05639771981	0.377875585412	0.419429593152	1.54874396631	-1.26258704744	-0.162160143413	-0.462369685002	-0.705909789868	0.114498121626	-0.279779657765	0.612549144724	-0.118399959295	0.132926523168	0.610209336075	0.219206815801	0.614856432888	-22.2695261134	57.1476764273	-12.418533733
8	6.74335344938	3.30842708103	0.792718303952	7.88898970392	0.185105388285	5.16902987872	0.544737034886	1.03876180986	-0.736615934492	0.336169383057	0.0456783080665	-0.66926804711	0.342895121794	0.581270775871	-0.444376206061	0.362603359501	0.036424001001	0.0404201895338	0.61192006473	0.0189092902671	0.579461162812	7.42171449688	26.3678949864	-1.57365114996
9	5.96159403831	-0.415243723654	-0.436575661032	2.05187272743	0.158836483002	3.94992141278	0.370196175892	1.02686432524	-0.682709290233	-0.56552351789	-0.342669122948	-0.505685176176	0.470519370652	-0.541139895079	-0.00699167391769	0.376308172319	0.0754482215389	0.104580734772	0.717959297538	-0.0160284171428	0.499210878819	0.65009134357	30.7418953423	-6.23622601575
10	4.19821794162	-4.62523156492	-2.65305618421	6.17210936445	3.74990484783	2.3127488556	0.507659430293	1.75170169108	-0.320047378835	-1.1227201833	-0.855566590277	-0.310269649326	-0.232268402187	-0.346738734984	-0.444837255876	0.598978674597	0.435275819256	0.377259820562	1.23580022977	0.231322591364	0.674393270952	5.26081228497	35.5282434518	-13.310680567
11	1.53030317724	-0.000338245958022	0.576396093994	2.39775602756	-0.816716441634	1.73349337627	0.213597322844	1.1035925065	0.475403169078	-0.444740204799	-0.33862983048	-0.476699713991	-0.473743410198	-0.417995955162	-0.305205316822	0.346493656548	0.204458259159	0.173889688444	0.985014896947	0.0941860963196	0.555804220756	-3.9678656904	43.655075939	-4.60547950453
12	2.72840117254	-0.331213099573	-0.486599819271	2.21770032205	-0.0505457789696	2.73006724626	0.317392336676	-0.201132576921	0.271500582982	-0.00829152837989	-0.269326981103	-0.557799384263	-0.0931725271667	-0.011123777025	-0.0439247321129	0.269830976782	0.000577506027574	0.0345297932148	0.52784509805	0.0374707390291	0.520323632818	-0.450852347279	39.0174785035	7.50394542632
13	3.9931055236	0.0749045770865	-0.542226852485	3.69449627176	1.13183939755	5.459497032	0.0688522585888	-0.191898012416	0.270473627923	0.308174118129	-0.028630486475	-0.299780080894	0.0668935590462	0.177637352006	-0.0216772501913	0.292519350668	-0.00582723809683	-0.00363390896014	0.620393542683	0.015998268349	0.437013514688	-0.670858792715	40.1353878521	14.5640482746
14	4.91906874159	-0.208192697375	0.132269304801	3.36595861613	0.722549865157	4.68086550046	0.223582683947	-0.798194045158	0.545191992098	0.637155810214	-0.178836827451	-0.27360106316	0.438557197997	0.187852152878	-0.0968810942783	0.350050573782	-0.0820563881984	-0.00273520581338	0.610796156685	0.00727852990767	0.374505191601	-2.16144627656	39.3784507722	19.8169043193

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 9 )	A	A	1 - 9	1 - 9
2	2	chain 'A' and (resid 10 through 59 )	A	A	10 - 59	10 - 59
3	3	chain 'A' and (resid 60 through 70 )	A	A	60 - 70	60 - 70
4	4	chain 'A' and (resid 71 through 87 )	A	A	71 - 87	71 - 87
5	5	chain 'A' and (resid 88 through 108 )	A	A	88 - 108	88 - 108
6	6	chain 'A' and (resid 109 through 139 )	A	A	109 - 139	109 - 139
7	7	chain 'A' and (resid 140 through 168 )	A	A	140 - 168	140 - 168
8	8	chain 'B' and (resid 1 through 9 )	B	B	1 - 9	1 - 9
9	9	chain 'B' and (resid 10 through 59 )	B	B	10 - 59	10 - 59
10	10	chain 'B' and (resid 60 through 70 )	B	B	60 - 70	60 - 70
11	11	chain 'B' and (resid 71 through 87 )	B	B	71 - 87	71 - 87
12	12	chain 'B' and (resid 88 through 108 )	B	B	88 - 108	88 - 108
13	13	chain 'B' and (resid 109 through 139 )	B	B	109 - 139	109 - 139
14	14	chain 'B' and (resid 140 through 168 )	B	B	140 - 168	140 - 168

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