PDB-8ijo: Structure of DNA binding domain of McrBC endonuclease bound to DN...

ID or keywords:

Entry

Database: PDB / ID: 8ijo

Title

Structure of DNA binding domain of McrBC endonuclease bound to DNA: Y41F-L68F double mutant

Components

DNA (5'-D(*GP*AP*GP*AP*CP*CP*GP*GP*TP*AP*GP*C)-3')
DNA (5'-D(*GP*CP*TP*AP*CP*CP*GP*GP*TP*CP*TP*C)-3')
Type IV methyl-directed restriction enzyme EcoKMcrB subunit

Keywords

DNA BINDING PROTEIN / McrB-NTD / 5-methylcytosine / Restriction endonucleases

Function / homology

Function and homology information

restriction endodeoxyribonuclease activity / endonuclease complex / double-stranded methylated DNA binding / hemi-methylated DNA-binding / Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters / DNA restriction-modification system / DNA catabolic process / endonuclease activity / GTPase activity / GTP binding ...
Similarity search - Function

Biological species

Escherichia coli K-12 (bacteria)
DNA molecule (others)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.65 Å

Authors

Adhav, V.A. / Saikrishnan, K.

Funding support

1items

Citation

Journal: To Be Published
Title: Structural basis of target recognition by the DNA binding domain of McrBC
Authors: Adhav, V.A. / Saikrishnan, K.

History

Deposition	Feb 27, 2023	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Feb 28, 2024	Provider: repository / Type: Initial release

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8ijo.cif.gz	240.6 KB	Display	PDBx/mmCIF format
PDB format	pdb8ijo.ent.gz	158.8 KB	Display	PDB format
PDBx/mmJSON format	8ijo.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ijo_validation.pdf.gz	1.2 MB	Display	wwPDB validaton report
Full document	8ijo_full_validation.pdf.gz	1.2 MB	Display
Data in XML	8ijo_validation.xml.gz	18 KB	Display
Data in CIF	8ijo_validation.cif.gz	27 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ij/8ijo ftp://data.pdbj.org/pub/pdb/validation_reports/ij/8ijo	HTTPS FTP

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Related structure data

Related structure data	8ijpC 8ik4C 8ik8C 8ikdC 3sseS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	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
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PDB pages

PDBj /

wwPDB /

NCBI

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Deposited unit

A: Type IV methyl-directed restriction enzyme EcoKMcrB subunit

B: Type IV methyl-directed restriction enzyme EcoKMcrB subunit

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

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

hetero molecules

47.7 kDa, 4 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)	36.149, 68.899, 143.329
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

#1: Protein	Type IV methyl-directed restriction enzyme EcoKMcrB subunit / EcoKMcrBC / 5-methylcytosine-specific restriction enzyme B Mass: 19677.938 Da / Num. of mol.: 2 / Mutation: Y41F,L68F Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Strain: K12 / Gene: mcrB, rglB, b4346, JW5871 / Production host: Escherichia coli BL21 (bacteria) References: UniProt: P15005, Hydrolases; Acting on ester bonds; Endodeoxyribonucleases producing 5'-phosphomonoesters
#2: DNA chain	DNA (5'-D(GPAPGPAPCPCPGPGPTPAPGPC)-3') Mass: 4016.623 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#3: DNA chain	DNA (5'-D(GPCPTPAPCPCPGPGPTPCPTPC)-3') Mass: 3927.561 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) DNA molecule (others)
#4: Chemical	ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER Mass: 209.240 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₈H₁₉NO₅ / Feature type: SUBJECT OF INVESTIGATION / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 325 / Source method: isolated from a natural source / Formula: H₂O
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: 1.89 Å³/Da / Density % sol: 34.81 %
Crystal grow	Temperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5.5 / Details: 0.1-0.2 M Bis-Tris pH 5.5 and 12-24% PEG 4000

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å
Detector	Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 21, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.65→71.66 Å / Num. obs: 44144 / % possible obs: 100 % / Redundancy: 9.1 % / B_iso Wilson estimate: 21.71 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.085 / Net I/σ(I): 12.4
Reflection shell	Resolution: 1.65→1.68 Å / Redundancy: 8.5 % / R_merge(I) obs: 0.736 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 2123 / CC_1/2: 0.824 / % possible all: 100

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
MOSFLM		data reduction
Aimless		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3SSE

3sse

Resolution: 1.65→49.67 Å / SU ML: 0.1528 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 18.4237
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.194	4301	9.76 %
R_work	0.1568	39758	-
obs	0.1605	44059	99.95 %

Solvent computation

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

Displacement parameters

B_iso mean: 35.27 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→49.67 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2501	486	28	325	3340

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0123	3740
X-RAY DIFFRACTION	f_angle_d	1.1662	5282
X-RAY DIFFRACTION	f_chiral_restr	0.0719	555
X-RAY DIFFRACTION	f_plane_restr	0.0095	510
X-RAY DIFFRACTION	f_dihedral_angle_d	23.4994	836

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 (%)
1.65-1.67	0.2707	126	0.2243	1287	X-RAY DIFFRACTION	100
1.67-1.69	0.2725	157	0.2179	1293	X-RAY DIFFRACTION	99.93
1.69-1.71	0.2629	118	0.2091	1321	X-RAY DIFFRACTION	100
1.71-1.73	0.2267	141	0.2038	1329	X-RAY DIFFRACTION	99.93
1.73-1.75	0.2595	134	0.2003	1282	X-RAY DIFFRACTION	100
1.75-1.78	0.2498	143	0.2005	1308	X-RAY DIFFRACTION	100
1.78-1.8	0.2674	138	0.2284	1343	X-RAY DIFFRACTION	100
1.8-1.83	0.2467	148	0.2146	1270	X-RAY DIFFRACTION	100
1.83-1.86	0.2076	153	0.1861	1299	X-RAY DIFFRACTION	99.86
1.86-1.89	0.2152	128	0.1699	1330	X-RAY DIFFRACTION	99.93
1.89-1.92	0.2092	153	0.16	1315	X-RAY DIFFRACTION	99.86
1.92-1.96	0.1983	136	0.1568	1284	X-RAY DIFFRACTION	100
1.96-1.99	0.2055	179	0.1613	1297	X-RAY DIFFRACTION	100
1.99-2.03	0.1895	141	0.1592	1309	X-RAY DIFFRACTION	100
2.03-2.08	0.217	127	0.171	1318	X-RAY DIFFRACTION	100
2.08-2.13	0.2275	139	0.1687	1333	X-RAY DIFFRACTION	100
2.13-2.18	0.2037	141	0.1796	1294	X-RAY DIFFRACTION	100
2.18-2.24	0.192	152	0.1644	1323	X-RAY DIFFRACTION	99.93
2.24-2.31	0.1974	124	0.1512	1325	X-RAY DIFFRACTION	100
2.31-2.38	0.1978	148	0.1491	1340	X-RAY DIFFRACTION	100
2.38-2.46	0.1736	148	0.1555	1313	X-RAY DIFFRACTION	99.93
2.46-2.56	0.226	144	0.1614	1331	X-RAY DIFFRACTION	100
2.56-2.68	0.213	127	0.16	1345	X-RAY DIFFRACTION	100
2.68-2.82	0.1936	147	0.1543	1317	X-RAY DIFFRACTION	99.93
2.82-3	0.1771	142	0.1589	1365	X-RAY DIFFRACTION	100
3-3.23	0.1958	148	0.1512	1335	X-RAY DIFFRACTION	100
3.23-3.55	0.182	157	0.1375	1343	X-RAY DIFFRACTION	100
3.56-4.07	0.1432	142	0.1295	1380	X-RAY DIFFRACTION	100
4.07-5.12	0.1564	141	0.1177	1391	X-RAY DIFFRACTION	100
5.13-49.67	0.2058	179	0.1791	1438	X-RAY DIFFRACTION	99.2

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	6.38163429948	1.4446665061	-4.04294711733	3.06261902043	-2.8560974801	3.92971848046	-0.475846868355	1.3511132515	-0.831289868476	-1.21678420399	0.76247353488	-0.683717465205	0.379999963043	0.437958980613	-0.327091303208	0.416497510034	0.0532021101648	0.0879903305435	0.402821592317	-0.0982147677885	0.291614424885	24.4057374481	-3.51477453228	-29.1811825
2	5.63790933228	5.17347713973	-4.25084081783	4.73859106087	-3.92174391307	3.24621743352	-0.15847442353	1.25337119177	1.18987292325	-0.197378162436	0.26731323164	0.1743375352	-0.0365396098654	0.174769769276	-0.0226908742854	0.202972201634	-0.0145562476776	-0.0177364356524	0.328131045346	0.0860768713891	0.307727347187	26.4474568405	9.12240096344	-21.1500825766
3	6.6975037316	-0.979191685612	2.23926367353	2.77427254996	-0.816049721427	5.77378195071	0.0089773980589	0.228475116793	0.167045090785	-0.134385330964	-0.0889649866227	-0.0949133190733	-0.149100742716	0.30756155984	0.0737277718009	0.152351877504	-0.023132308039	0.0313028394296	0.126819763283	0.0156452595955	0.1484685048	18.5962245447	8.24996628617	-20.4323745943
4	4.83259945659	-1.72794902287	0.39208554005	2.02642290045	-1.44232579453	4.98740761773	0.137821928838	0.524383546097	-0.579156904641	-0.602960678583	-0.150864116609	0.102657240934	0.577138423656	0.216034981935	0.0136902039868	0.246447800899	-0.0291757768342	0.0133634796262	0.219961068654	-0.0694577428809	0.213733770799	10.180802731	-3.02847644239	-28.3952460797
5	4.83411005717	0.979393816122	0.506248311975	2.90890099504	-0.83875560107	3.24094488326	-0.357252341801	1.85527790498	-0.182112200284	-1.0474837653	0.639926112623	0.0774135858322	0.424161933744	0.107703652846	-0.063170275727	0.435877135183	-0.164810632048	-0.0192106092367	0.416554815339	-0.0222147638416	0.127614934517	14.1135878847	-1.88537800053	3.29016873752
6	3.65826242347	-0.829159037037	1.41601205722	2.46190117658	0.0214286399495	3.0375030598	-0.19318207979	-1.6054674598	-0.428767380727	0.525479390846	0.190226492263	-0.00353903723077	0.461403588069	-0.385596901153	-0.0703592730557	0.299039741297	0.0165782967584	-0.0171752833807	0.455065935558	0.163814447648	0.135500455694	14.1299318009	-1.8216109115	3.31061354466
7	5.39301963814	-3.79708330471	3.58082875941	8.61076025699	-4.20752793919	2.99136492076	-0.0453633594661	-0.0477805945122	0.144841382932	-0.0902274723616	0.153399219453	-0.0386825179876	-0.16039106403	0.354802842583	-0.0907811682829	0.170867930597	-0.0427067685032	-0.00671885170847	0.181058843361	-0.0111375728528	0.17284133497	26.0850055154	4.42720373001	26.6938210546
8	7.92774537685	-5.17584920339	5.68929557383	8.48536401565	-6.23859063912	8.68783694647	-0.000804440292131	0.434372705907	0.216626000108	0.0997771535314	-0.180835792989	-0.259667948737	-0.251387049077	0.563213863357	0.205066940773	0.186883259357	-0.0739935193827	0.0278270997454	0.317718032174	0.0153198875956	0.188125061072	27.4759292163	3.3120379724	17.0296428993
9	2.74593473838	-0.0899616980034	0.630242496249	3.39452012922	-0.558221457013	2.46314954494	-0.0320457467407	0.157303651302	-0.155442201801	-0.0911577151005	0.058319721096	-0.180973142248	0.272977776348	0.18250889884	-0.0298643837759	0.184089003811	0.0149056113448	0.00890200313708	0.111815551927	-0.0105692664974	0.114775492803	20.309961028	-5.46588064758	20.0198945095
10	4.87982249136	-0.189279092909	0.349525613492	5.85468275564	1.01407041347	4.22910528283	-0.0417980891192	-0.0664280533892	0.199536969867	0.135645888715	-0.00731044191501	-0.162795287287	-0.0898252410642	-0.21321574658	0.0352648484016	0.141243498796	0.00568884389678	-0.00589952433139	0.101032007166	0.0270490674351	0.0986923380352	12.5449601528	0.62741700637	26.0252943911
11	2.62200425335	-0.8641210812	0.767878919104	1.07193940236	-1.55914235401	2.40329866136	0.26610082089	0.631227443021	-0.596294963156	-0.216987054644	0.158950291722	0.68529348668	0.959613840926	-0.101393185247	-0.243050253479	0.45602503413	-0.0942014632463	-0.0100300033604	0.169046300943	-0.0504932966572	0.321800485176	8.75118146064	-13.5536053359	19.7505260927
12	7.5601732279	-1.70777054444	-0.135830337521	6.05894499623	-3.31900431376	5.47885221923	-0.274784570155	-0.797061375789	-1.13300358477	1.50517374131	0.58867082566	0.60972226205	0.317771460919	-0.426980799387	-0.309018450001	0.434649461381	-0.0274291341132	0.0049736638164	0.291400475304	0.133360008369	0.306659805222	4.14467257085	-10.6176536811	33.9572191725
13	5.93384498026	-5.57174813283	-5.82959876631	9.25877999743	5.84904094222	8.56134741433	0.110115760667	0.109957028331	0.171562499822	-0.0668015907467	-0.121337719624	0.297342060358	-0.0664868990739	-0.357060790667	0.0128369818496	0.108993733963	-0.0314265116292	-0.0323296761682	0.163645349736	0.0143742004188	0.162081215468	2.91321043983	2.30056188123	25.3227742554
14	6.95266058326	6.94561284482	5.24560887392	8.67971679563	5.65238556126	7.74352265042	0.140824133655	-0.390884987768	-0.0225113692107	0.528879207721	-0.126584195085	-0.0664146181653	0.0154948444213	-0.296604822412	-0.005950650442	0.147628756246	0.0416166684427	-0.0017792255737	0.133332245543	-0.00249239576197	0.168851137658	13.4336690823	4.52787631007	33.4203922579
15	4.41990885434	3.12028030297	0.727090023845	6.73877918843	0.89514883158	2.31271564915	0.103488725164	-0.0229708009632	-0.297460165056	0.144952759828	-0.0611508890088	-0.179919269145	0.462357034935	-0.0275376725218	-0.013379449728	0.254494565395	0.0431351614983	-0.00331518060179	0.125326441073	0.0342476079112	0.158882344797	17.3430368001	-11.7864786436	32.1643963447
16	8.87496307346	4.64811094027	5.52988436258	9.21510353434	4.5721583986	6.68914819727	-0.118902107467	0.514528753469	0.370006292246	-0.283657171531	0.0902148533557	0.296109330066	-0.25428972686	-0.454584341881	0.101937803604	0.158748137724	0.0511433362954	0.0193719617668	0.317558116297	0.0736996416333	0.187542758112	1.61091003077	8.77108858431	-18.946661795
17	4.1310325955	1.2708988634	2.08359915833	2.32814748777	1.5232839026	5.43328254095	0.0226643620835	-0.293181376004	-0.125746980508	0.0594470676026	0.0220784179409	0.0635755788714	0.202650024198	-0.472097554385	-0.0162012148087	0.159713309485	-0.0103128724862	0.00345793528336	0.187083906351	0.0479525607425	0.116200739846	5.25278859777	1.96442622338	-12.656346845
18	4.03229620721	0.529310677098	0.102020857321	5.48710077668	-0.470496211911	4.82257624308	0.154272369113	-0.257265585226	-0.34431034931	0.222391838198	-0.21319565782	0.0247345344905	0.196526243421	0.0926432347276	0.0849787319415	0.149400161545	0.00565246012445	-0.0291259711032	0.127793986859	0.0285146440017	0.13724342384	13.5373660891	-0.410283660729	-15.6745155213
19	5.05526009189	-1.29723585219	0.292885220855	6.0312292995	0.160506943176	4.7390577048	0.0413486387796	-0.266832335143	-0.565300989779	-0.0803509703486	-0.0485392709581	-0.387278887707	0.703393831299	0.262946655144	0.0490905161414	0.22033255244	0.0318865542416	-0.00188484200514	0.142146413563	0.0157975681156	0.219744049711	18.0353632797	-2.91408567215	-17.8178979465

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 'B' and (resid 93 through 101 )	B	B	93 - 101	93 - 101
2	2	chain 'B' and (resid 102 through 110 )	B	B	102 - 110	102 - 110
3	3	chain 'B' and (resid 111 through 133 )	B	B	111 - 133	111 - 133
4	4	chain 'B' and (resid 134 through 153 )	B	B	134 - 153	134 - 153
5	5	chain 'C' and (resid 2 through 13 )	C	C	2 - 13
6	6	chain 'D' and (resid 2 through 13 )	D	D	2 - 13
7	7	chain 'A' and (resid 2 through 17 )	A	A	2 - 17	1 - 16
8	8	chain 'A' and (resid 18 through 27 )	A	A	18 - 27	17 - 26
9	9	chain 'A' and (resid 28 through 62 )	A	A	28 - 62	27 - 61
10	10	chain 'A' and (resid 63 through 82 )	A	A	63 - 82	62 - 81
11	11	chain 'A' and (resid 83 through 92 )	A	A	83 - 92	82 - 91
12	12	chain 'A' and (resid 93 through 101 )	A	A	93 - 101	92 - 100
13	13	chain 'A' and (resid 102 through 120 )	A	A	102 - 120	101 - 119
14	14	chain 'A' and (resid 121 through 133 )	A	A	121 - 133	120 - 132
15	15	chain 'A' and (resid 134 through 160 )	A	A	134 - 160	133 - 159
16	16	chain 'B' and (resid 1 through 17 )	B	B	1 - 17	1 - 17
17	17	chain 'B' and (resid 18 through 53 )	B	B	18 - 53	18 - 53
18	18	chain 'B' and (resid 54 through 73 )	B	B	54 - 73	54 - 73
19	19	chain 'B' and (resid 74 through 92 )	B	B	74 - 92	74 - 92

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