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

ID or keywords:

Entry

Database: PDB / ID: 8syj

Title

Structure of apurinic/apyrimidinic DNA lyase TK0353 from Thermococcus kodakarensis (Iodide crystal form)

Components

TK0353

Keywords

LYASE / apurinic/apyrimidinic DNA lyase DNA binding protein

Function / homology

IODIDE ION / Uncharacterized protein

Function and homology information

Biological species

Thermococcus kodakarensis (archaea)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 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	May 25, 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sy/8syj ftp://data.pdbj.org/pub/pdb/validation_reports/sy/8syj	HTTPS FTP

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Related structure data

Related structure data	8gm6C 8gm7C 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

C: TK0353

D: TK0353

hetero molecules

86.2 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: TK0353

hetero molecules

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

2

B: TK0353

hetero molecules

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

3

C: TK0353

hetero molecules

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

4

D: TK0353

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.554, 89.116, 128.043
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁
Space group name Hall	P2ac2ab
Symmetry operation	#1: x,y,z #2: x+1/2,-y+1/2,-z #3: -x,y+1/2,-z+1/2 #4: -x+1/2,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 2 through 4 or (resid 5...
d_2	ens_1	(chain "D" and (resid 2 through 39 or resid 41...
d_1	ens_2	(chain "B" and (resid 1 through 36 or (resid 37...
d_2	ens_2	(chain "C" and ((resid 1 and (name N or name...

NCS domain segments:

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
d_1	1	ens_1	TYR	TYR	LEU	LEU	A	A	2 - 39	2 - 39
d_1	2	ens_1	TYR	TYR	SER	SER	A	A	41 - 49	41 - 49
d_1	3	ens_1	GLU	GLU	GLU	GLU	A	A	51 - 57	51 - 57
d_1	4	ens_1	THR	THR	ASN	ASN	A	A	59 - 77	59 - 77
d_1	5	ens_1	VAL	VAL	ALA	ALA	A	A	79 - 124	79 - 124
d_1	6	ens_1	LEU	LEU	GLU	GLU	A	A	126 - 167	126 - 167
d_1	7	ens_1	ARG	ARG	ARG	ARG	A	A	169	169
d_2	1	ens_1	TYR	TYR	LEU	LEU	D	D	2 - 39	2 - 39
d_2	2	ens_1	TYR	TYR	SER	SER	D	D	41 - 49	41 - 49
d_2	3	ens_1	GLU	GLU	GLU	GLU	D	D	51 - 57	51 - 57
d_2	4	ens_1	THR	THR	ASN	ASN	D	D	59 - 77	59 - 77
d_2	5	ens_1	VAL	VAL	ALA	ALA	D	D	79 - 124	79 - 124
d_2	6	ens_1	LEU	LEU	GLU	GLU	D	D	126 - 167	126 - 167
d_2	7	ens_1	ARG	ARG	ARG	ARG	D	D	169	169
d_1	1	ens_2	MET	MET	LEU	LEU	B	B	1 - 39	1 - 39
d_1	2	ens_2	TYR	TYR	ASN	ASN	B	B	41 - 77	41 - 77
d_1	3	ens_2	VAL	VAL	VAL	VAL	B	B	79 - 165	79 - 165
d_2	1	ens_2	MET	MET	LEU	LEU	C	C	1 - 39	1 - 39
d_2	2	ens_2	TYR	TYR	ASN	ASN	C	C	41 - 77	41 - 77
d_2	3	ens_2	VAL	VAL	VAL	VAL	C	C	79 - 165	79 - 165

NCS ensembles :

ID
ens_1
ens_2

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.232097621803, -0.750721033615, -0.618505152477), (0.970060325612, 0.131900012253, 0.203924867146), (-0.0715098498532, -0.647317786296, 0.758858369473)	-45.2101485676, 74.6468310319, 2.20623681322
2	given	(0.205231197001, -0.761701479784, -0.614565709645), (-0.973885358094, -0.0966417322116, -0.205445089707), (0.0970951341061, 0.640680287889, -0.761643816783)	-46.5328081055, -75.3098849246, -6.4324672629

#1: Protein	TK0353 Mass: 19643.920 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Thermococcus kodakarensis (archaea) / Gene: TK0353 / Production host: Escherichia coli (E. coli) / References: UniProt: Q5JCX2
#2: Chemical	... ChemComp-IOD / IODIDE ION / Iodide Mass: 126.904 Da / Num. of mol.: 46 / Source method: obtained synthetically / Formula: I
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: SO₄
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 150 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.3 Å³/Da / Density % sol: 46.57 %
Crystal grow	Temperature: 297 K / Method: vapor diffusion, hanging drop Details: 2.5 M ammonium sulfate cryoprotected by inclusion of 1.5 M lithium sulfate and soaked in the presence of 0.1 M sodium iodide

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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: 1.28 Å
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 20, 2018
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.28 Å / Relative weight: 1
Reflection	Resolution: 2.2→40 Å / Num. obs: 70908 / % possible obs: 99.8 % / Redundancy: 6.1 % / B_iso Wilson estimate: 42.98 Å² / CC_1/2: 0.997 / R_merge(I) obs: 0.127 / R_pim(I) all: 0.051 / Net I/σ(I): 8.2
Reflection shell	Resolution: 2.2→2.27 Å / R_merge(I) obs: 1.27 / Mean I/σ(I) obs: 1.6 / Num. unique obs: 6310 / CC_1/2: 0.809 / R_pim(I) all: 0.561

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Processing

Software

Name	Version	Classification
PHENIX	1.20.1_4487	refinement
DIALS	2.2.5	data reduction
DIALS	2.2.5	data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.2→38.49 Å / SU ML: 0.3527 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.4735
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.26	7072	9.97 %
R_work	0.2253	63836	-
obs	0.2288	70908	99.59 %

Solvent computation

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

Displacement parameters

B_iso mean: 55.29 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→38.49 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5151	0	151	150	5452

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0063	5414
X-RAY DIFFRACTION	f_angle_d	0.9039	7325
X-RAY DIFFRACTION	f_chiral_restr	0.0534	805
X-RAY DIFFRACTION	f_plane_restr	0.0076	936
X-RAY DIFFRACTION	f_dihedral_angle_d	13.3491	2035

Refine LS restraints NCS

Ens-ID	Dom-ID	Asym-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	A	X-RAY DIFFRACTION	Torsion NCS	0.460538417356
ens_2	d_2	B	B	X-RAY DIFFRACTION	Torsion NCS	0.62293233735

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 (%)
2.2-2.23	0.3939	261	0.3776	2025	X-RAY DIFFRACTION	95.69
2.23-2.25	0.3306	180	0.3575	2116	X-RAY DIFFRACTION	98.97
2.25-2.28	0.3934	269	0.3276	2169	X-RAY DIFFRACTION	99.15
2.28-2.31	0.3592	229	0.3202	2092	X-RAY DIFFRACTION	99.83
2.31-2.34	0.4033	246	0.3217	2163	X-RAY DIFFRACTION	100
2.34-2.37	0.3417	252	0.3003	2081	X-RAY DIFFRACTION	99.66
2.37-2.41	0.3238	229	0.2998	2140	X-RAY DIFFRACTION	99.79
2.41-2.44	0.3282	230	0.2932	2162	X-RAY DIFFRACTION	99.58
2.44-2.48	0.3191	217	0.2955	2126	X-RAY DIFFRACTION	99.79
2.48-2.52	0.3303	259	0.2867	2086	X-RAY DIFFRACTION	99.36
2.52-2.56	0.3209	207	0.2803	2158	X-RAY DIFFRACTION	99.45
2.56-2.61	0.2871	247	0.2933	2122	X-RAY DIFFRACTION	99.79
2.61-2.66	0.3462	240	0.2814	2116	X-RAY DIFFRACTION	99.92
2.66-2.71	0.3617	248	0.2853	2146	X-RAY DIFFRACTION	99.83
2.71-2.77	0.3523	205	0.2891	2162	X-RAY DIFFRACTION	99.66
2.77-2.84	0.3439	227	0.2786	2108	X-RAY DIFFRACTION	99.62
2.84-2.91	0.3043	259	0.2686	2139	X-RAY DIFFRACTION	99.92
2.91-2.99	0.2744	233	0.2452	2121	X-RAY DIFFRACTION	99.87
2.99-3.08	0.2651	222	0.2434	2149	X-RAY DIFFRACTION	99.96
3.08-3.17	0.2837	245	0.2279	2155	X-RAY DIFFRACTION	100
3.17-3.29	0.2981	239	0.2332	2122	X-RAY DIFFRACTION	100
3.29-3.42	0.2225	227	0.2277	2146	X-RAY DIFFRACTION	99.92
3.42-3.57	0.2578	245	0.2047	2126	X-RAY DIFFRACTION	99.79
3.58-3.76	0.2219	259	0.1767	2108	X-RAY DIFFRACTION	100
3.76-4	0.2254	197	0.1703	2183	X-RAY DIFFRACTION	100
4-4.31	0.1804	267	0.1593	2087	X-RAY DIFFRACTION	99.96
4.31-4.74	0.2031	217	0.1572	2160	X-RAY DIFFRACTION	99.66
4.74-5.42	0.2098	256	0.1814	2107	X-RAY DIFFRACTION	99.66
5.42-6.82	0.225	225	0.2299	2140	X-RAY DIFFRACTION	99.96
6.83-38.49	0.247	235	0.2241	2121	X-RAY DIFFRACTION	99.24

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	1.68301480971	-0.14866408071	-0.546276970067	4.40513569656	-1.57806740005	2.65002076283	0.121377020761	0.124479258032	-0.34839702618	-0.423277773455	0.131616074317	0.0693921659277	0.147319126002	0.286938807367	-1.24881277196E-5	0.324477949323	0.0677266770472	-0.0982970396358	0.347445064794	-0.143568360438	0.436064740574	-60.921593274	-18.0217733489	-45.3923950915
2	0.304375280339	0.0594843125238	-0.0262255383328	0.0181470051138	0.0407823686856	0.252156340068	0.423775755184	-0.171535178512	-0.244948946139	-0.0206915468551	-0.117231805924	-0.174244112747	-0.275832903741	0.159703273561	0.000270633583397	0.31491481103	-0.0384034119253	-0.0104219543747	0.344062915505	0.00719056288964	0.402982931002	-51.4272405638	-6.24047164747	-27.4385519899
3	2.86222411632	0.0156194869271	0.234309536475	2.30790830897	2.36433640496	3.13757879957	0.0626078547565	-0.440707374581	-0.290622638316	0.0268497276537	0.288647807091	0.19648854618	-0.424576881614	-0.485625575528	0.0206408952896	0.267037280812	0.0251595882716	0.00422993009794	0.401111991432	0.0276743236166	0.329053900429	-63.5647504807	-4.55976951294	-30.0993486925
4	3.68607752503	0.177807791113	0.35251960213	1.13776436275	-0.454181683185	0.246634937667	0.409709393529	-0.866906087475	0.497064072587	-0.455694813268	-0.304201949342	-0.250115223147	-0.51202903564	-0.391854012182	-0.110514548042	0.52431156576	0.188786837794	-0.028646282762	0.666678063879	-0.22352727794	0.432442628552	-58.7986876807	0.518542576743	-18.3369923193
5	3.31632445289	-1.50139429903	0.0723509520585	3.25880602928	0.955987405848	2.54887525695	-0.157599360827	0.2237733331	0.173470728389	0.00240577449171	0.0243786727327	-0.246220329568	-0.233491651495	0.645375634664	-0.00446274509762	0.405610318342	-0.164684380476	0.00567894973078	0.347329218327	-0.039011622897	0.335146949632	-18.1701221635	3.9227796087	-16.8247325357
6	1.8363441139	0.0208586097794	-1.53639545485	0.519694854851	0.87735338538	2.82981627207	-0.0975453087606	-0.0654467004712	0.533043704263	0.138112387262	-0.0918017243458	0.388786989586	-1.30697672358	-0.787769932066	0.0606175287995	0.968696957074	0.135060529009	-0.110420327906	0.228495198914	-0.140070047725	0.537235347445	-35.3763419094	18.1272589788	-11.5205501795
7	1.65218009454	0.618827767869	0.571315002165	2.21981498871	0.67842520683	2.53841954564	0.0140072302411	-0.344619634206	0.189835203603	0.0457849772086	-0.235545979905	0.0317086413566	-0.603744946569	-1.00627274582	0.0140090105846	0.452906235816	0.0636786845571	-0.0614030828718	0.423556110337	-0.0841296424075	0.333875059379	-37.8176903823	6.2226026959	-12.4887156029
8	0.0881365125683	0.408781095633	-0.148138979941	1.89055510228	-0.67293565188	0.242071520253	-0.287515592014	-0.945174830675	0.403457455088	-0.79849122611	-0.63928901127	1.24024619242	-0.593566904934	-1.14644676552	0.122588703968	0.546806719773	0.271237435691	-0.236255645596	0.93676092391	-0.502637872173	0.757962095733	-48.5438033233	11.3446826029	-9.97808879646
9	4.18413586613	0.905442579636	0.561363856029	3.76942779239	1.69317401397	3.56902333104	0.0311855232419	-0.108627799953	0.0285281098216	0.0279654008709	0.0701347738981	-0.142214596536	0.510564285959	0.403391360875	0.00242923366778	0.42429554767	0.0655861777008	-0.0412494653739	0.265510497058	-0.0687436464096	0.293430464899	-17.6863140147	-4.78965601594	10.97252405
10	4.22187459321	-0.386312121617	1.88601555039	1.13703604141	0.185166139448	0.957295591965	0.452104099171	0.0353446491195	-0.947161113	0.255763436678	0.258173322836	-0.0270854369228	0.845421559114	-0.509745947973	0.54801443668	1.24252527226	-0.351128925407	0.0104435975111	0.52360862897	-0.0692430791836	0.650397378319	-35.328723491	-18.7383942176	5.90987556012
11	1.24565312091	-1.55605125799	-0.130461189296	2.22414175635	0.56416109272	0.60070671562	0.0498294588782	0.552834560981	-0.0637888989362	-0.0445864896803	-0.118805898466	0.239704880606	0.54920194829	-1.22841149889	0.00551089564089	0.522509662758	-0.286793612046	-0.0155359460974	0.713082292366	-0.0534783382103	0.359755640622	-37.3913311025	-6.79379526469	6.97446487112
12	1.39608178695	-1.16069442336	0.125467884094	2.92593224055	1.92715475242	2.11870475113	-0.140950982656	-0.613053919838	-0.266441231614	0.309664858069	-0.15235320229	0.773935740919	0.62245656991	-0.683589407213	0.0889748896996	0.589959581439	-0.407079167196	0.0326159406287	1.14270567273	-0.197142981424	0.643685549465	-48.4945437769	-11.5076286698	4.23937262942
13	2.34209229463	0.520172952348	-0.367657020044	2.75456537685	-0.348082625558	2.19785413487	-0.331252120636	0.118094489961	-0.714089464836	-0.360076096403	0.208264431543	-0.317952202205	0.873455447192	-0.340923312937	-0.0750006541028	0.542794216874	-0.141151158202	0.0741086172857	0.222674964627	-0.0223653903508	0.542269519535	-35.6846609804	-17.9084416656	-24.7958504653
14	0.0777865920882	-0.0874458612014	-0.0383756521465	0.133748597653	-0.111298090465	0.372967059639	0.367366596953	0.305018820551	-0.131161700563	-0.224550788528	0.0871837178498	-0.196016571247	0.528639653569	-0.63532672623	-0.00224394454274	0.406563900424	-0.134068335514	-0.00860339517462	0.608311576947	-0.0770171155273	0.390553710116	-44.5088650122	-6.12471015726	-42.5829893314
15	3.00423090636	0.456779586495	-0.00733375811672	1.23203361304	-1.6861273685	2.64271999572	-0.166062328029	0.749806503676	-0.1425025552	-0.113183899549	0.144270236681	-0.172908995107	0.129085267865	-0.00787559573526	-0.000466293704668	0.293325150598	-0.0441729326566	0.0292058900856	0.444385908659	-0.0629778887408	0.389641120184	-32.3944490533	-4.23116165429	-39.5753595102
16	0.761810899469	-0.475044242064	0.254437349401	0.28028603737	-0.127369721921	0.441321534442	0.0474096534484	0.935732954592	0.309560834444	0.131693616444	-0.126632787851	0.360128678	-0.291119992763	-0.102680862893	-0.00236876797965	0.468127072706	-0.173480304235	-0.0394064802923	0.966348548751	0.0867207741915	0.398326830383	-37.2072669335	0.798112502365	-51.2666657677

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 82 )	A	A	1 - 82	1 - 82
2	2	chain 'A' and (resid 83 through 96 )	A	A	83 - 96	83 - 96
3	3	chain 'A' and (resid 97 through 151 )	A	A	97 - 151	97 - 151
4	4	chain 'A' and (resid 152 through 169 )	A	A	152 - 169	152 - 169
5	5	chain 'B' and (resid 1 through 82 )	B	B	1 - 82	1 - 82
6	6	chain 'B' and (resid 83 through 96 )	B	B	83 - 96	83 - 96
7	7	chain 'B' and (resid 97 through 151 )	B	B	97 - 151	97 - 151
8	8	chain 'B' and (resid 152 through 165 )	B	B	152 - 165	152 - 165
9	9	chain 'C' and (resid 1 through 82 )	C	C	1 - 82	1 - 82
10	10	chain 'C' and (resid 83 through 96 )	C	C	83 - 96	83 - 96
11	11	chain 'C' and (resid 97 through 151 )	C	C	97 - 151	97 - 151
12	12	chain 'C' and (resid 152 through 165 )	C	C	152 - 165	152 - 165
13	13	chain 'D' and (resid 1 through 82 )	D	D	1 - 82	1 - 82
14	14	chain 'D' and (resid 83 through 96 )	D	D	83 - 96	83 - 96
15	15	chain 'D' and (resid 97 through 151 )	D	D	97 - 151	97 - 151
16	16	chain 'D' and (resid 152 through 169 )	D	D	152 - 169	152 - 169

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