PDB-8ik8: Structure of DNA binding domain of McrBC endonuclease bound to DN...

ID or keywords:

Entry

Database: PDB / ID: 8ik8

Title

Structure of DNA binding domain of McrBC endonuclease bound to DNA: L68F 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 endonuclease

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 catabolic process / DNA restriction-modification system / 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: 1.8 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 28, 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	8ik8.cif.gz	212.1 KB	Display	PDBx/mmCIF format
PDB format	pdb8ik8.ent.gz	138.3 KB	Display	PDB format
PDBx/mmJSON format	8ik8.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ik8_validation.pdf.gz	471 KB	Display	wwPDB validaton report
Full document	8ik8_full_validation.pdf.gz	473.6 KB	Display
Data in XML	8ik8_validation.xml.gz	18.3 KB	Display
Data in CIF	8ik8_validation.cif.gz	27.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ik/8ik8 ftp://data.pdbj.org/pub/pdb/validation_reports/ik/8ik8	HTTPS FTP

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Related structure data

Related structure data	8ijoC 8ijpC 8ik4C 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

47.8 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)	74.662, 36.123, 142.805
Angle α, β, γ (deg.)	90.000, 98.633, 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

Components on special symmetry positions

ID	Model	Components
1	1	A-242- HOH

#1: Protein	Type IV methyl-directed restriction enzyme EcoKMcrB subunit / EcoKMcrBC / 5-methylcytosine-specific restriction enzyme B Mass: 19693.938 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli K-12 (bacteria) / 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 / Comment: pH buffer*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 336 / 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: 2.01 Å³/Da / Density % sol: 38.84 %
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 20, 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: 1.8→47.06 Å / Num. obs: 66256 / % possible obs: 99.4 % / Redundancy: 3.9 % / B_iso Wilson estimate: 23.95 Å² / CC_1/2: 0.995 / R_merge(I) obs: 0.086 / Net I/σ(I): 8
Reflection shell	Resolution: 1.8→1.84 Å / Redundancy: 3.4 % / R_merge(I) obs: 0.77 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1994 / CC_1/2: 0.71 / % possible all: 98.9

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Processing

Software

Name	Version	Classification
PHENIX	1.19.2_4158	refinement
XDS		data reduction
SCALA		data scaling
PHASER		phasing
Coot		model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3SSE

3sse

Resolution: 1.8→47.06 Å / SU ML: 0.1777 / Cross valid method: FREE R-VALUE / σ(F): 0.21 / Phase error: 26.0413
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.222	3281	4.96 %
R_work	0.1845	62908	-
obs	0.1863	66189	96.89 %

Solvent computation

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

Displacement parameters

B_iso mean: 41.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.8→47.06 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2493	486	28	336	3343

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0152	3142
X-RAY DIFFRACTION	f_angle_d	1.341	4358
X-RAY DIFFRACTION	f_chiral_restr	0.0804	449
X-RAY DIFFRACTION	f_plane_restr	0.0108	471
X-RAY DIFFRACTION	f_dihedral_angle_d	20.0276	590

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 (%)
1.8-1.83	0.321	173	0.2984	2519	X-RAY DIFFRACTION	92.99
1.83-1.86	0.3833	175	0.2953	2552	X-RAY DIFFRACTION	92.63
1.86-1.89	0.353	138	0.2983	2690	X-RAY DIFFRACTION	91.23
1.89-1.92	0.3667	146	0.278	2533	X-RAY DIFFRACTION	92.76
1.92-1.95	0.291	133	0.2724	2676	X-RAY DIFFRACTION	95.74
1.95-1.99	0.3123	126	0.263	2788	X-RAY DIFFRACTION	95.42
1.99-2.03	0.2715	141	0.2313	2667	X-RAY DIFFRACTION	96.46
2.03-2.08	0.2739	156	0.2487	2734	X-RAY DIFFRACTION	95.6
2.08-2.12	0.2546	131	0.2187	2723	X-RAY DIFFRACTION	96.61
2.12-2.18	0.2847	139	0.233	2712	X-RAY DIFFRACTION	96.68
2.18-2.24	0.2679	161	0.2032	2720	X-RAY DIFFRACTION	98.23
2.24-2.3	0.3096	140	0.2158	2838	X-RAY DIFFRACTION	98.25
2.3-2.38	0.2433	178	0.1971	2717	X-RAY DIFFRACTION	99.04
2.38-2.46	0.2522	154	0.2036	2796	X-RAY DIFFRACTION	98.4
2.46-2.56	0.2219	134	0.1957	2829	X-RAY DIFFRACTION	98.93
2.56-2.68	0.1767	126	0.2041	2769	X-RAY DIFFRACTION	99.28
2.68-2.82	0.2644	120	0.2009	2868	X-RAY DIFFRACTION	99.14
2.82-2.99	0.2573	130	0.1861	2850	X-RAY DIFFRACTION	98.87
2.99-3.22	0.2027	137	0.1728	2761	X-RAY DIFFRACTION	98.77
3.22-3.55	0.1658	140	0.1488	2769	X-RAY DIFFRACTION	98.44
3.55-4.06	0.1838	147	0.1338	2791	X-RAY DIFFRACTION	97.84
4.06-5.12	0.1546	122	0.1318	2832	X-RAY DIFFRACTION	98.66
5.12-47.06	0.1735	134	0.1685	2774	X-RAY DIFFRACTION	98.81

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	2.92863244561	0.334179957609	-0.0203271273013	1.03376538571	1.34345553721	5.09613660386	0.0424251606021	0.262843008659	0.142870684749	-0.148463767577	0.058273754485	0.41956855032	0.118284902883	0.445605700988	0.147094602526	1.26873611039	-0.0284204774463	-0.0947548329278	0.411083211708	-0.0919365330918	-0.0490338030157	1.37934585233	-10.9889426926	5.60102591483
2	5.52553857149	0.415309987705	1.34508451106	0.125573438399	0.519139302978	1.94832364436	0.296248983723	0.750782182342	-0.421902595664	-1.10294647113	-0.0376151582126	-0.336253040503	0.402595820771	0.389700597096	-0.197657436408	0.853178045414	0.046582029367	-4.04549209868E-5	0.333463390618	-0.0261356257934	0.251625879364	11.3240377768	-7.68277891402	36.8438754884
3	5.00665633645	0.346147627844	-0.0558250068734	5.98171350943	3.9034200673	6.37660110986	-0.177590583375	0.0320009322633	-0.159844547049	0.011701355834	0.22202477209	-0.674933847803	-0.36939674886	1.09242725862	-0.102509182869	0.62016086625	-0.0448162915582	-0.0710559441875	0.345105602942	0.0263760998536	0.249213222676	10.6530594066	-3.83212216544	35.3660104809
4	5.34456241	2.04081066143	0.907069962267	8.4199036843	0.966492620329	8.43955261854	0.0828367166656	-0.459352201472	-0.130689455373	0.265834367125	-0.163551284502	-0.0819286777516	-0.614458655369	-0.210817846046	0.0551534817034	0.210461742394	0.0259573078851	0.0287490542045	0.149696189408	0.0187152229839	0.180492783321	11.3216257258	7.31113445503	61.1012879893
5	5.80276564755	0.973958262829	5.09802493383	2.21272315294	2.36737720449	7.84760105906	-0.494932633439	0.00923238806051	0.429727951555	-0.429768486229	0.0744883198719	0.704679402779	-0.899173016876	-0.399691872373	0.414963688934	0.453987634507	0.0258880263079	-0.0215088222843	0.23852742432	0.0176935258949	0.251801935164	8.29268218317	7.60649288914	50.8362360071
6	1.29635164061	0.224174100162	0.580831244244	2.01253669897	0.922312243245	1.71345429933	-0.0544897097998	0.182231185973	0.259472765648	-0.319751787627	-0.052123429348	-0.262203395718	-0.131117584183	0.431583871448	0.0607360839128	0.208597871999	-0.0161221833588	0.0427876269016	0.231827454782	0.0511803858644	0.187206059016	18.7126533346	1.17275601746	51.9406425473
7	6.52434175437	1.25565007575	-0.724185866963	3.92480790899	-0.00260556133426	3.14462800527	-0.0580305853814	-0.0373047173686	0.0808373673168	-0.214682495691	0.0543101753922	0.00699903824486	0.0933550659797	-0.0128722048454	-0.000385183458564	0.150400830045	0.00822747723754	0.0108464166183	0.134832564114	0.00959296381645	0.104612367919	13.1267819795	-6.01898662711	57.3096706301
8	2.06668843353	-0.613757855457	0.647353895771	2.4815881899	-0.115311942798	1.76663013454	0.0432671042093	0.233091912878	-0.125540408318	-0.471077608586	-0.141046956494	-0.299742583622	0.190242987815	0.503997325647	0.0339606152658	0.197417318612	0.0158118793412	0.0690277314457	0.283465951928	0.0250756243063	0.235531357937	21.5582780942	-9.04737143118	55.1605961857
9	3.44202056188	3.73742089841	0.519717739356	5.90041690716	0.90825952957	1.73504955035	-0.0654401698645	-0.371011807661	0.0277623914222	0.0962366550074	-0.413712884987	-1.62435571771	-0.180296699902	0.954530548404	0.202219182959	0.345731737188	-0.0187867102573	-0.0497266272122	0.426514261738	0.0676055082736	0.51542907034	27.3785470735	-14.6709376392	64.7042774684
10	4.79773906972	2.96231989164	-1.77486492915	6.87901347911	-3.67591747	2.49798231836	-0.0052298434878	0.142995218234	-0.0581882107133	-0.259273713612	0.113729861297	-0.0593141521214	0.552439449007	0.148604797241	-0.0630019177682	0.29606398041	0.0075569998952	0.0271717457344	0.122502757429	-0.00386437093368	0.167487105077	12.4607032536	-16.0536797001	58.7777814539
11	7.37295088021	-2.120371017	0.760801484503	5.24912988484	-0.583605601294	2.64839349447	-0.225036864062	-0.287393724032	-0.126865920415	0.581290482182	0.152924634272	0.357668414752	-0.201275343735	-0.229201685462	0.133627016626	0.255703998706	-0.0198783267261	0.0606705892738	0.186172781183	0.0183682319749	0.147157758958	11.0680118985	-6.00641311877	67.0634688462
12	2.76065319162	0.355091253927	-0.739361179239	3.69271270977	0.15961815536	4.35955894047	-0.0762939628532	0.106340302635	0.327057151148	0.00571424606215	0.109026616828	-0.750404932361	-0.0613291022333	0.704383219206	-0.0577971224339	0.25153971708	-0.0514040551253	-0.0202277763818	0.304176432833	0.0388317029814	0.334238328393	26.505297596	0.840094154738	64.1080633988
13	3.18887620845	1.8139299774	1.83868155684	3.02474559751	3.58583635233	4.62024405999	0.165575015339	0.419503186035	-0.251492432204	-0.399271952487	-0.0127296241238	0.564545449975	0.373485641052	-0.186721490004	0.734986090986	1.05088579546	-0.106735259107	-0.19737555487	0.30191015798	0.0245589437997	0.288747459365	-5.99103992999	-18.2367978466	18.2941665995
14	1.8914597274	1.05759631834	1.49408149999	1.58422927972	0.148274504559	2.57085921363	0.287972917355	0.131454588343	-0.304780390358	-0.33835306856	-0.0687517352618	-0.219495053506	0.690663736411	0.340331936025	-0.0584023081428	0.870385746747	0.0370280157687	-0.0979983739621	0.262653025768	-0.00715770085743	0.253298679526	2.56849164131	-15.1596870542	21.8565372249
15	5.32712497786	-1.1440627501	0.524981932284	2.05046653602	-0.435378458424	3.78865217879	-0.0443278006937	0.503527187136	0.110490553052	-0.433502502429	-0.00277202100274	-0.153905180318	-0.340434377144	0.460001125857	0.0302437354405	0.771019847364	-0.107353612973	-0.0566275321054	0.320672189202	-0.00987344719962	0.197145965775	4.44060907869	-3.49660745401	14.7953817669
16	1.88944658686	1.62680983465	0.256236662064	6.49507683974	-0.379085909236	0.484908746072	-0.33829799528	0.0118209879608	0.662912281821	-0.145608061318	-0.186521403303	0.756865787323	-0.332382434221	-0.194103413775	-0.582345124233	1.10003062375	-0.0699672624065	-0.163983029492	0.125838734497	0.0285230193917	0.364095548799	-3.21970714695	4.49710441168	18.5298933181
17	4.31336950973	-0.0144477553376	-4.79862587422	2.87234285414	-1.97170569453	6.77382828328	-0.379385072289	0.49458058473	-0.345125216465	-0.361785673301	-0.0273144035088	0.791826655871	0.44444891275	-0.677216640341	-0.672770952102	1.09977853976	-0.0793298695503	-0.23035532602	0.389599574837	0.0164352441109	0.245446866843	-9.14186213478	-5.51630149494	12.5184115676

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 134 through 152 )	B	B	134 - 152	132 - 150
2	2	chain 'C' and (resid 2 through 13 )	C	C	2 - 13
3	3	chain 'D' and (resid 2 through 13 )	D	D	2 - 13
4	4	chain 'A' and (resid 1 through 17 )	A	A	1 - 17	1 - 17
5	5	chain 'A' and (resid 18 through 27 )	A	A	18 - 27	18 - 27
6	6	chain 'A' and (resid 28 through 62 )	A	A	28 - 62	28 - 62
7	7	chain 'A' and (resid 63 through 73 )	A	A	63 - 73	63 - 73
8	8	chain 'A' and (resid 74 through 92 )	A	A	74 - 92	74 - 92
9	9	chain 'A' and (resid 93 through 101 )	A	A	93 - 101	93 - 101
10	10	chain 'A' and (resid 102 through 120 )	A	A	102 - 120	102 - 120
11	11	chain 'A' and (resid 121 through 133 )	A	A	121 - 133	121 - 133
12	12	chain 'A' and (resid 134 through 158 )	A	A	134 - 158	134 - 158
13	13	chain 'B' and (resid 2 through 17 )	B	B	2 - 17	1 - 16
14	14	chain 'B' and (resid 18 through 53 )	B	B	18 - 53	17 - 52
15	15	chain 'B' and (resid 54 through 101 )	B	B	54 - 101	53 - 99
16	16	chain 'B' and (resid 102 through 120 )	B	B	102 - 120	100 - 118
17	17	chain 'B' and (resid 121 through 133 )	B	B	121 - 133	119 - 131

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