PDB-7tz1: Crystal Structure of a Mycobacteriophage Cluster A2 Immunity Repr...

ID or keywords:

Entry

Database: PDB / ID: 7tz1

Title

Crystal Structure of a Mycobacteriophage Cluster A2 Immunity Repressor:DNA Complex

Components

DNA (5'-D(P*CP*CP*CP*GP*CP*TP*TP*GP*AP*CP*AP*GP*CP*CP*AP*CP*CP*GP*AP*AP*A)-3')
DNA (5'-D(P*TP*TP*TP*CP*GP*GP*TP*GP*GP*CP*TP*GP*TP*CP*AP*AP*GP*CP*GP*GP*G)-3')
Immunity repressor

Keywords

GENE REGULATION/DNA / Immunity repressor / helix-turn-helix motif / DNA binding protein / GENE REGULATION / GENE REGULATION-DNA complex

Function / homology

DNA / DNA (> 10) / Immunity repressor

Function and homology information

Biological species

Mycobacterium phage TipsytheTRex (virus)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.79 Å

Authors

McGinnis, R.J. / Brambley, C.A. / Stamey, B. / Green, W.C. / Gragg, K.N. / Cafferty, E.R. / Terwilliger, T.C. / Hammel, M. / Hollis, T.J. / Miller, J.M. ...

Funding support

United States, 1items

Citation

Journal: Nat Commun / Year: 2022
Title: A monomeric mycobacteriophage immunity repressor utilizes two domains to recognize an asymmetric DNA sequence.
Authors: McGinnis, R.J. / Brambley, C.A. / Stamey, B. / Green, W.C. / Gragg, K.N. / Cafferty, E.R. / Terwilliger, T.C. / Hammel, M. / Hollis, T.J. / Miller, J.M. / Gainey, M.D. / Wallen, J.R.

History

Deposition	Feb 15, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 20, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jul 27, 2022	Group: Database references / Category: citation / citation_author Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.identifier_ORCID / _citation_author.name

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7tz1.cif.gz	156.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7tz1.ent.gz	103.7 KB	Display	PDB format
PDBx/mmJSON format	7tz1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7tz1_validation.pdf.gz	447.7 KB	Display	wwPDB validaton report
Full document	7tz1_full_validation.pdf.gz	453.8 KB	Display
Data in XML	7tz1_validation.xml.gz	10.2 KB	Display
Data in CIF	7tz1_validation.cif.gz	13 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/tz/7tz1 ftp://data.pdbj.org/pub/pdb/validation_reports/tz/7tz1	HTTPS FTP

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Related structure data

Related structure data	7r6rC C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	SASBDB: SASDLS7associated SAS data

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Links

PDB pages	PDBj / wwPDB / NCBI
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: Immunity repressor

B: DNA (5'-D(P*TP*TP*TP*CP*GP*GP*TP*GP*GP*CP*TP*GP*TP*CP*AP*AP*GP*CP*GP*GP*G)-3')

C: DNA (5'-D(P*CP*CP*CP*GP*CP*TP*TP*GP*AP*CP*AP*GP*CP*CP*AP*CP*CP*GP*AP*AP*A)-3')

36.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software
Evidence: SAXS, SAXS and MALS confirm a monomer in solution

Unit cell

Length a, b, c (Å)	131.267, 44.170, 89.448
Angle α, β, γ (deg.)	90.000, 102.900, 90.000
Int Tables number	5
Space group name H-M	C121
Space group name Hall	C2y
Symmetry operation	#1: x,y,z #2: -x,y,-z #3: x+1/2,y+1/2,z #4: -x+1/2,y+1/2,-z

#1: Protein	Immunity repressor Mass: 23924.055 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium phage TipsytheTRex (virus) Gene: SEA_TIPSYTHETREX_75 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: A0A2D1GKF7
#2: DNA chain	DNA (5'-D(PTPTPTPCPGPGPTPGPGPCPTPGPTPCPAPAPGPCPGPGPG)-3') Mass: 6526.192 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source*: (synth.) Mycobacterium phage TipsytheTRex (virus)
#3: DNA chain	DNA (5'-D(PCPCPCPGPCPTPTPGPAPCPAPGPCPCPAPCPCPGPAPAPA)-3') Mass: 6362.128 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source*: (synth.) Mycobacterium phage TipsytheTRex (virus)
Has ligand of interest	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: 3.46 Å³/Da / Density % sol: 64.45 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop Details: 5-12% PEG 8,000, 0.1-0.3 M CaCl2, and 0.1M HEPES pH 7.5

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 0.97969 Å
Detector	Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 27, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97969 Å / Relative weight: 1
Reflection	Resolution: 2.79→46.83 Å / Num. obs: 10973 / % possible obs: 85.37 % / Redundancy: 1.9 % / B_iso Wilson estimate: 65.9 Å² / CC_1/2: 0.996 / CC star: 0.999 / Net I/σ(I): 11
Reflection shell	Resolution: 2.79→2.89 Å / Num. unique obs: 521 / CC_1/2: 0.739

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
HKL-3000		data reduction
HKL-3000		data scaling
AutoSol		phasing

Refinement

Method to determine structure:

SAD / Resolution: 2.79→46.83 Å / SU ML: 0.367 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.3491
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.2452	2067	10.18 %
R_work	0.1986	18233	-
obs	0.2033	10888	83.02 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 82.65 Å²

Refinement step

Cycle: LAST / Resolution: 2.79→46.83 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1396	861	0	0	2257

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0128	2394
X-RAY DIFFRACTION	f_angle_d	1.7762	3415
X-RAY DIFFRACTION	f_chiral_restr	0.0911	367
X-RAY DIFFRACTION	f_plane_restr	0.0111	292
X-RAY DIFFRACTION	f_dihedral_angle_d	30.8686	602

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 (%)
2.79-2.85	0.3683	62	0.3584	466	X-RAY DIFFRACTION	33.19
2.85-2.92	0.3337	77	0.3256	632	X-RAY DIFFRACTION	43.13
2.92-3	0.4666	84	0.3181	775	X-RAY DIFFRACTION	52.03
3-3.09	0.3079	111	0.29	868	X-RAY DIFFRACTION	61.07
3.09-3.19	0.2859	129	0.257	1142	X-RAY DIFFRACTION	78.36
3.19-3.3	0.2369	148	0.2349	1343	X-RAY DIFFRACTION	89.44
3.3-3.44	0.2526	161	0.2274	1388	X-RAY DIFFRACTION	95.97
3.44-3.59	0.2619	160	0.2158	1443	X-RAY DIFFRACTION	97.39
3.59-3.78	0.2365	162	0.2177	1421	X-RAY DIFFRACTION	99.25
3.78-4.02	0.2441	162	0.1752	1460	X-RAY DIFFRACTION	98.24
4.02-4.33	0.2148	163	0.1612	1458	X-RAY DIFFRACTION	99.2
4.33-4.76	0.2081	162	0.1741	1455	X-RAY DIFFRACTION	99.75
4.77-5.45	0.2036	161	0.1761	1462	X-RAY DIFFRACTION	99.63
5.45-6.86	0.2311	164	0.1921	1459	X-RAY DIFFRACTION	99.94
6.87-46.83	0.2688	161	0.1863	1461	X-RAY DIFFRACTION	98.9

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	2.3688275433	-0.163916973029	0.61269800334	0.731338175449	-0.131636101194	3.63193421781	0.142683185777	0.228382836359	-0.396347021327	0.256756510436	-0.668128626883	-0.447717677903	0.792009947991	0.476026209947	-0.648105243285	0.298389650817	0.0195632921648	-0.472704512053	0.63228946877	-0.113758593177	0.920939965259	47.519047024	2.91283988631	81.6008482133
2	1.80266072633	0.542699568148	1.33782671733	1.46935227439	-1.48707450595	4.21472176593	0.374446717017	0.113465760175	0.551974318391	0.2261877945	-0.20695226633	-0.0331158761671	-0.347089760355	0.308114893359	0.0925935622679	-0.0169222823857	0.0691513652273	-0.0491443496206	0.545556936061	0.123142760351	0.957193994552	48.4642333622	11.5271449271	81.7594492981
3	1.74002991653	0.960732230105	1.54409925192	2.28210974305	-0.108614121595	3.34003837699	0.560287755138	0.273116050213	-0.228417547432	-0.662745190592	-0.239374173266	-0.870259124935	0.275475686076	0.397651806912	-0.263235698398	0.383247152863	0.284843977009	-0.0194068844293	1.03742921036	-0.102528755599	0.657041099985	51.7261838642	7.35030801866	72.057798679
4	3.24131115198	0.0388097041015	1.79143484565	2.33202827841	-0.587726660485	4.32699962578	0.484837789447	-0.163357125019	-0.705530152974	-0.126472662697	-0.309725389123	0.387111761555	0.196687413738	0.428092668831	-0.368280205635	0.633050017617	0.195576866273	-0.106887991925	1.00887860044	-0.29746926908	0.639613956185	38.7633321124	4.14476726018	65.0980969674
5	3.08767505558	0.157427381425	1.68144982059	3.39323856707	-0.706705839444	2.94377257954	-0.132381327717	0.96788656502	0.634413583482	-0.342019459373	0.126167018266	-0.120270545575	-0.0540249735915	-0.120806106376	-0.0294162410418	0.521091643244	0.200327828263	-0.082377835551	1.25100635576	0.0580626317676	0.555143831933	36.7977573951	17.9736435221	57.0542294697
6	2.89628300006	-0.374956635235	1.42447306009	2.84754204587	-1.21538135739	3.41679870253	-0.141420502113	0.460205016609	-0.612945251067	-0.416416124892	0.591362554765	0.193881593211	0.553588211426	-0.442264865674	-0.307310727014	0.413650919088	0.030797132317	-0.163420306129	1.07497604148	-0.0943315106812	0.774122013248	28.127998114	9.2446814705	61.9630545752
7	0.195301511588	-0.506230646577	-0.526616844771	3.14032056216	3.33219585425	3.70791631899	-0.113195213877	0.0645015711507	-0.37174228278	-0.361308928807	0.0358707698891	0.171891563207	0.826969485295	-0.664002665543	-0.517152898806	1.00076119418	0.0176065784999	-0.320762825917	1.42151177679	0.191945214848	0.994509789306	23.5277350573	4.20523904438	70.2846267606
8	4.24816729752	0.296440420826	1.0088314749	3.54073964144	0.425020972147	3.23092039872	0.31496656785	0.331276260617	0.70688610975	-0.41265119693	0.39380198799	0.905609625891	0.296968665005	-1.08590959747	-0.237329949302	0.535135627652	0.0304978962142	-0.172324320301	1.14582330222	-0.0356239994963	0.932120441448	18.9191378561	12.4271526249	62.1194425161
9	4.22956255288	0.26247475235	0.128485461265	3.85334991588	0.400323171691	1.43259216624	0.140576231956	0.738630770233	0.186417417801	-1.1004556534	-0.348071723327	1.13129365362	0.0620352307286	-0.232232128383	-0.315118099658	0.772152073838	0.18179506142	-0.285211157911	1.73328111028	0.176407124433	0.722077922187	22.438184473	15.2671086799	49.4616935392
10	3.74538012974	0.0451078013994	1.68981921686	2.99008554342	-0.476484551846	4.28911414864	-0.316446162606	0.590783240175	0.51242615753	-0.583573880689	-0.0941045835316	0.184715839059	-0.371628242527	-0.426710752304	0.158847950136	0.8716503461	0.286045957573	-0.106092717424	1.35385915138	0.315488513153	0.847602319088	31.0612159659	25.8690747306	52.8245033302
11	2.70325108368	0.401800823289	0.965429693936	2.73460431093	1.72310828063	4.2765815855	0.351114641268	1.36731866942	-0.23970752407	-1.84884500251	0.176242221449	0.794484278882	0.290603899278	-0.23402018053	0.0795855427087	1.0554897957	0.141076723311	-0.435477070643	1.48922127516	0.0996881309898	0.804582448049	23.849269403	13.8244138971	46.0802061598
12	3.96406854636	0.774896177483	1.34751025316	3.36999831602	-0.86857417375	3.9359664725	-0.142801429611	1.53533718489	-0.697521972972	-1.37017410952	-0.14240157407	0.166917553071	0.71787798015	-0.255163413423	-0.50966156112	1.0810618779	0.264042338977	-0.258143261552	1.23531491938	-0.348159479392	0.716668717613	31.4353420551	9.12345169243	47.1498275324
13	2.99657086714	0.394676955546	2.02542479477	3.57410639444	-0.552424662916	4.57511608913	0.135355805052	0.624276882582	-1.11338987078	-0.651830230222	-0.216651367549	0.942682230023	0.886397430357	-0.849843103738	-0.467863125782	0.920830491129	-0.0683287421359	-0.426414018821	1.34920908877	-0.124698403063	0.964825685424	22.0275652489	2.13461659936	56.4045045396
14	6.69984855098	-0.848399520606	0.414638318193	3.7942687717	0.0414162008342	1.71982199208	-0.338400625559	-0.579813970154	0.235466024926	0.282285922482	-0.0361806054202	0.963644869553	-0.081706359817	-0.738555222487	-0.909601364022	0.33846122783	0.436993519778	0.0115244201382	1.2584208499	0.139612766024	1.40973919252	15.1443694823	22.5819745402	69.2510185853
15	6.89200491445	-2.27219155981	1.00669934715	2.3385323907	-0.708926566331	0.23222775313	-0.46381878015	0.274021684341	0.845590853434	0.516593225005	-0.126481392004	-0.776280854799	-0.831143903739	-0.383388299517	0.168729222369	0.50466778233	0.192274792811	-0.12893754049	0.91231336821	0.00133631601828	0.991768864423	33.2555019003	25.4480382143	70.3108903352
16	7.72383066122	-1.62373689486	-0.43124867416	3.53254093529	0.51356139202	3.93373810252	0.32963542534	0.58761195448	0.879375656603	-0.33759501339	-0.0677289443346	-1.05216530045	0.0416775847238	0.850728513999	0.176406639226	0.170648840861	0.274144945072	-0.182047706708	1.2346642832	-0.00319829952478	0.768613926955	47.5250591464	13.6518180147	67.9872731023
17	6.00584390005	-1.10224514586	1.70900615577	1.63943145683	-0.59307204167	1.81950806625	-0.249117121018	0.542381955814	0.197021393275	0.208456831882	-0.0415675728786	-0.998013420812	0.216930286699	0.725128994477	0.411294820333	0.435544921141	0.344521561789	-0.143017367862	1.56391721708	0.0587103630914	1.20279034195	66.5639886415	13.1389821751	71.2210347629
18	7.44069606218	-0.694722993571	1.42326405596	8.04863208144	-1.29558288083	0.445885725488	0.379761942084	1.52026670307	-0.306165696422	-1.14291981788	-0.276385744432	-1.22846825286	0.419705984405	0.751700572943	0.0253164875444	0.250747367705	0.331431087803	0.0206216974041	1.52532244655	-0.170671212552	1.17411914597	64.3767679638	5.99486284561	70.8741840401
19	4.19738850111	-0.44256561511	1.70942888381	2.12327751213	-0.50807276121	1.47598491828	0.0171252773347	0.426078989447	0.525360757461	-0.152379420162	-0.178340714225	-0.129125531142	-0.109627478859	0.169360794729	0.00801048086733	0.276160907285	0.247497218447	-0.115684622133	1.08612865458	0.0280061947357	0.811465384202	44.3616751997	18.8225066272	68.366821747
20	3.5123737821	-1.2858299556	0.65690815729	1.49705603766	-0.360650838277	0.27415586662	-0.128144852817	0.00828831892225	0.611909788687	0.0763956506835	0.122979837884	1.15428169283	-0.310270036046	-0.625703501067	-0.549046743574	0.369042303924	0.515982732475	-0.139234593769	1.31062115109	-0.108216011589	1.33342032264	18.595834731	28.5251252954	70.6178772336

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 15 through 33 )	A	A	15 - 33	1 - 19
2	2	chain 'A' and (resid 34 through 44 )	A	A	34 - 44	20 - 30
3	3	chain 'A' and (resid 45 through 55 )	A	A	45 - 55	31 - 41
4	4	chain 'A' and (resid 56 through 68 )	A	A	56 - 68	42 - 54
5	5	chain 'A' and (resid 69 through 80 )	A	A	69 - 80	55 - 66
6	6	chain 'A' and (resid 81 through 95 )	A	A	81 - 95	67 - 81
7	7	chain 'A' and (resid 96 through 102 )	A	A	96 - 102	82 - 88
8	8	chain 'A' and (resid 103 through 117 )	A	A	103 - 117	89 - 103
9	9	chain 'A' and (resid 118 through 125 )	A	A	118 - 125	104 - 111
10	10	chain 'A' and (resid 126 through 139 )	A	A	126 - 139	112 - 125
11	11	chain 'A' and (resid 140 through 149 )	A	A	140 - 149	126 - 135
12	12	chain 'A' and (resid 150 through 163 )	A	A	150 - 163	136 - 149
13	13	chain 'A' and (resid 164 through 181 )	A	A	164 - 181	150 - 167
14	14	chain 'B' and (resid 22 through 26 )	B	B	22 - 26
15	15	chain 'B' and (resid 27 through 31 )	B	B	27 - 31
16	16	chain 'B' and (resid 32 through 36 )	B	B	32 - 36
17	17	chain 'B' and (resid 37 through 42 )	B	B	37 - 42
18	18	chain 'C' and (resid 60 through 64 )	C	C	60 - 64
19	19	chain 'C' and (resid 65 through 74 )	C	C	65 - 74
20	20	chain 'C' and (resid 75 through 80 )	C	C	75 - 80

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