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

ID or keywords:

Entry

Database: PDB / ID: 8ijp

Title

Structure of DNA binding domain of McrBC endonuclease bound to DNA: L68Y 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: 1.55 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	8ijp.cif.gz	240.8 KB	Display	PDBx/mmCIF format
PDB format	pdb8ijp.ent.gz	159 KB	Display	PDB format
PDBx/mmJSON format	8ijp.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8ijp_validation.pdf.gz	469.4 KB	Display	wwPDB validaton report
Full document	8ijp_full_validation.pdf.gz	471.8 KB	Display
Data in XML	8ijp_validation.xml.gz	18.1 KB	Display
Data in CIF	8ijp_validation.cif.gz	27.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ij/8ijp ftp://data.pdbj.org/pub/pdb/validation_reports/ij/8ijp	HTTPS FTP

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Related structure data

Related structure data	8ijoC 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
Related items in Molecule of the Month	#67 - Jul 2005 TATA-Binding Protein similarity (1) #168 - Dec 2013 DNA Helicase similarity (1) #255 - Mar 2021 Cisplatin and DNA similarity (1) #91 - Jul 2007 Thymine Dimers similarity (1) #122 - Feb 2010 Enhanceosome similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #181 - Jan 2015 Cascade and CRISPR similarity (1) #253 - Jan 2021 Expressome similarity (1) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (1) #135 - Mar 2011 Integrase similarity (1) #150 - Jun 2012 Sliding Clamps similarity (1) #180 - Dec 2014 TAL Effectors similarity (1) #227 - Nov 2018 Telomerase similarity (1) #48 - Dec 2003 Catabolite Activator Protein similarity (1) #84 - Dec 2006 Transposase similarity (1) #139 - Jul 2011 DNA Methyltransferase similarity (1) #155 - Nov 2012 Vitamin D Receptor similarity (1) #3 - Mar 2000 DNA Polymerase similarity (1) #40 - Apr 2003 RNA Polymerase similarity (1) #73 - Jan 2006 Topoisomerase similarity (1) #87 - Mar 2007 Zinc Fingers similarity (1) #119 - Nov 2009 Designed DNA Crystal similarity (1) #125 - May 2010 Parvoviruses similarity (1) #131 - Nov 2010 Inteins similarity (1) #160 - Apr 2013 Actinomycin similarity (1) #190 - Oct 2015 Two-component Systems similarity (1) #23 - Nov 2001 DNA similarity (1) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (1) #257 - May 2021 Fetal Hemoglobin similarity (1) #258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (1) #31 - Jul 2002 p53 Tumor Suppressor similarity (1) #33 - Sep 2002 HIV Reverse Transcriptase similarity (1) #39 - Mar 2003 lac Repressor similarity (1) #45 - Sep 2003 Estrogen Receptor similarity (1) #55 - Jul 2004 DNA Ligase similarity (1) #7 - Jul 2000 Nucleosome similarity (1) #8 - Aug 2000 Restriction Enzymes similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (1) #241 - Jan 2020 Twenty Years of Molecules similarity (1)

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)	36.069, 68.910, 143.829
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: 19709.938 Da / Num. of mol.: 2 / Mutation: L68Y 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.: 318 / 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: 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: Jan 27, 2020
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9795 Å / Relative weight: 1
Reflection	Resolution: 1.55→68.91 Å / Num. obs: 53142 / % possible obs: 99.9 % / Redundancy: 12.1 % / B_iso Wilson estimate: 20.39 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.076 / Net I/σ(I): 15.7
Reflection shell	Resolution: 1.55→1.58 Å / Redundancy: 12.3 % / R_merge(I) obs: 0.869 / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2591 / CC_1/2: 0.916 / % possible all: 99.6

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3SSE

3sse

Resolution: 1.55→62.15 Å / SU ML: 0.1618 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.6861
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1924	5293	9.98 %
R_work	0.1581	47753	-
obs	0.1615	53046	99.89 %

Solvent computation

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

Displacement parameters

B_iso mean: 34.94 Å²

Refinement step

Cycle: LAST / Resolution: 1.55→62.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2510	486	28	318	3342

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0126	3765
X-RAY DIFFRACTION	f_angle_d	1.2518	5317
X-RAY DIFFRACTION	f_chiral_restr	0.0751	555
X-RAY DIFFRACTION	f_plane_restr	0.0096	516
X-RAY DIFFRACTION	f_dihedral_angle_d	25.4312	843

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 (%)
1.55-1.57	0.3138	182	0.2596	1588	X-RAY DIFFRACTION	99.49
1.57-1.59	0.2893	164	0.2479	1539	X-RAY DIFFRACTION	99.94
1.59-1.61	0.2842	146	0.2348	1597	X-RAY DIFFRACTION	100
1.61-1.63	0.2493	173	0.224	1565	X-RAY DIFFRACTION	100
1.63-1.65	0.2649	190	0.2105	1574	X-RAY DIFFRACTION	99.94
1.65-1.67	0.2367	181	0.1991	1530	X-RAY DIFFRACTION	100
1.67-1.69	0.2447	165	0.2039	1593	X-RAY DIFFRACTION	99.89
1.69-1.72	0.2462	192	0.2166	1583	X-RAY DIFFRACTION	99.94
1.72-1.75	0.2595	158	0.2017	1545	X-RAY DIFFRACTION	99.94
1.75-1.77	0.2253	173	0.1974	1575	X-RAY DIFFRACTION	100
1.77-1.8	0.2171	173	0.1752	1617	X-RAY DIFFRACTION	100
1.8-1.84	0.1987	195	0.1652	1502	X-RAY DIFFRACTION	100
1.84-1.87	0.1983	159	0.161	1603	X-RAY DIFFRACTION	99.66
1.87-1.91	0.2149	179	0.1654	1580	X-RAY DIFFRACTION	99.94
1.91-1.95	0.1994	180	0.1662	1568	X-RAY DIFFRACTION	100
1.95-2	0.1988	174	0.1664	1602	X-RAY DIFFRACTION	100
2-2.05	0.1998	185	0.1691	1550	X-RAY DIFFRACTION	99.94
2.05-2.1	0.1961	175	0.1785	1598	X-RAY DIFFRACTION	99.89
2.1-2.17	0.2137	195	0.1615	1563	X-RAY DIFFRACTION	99.89
2.17-2.24	0.1958	163	0.1505	1595	X-RAY DIFFRACTION	99.94
2.24-2.32	0.1822	171	0.1508	1592	X-RAY DIFFRACTION	99.89
2.32-2.41	0.1986	183	0.1471	1606	X-RAY DIFFRACTION	100
2.41-2.52	0.2203	169	0.153	1589	X-RAY DIFFRACTION	100
2.52-2.65	0.1808	173	0.1529	1610	X-RAY DIFFRACTION	100
2.65-2.82	0.1682	182	0.1556	1599	X-RAY DIFFRACTION	99.94
2.82-3.03	0.1864	169	0.1512	1638	X-RAY DIFFRACTION	99.94
3.03-3.34	0.1983	185	0.1543	1609	X-RAY DIFFRACTION	100
3.34-3.82	0.1535	182	0.1296	1636	X-RAY DIFFRACTION	100
3.82-4.81	0.1443	167	0.1248	1682	X-RAY DIFFRACTION	100
4.82-62.15	0.2021	210	0.1718	1725	X-RAY DIFFRACTION	98.67

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	5.88943039843	-0.756651942375	-0.229605094559	3.9125292558	-0.727109623794	7.55541725364	-0.0886927618253	0.0578076644752	0.198513914628	0.0236140488594	0.0337770744786	-0.139696957831	-0.332173131072	0.432083349097	0.0473829264523	0.123832995189	-0.0737713930123	-0.0036934440205	0.171279003366	-0.01100613969	0.18032613078	26.5029673066	4.3798554885	23.0305032808
2	2.44975998571	-0.238173931509	0.282845656224	1.91503038617	-0.214041155969	3.29686490462	-0.0379610141357	0.075666819453	-0.0710229577863	-0.000465851731364	0.051919159443	-0.0333860525341	0.0857903690361	0.0381817859705	-0.0151396554383	0.143747904336	-0.00509103659329	-0.00407123622805	0.108926625115	0.00994343401244	0.132467965922	17.3061472693	-3.23984891462	22.2573800467
3	3.62220416832	-0.251308558595	-0.401776392125	1.78531050793	0.791804906771	3.85848864311	-0.0419937811371	-0.0715444949334	-0.313147974693	0.0387798672736	-0.00300048751569	0.241527058623	0.36522061516	-0.341382079039	-0.0233015453943	0.181780678308	-0.0434619677266	0.0130695774269	0.172723707156	0.0372691977089	0.204730228497	4.89048990844	-5.13264587021	25.5229827494
4	8.74824127003	6.31718647313	4.96201514145	4.64299863767	4.39013288437	7.70727908659	0.145697397801	-0.578279942045	-0.0828949343651	0.722355972238	-0.145584889067	-0.291712333283	-0.0744729598656	-0.278412537266	0.0196752476833	0.197401634108	0.0510421926356	-0.00407935065016	0.209728904866	0.000303662976074	0.179010264245	13.2473857408	4.88394453885	33.4497156566
5	4.39618585166	3.24520007827	0.775331102138	6.58153065818	0.282578979247	2.72743249593	0.155267861039	-0.0189975555993	-0.270833510073	0.260082159141	-0.0316933886925	-0.223851826888	0.51042799354	0.00723760612988	-0.075980316415	0.214990543338	0.0463159882798	-0.00792719352464	0.152868610691	0.0472140206155	0.163275010421	17.4116591185	-11.7944375187	32.2612252119
6	8.44633262241	4.27109650987	5.5856033575	7.8820075044	4.13940609433	8.90020644847	-0.169698233735	0.615287213264	0.410447435026	-0.362702346217	0.0364488410936	0.287259683273	-0.249036673367	-0.42542366045	0.144243174879	0.14717826174	0.0506536027962	0.0217179154709	0.311584850833	0.0439579440609	0.194046443092	1.53787225871	8.55639780471	-19.2333598381
7	5.08248303682	0.223553101018	1.23920209508	7.61917852992	5.35250580185	6.59109711409	0.0381201229815	-0.107401154467	-0.211371546106	-0.101203824193	-0.087170170716	0.06660279287	0.091371928719	-0.631558225906	0.0750047625992	0.188647988729	-0.0282545569862	0.00817440736962	0.267432706372	0.0605134228326	0.167965067573	1.90542977779	0.527138525887	-14.6811098866
8	2.79355122402	0.289042021509	0.388681417958	2.19728663883	0.524458893669	4.28819977707	0.0139898435853	-0.123223542226	-0.164384955269	-0.00638427759474	0.000338408554374	-0.0505822651205	0.0613835204769	0.012397884644	0.00708383236133	0.113290402177	0.00860070846887	-0.00952681365412	0.112859938024	0.020284574832	0.11318859224	12.6945838252	2.02430213164	-14.8823169237
9	0.953604775256	-1.6928870356	1.42362974469	7.11880424676	-2.80408267273	4.19926013243	0.185624748124	-0.0892093109976	-0.615943673244	0.0091935432294	0.0226133808724	-0.421144854849	1.23069611058	0.62555493596	-0.108746556064	0.370665464258	0.0791061781395	-0.00146353605476	0.236321233514	0.0504371551687	0.437309751	19.4232622038	-9.65397270512	-15.1207476879
10	4.66703221481	-0.293762269795	-4.66455003161	5.59856077232	-4.1291582729	8.16406455081	-0.263312904415	1.35154158579	-0.737972531735	-1.18818015299	0.524602892618	-0.412420824353	0.778551630355	0.494990409598	-0.150637571381	0.356106247908	0.0796309805342	0.0448994014663	0.437624725321	-0.133700239624	0.29910480832	24.1965224766	-3.63538394447	-29.4504016988
11	9.46067925563	5.67264511828	-4.17905423774	8.63051784227	-4.07901929795	6.09722189764	0.102332679008	0.00351868590715	0.422870117098	0.148272595483	-0.132783912014	0.00141983440677	-0.159651390672	0.452826616185	0.00910488122438	0.132425995224	0.0110549008436	-0.00118944902287	0.23813196332	0.0178302354831	0.223630866655	24.667956449	6.89613993904	-16.9704448961
12	8.69643460183	-3.63248526102	-0.85633867455	2.6335719644	2.88922067774	7.30024038993	0.0596139320747	0.580886739827	0.500455088512	-0.534385348544	-0.0567706352933	-0.301366755635	-0.580616636439	0.111180674142	0.0405336382562	0.24408547782	-0.0323187305408	0.00472809698683	0.2218088873	0.0559966215564	0.204598747379	14.8239502344	11.0251054566	-25.1024667333
13	8.67060760405	-5.10864387072	1.0324151199	3.14663929046	-1.10267332606	4.99299684293	0.279031241823	0.615469418929	-0.328376988192	-0.724532602612	-0.276401934459	0.00830499525254	0.375215152409	0.185100693832	0.00920407200508	0.238850437702	-0.046836087671	0.0297221850351	0.300043739704	-0.0960475636914	0.173070780545	9.92424328061	-2.0360658339	-28.9686250359
14	1.95729494097	1.3775243632	0.702441715621	2.11280210914	-0.572009737766	2.91633722755	-0.4315862572	1.20175411885	0.0131458839796	-0.933215190525	0.722214146691	-0.0111774479117	0.499986103543	0.141249632208	-0.00403840129696	0.438866692118	-0.185178570669	0.00395530855995	0.409725371453	-0.00359953492702	0.217634889403	14.0222098299	-2.0210681227	3.21110663439
15	1.10697680098	-0.195445006494	0.626419784043	2.73430997197	0.0526952189335	3.21562282584	-0.195697548888	-0.826918765692	-0.191579886024	0.476419635338	0.0871033782899	-0.0308553407152	0.336548177414	-0.154782942941	-0.016580562414	0.26162801376	0.0671404744068	0.0190135644647	0.31239660051	0.087011210375	0.154789064199	14.0595883394	-1.94817906299	3.22796743925

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 2 through 27 )	A	A	2 - 27	1 - 26
2	2	chain 'A' and (resid 28 through 82 )	A	A	28 - 82	27 - 81
3	3	chain 'A' and (resid 83 through 120 )	A	A	83 - 120	82 - 119
4	4	chain 'A' and (resid 121 through 133 )	A	A	121 - 133	120 - 132
5	5	chain 'A' and (resid 134 through 160 )	A	A	134 - 160	133 - 159
6	6	chain 'B' and (resid 1 through 17 )	B	B	1 - 17	1 - 17
7	7	chain 'B' and (resid 18 through 38 )	B	B	18 - 38	18 - 38
8	8	chain 'B' and (resid 39 through 82 )	B	B	39 - 82	39 - 82
9	9	chain 'B' and (resid 83 through 92 )	B	B	83 - 92	83 - 92
10	10	chain 'B' and (resid 93 through 101 )	B	B	93 - 101	93 - 101
11	11	chain 'B' and (resid 102 through 120 )	B	B	102 - 120	102 - 120
12	12	chain 'B' and (resid 121 through 133 )	B	B	121 - 133	121 - 133
13	13	chain 'B' and (resid 134 through 152 )	B	B	134 - 152	134 - 152
14	14	chain 'C' and (resid 2 through 13 )	C	C	2 - 13
15	15	chain 'D' and (resid 2 through 13 )	D	D	2 - 13

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