PDB-6uke: HhaI endonuclease in Complex with Iodine-Labelled DNA

ID or keywords:

Entry

Database: PDB / ID: 6uke

Title

HhaI endonuclease in Complex with Iodine-Labelled DNA

Components

DNA (5'-D(*CP*GP*(5IT)P*TP*GP*CP*GP*CP*TP*(5IT)P*GP*GP*A)-3')
DNA (5'-D(*TP*CP*CP*AP*AP*GP*CP*GP*CP*AP*AP*CP*G)-3')
HhaI Restriction Endonuclease

Keywords

HYDROLASE/DNA / restriction / modification /

protein-DNA complex / iodine phasing / HYDROLASE-DNA complex

Function / homology

ACETATE ION /

PHOSPHATE ION /

DNA / DNA (> 10) / Uncharacterized protein

Function and homology information

Biological species

Haemophilus parahaemolyticus (bacteria)

Method

X-RAY DIFFRACTION / AB INITIO PHASING / Resolution: 1.62 Å

Authors

Horton, J.R. / Cheng, X.

Funding support

United States, 1items

Citation

Journal: Nucleic Acids Res. / Year: 2020
Title: Structure of HhaI endonuclease with cognate DNA at an atomic resolution of 1.0 angstrom.
Authors: Horton, J.R. / Yang, J. / Zhang, X. / Petronzio, T. / Fomenkov, A. / Wilson, G.G. / Roberts, R.J. / Cheng, X.

History

Deposition	Oct 4, 2019	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 18, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 8, 2020	Group: Database references / Category: citation Item: _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2	Mar 4, 2020	Group: Database references / Category: citation Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3	Mar 13, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / struct_conn_type Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6uke.cif.gz	176.7 KB	Display	PDBx/mmCIF format
PDB format	pdb6uke.ent.gz	119.3 KB	Display	PDB format
PDBx/mmJSON format	6uke.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/uk/6uke ftp://data.pdbj.org/pub/pdb/validation_reports/uk/6uke	HTTPS FTP

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Related structure data

Related structure data	6ukfC 6ukgC 6ukhC 6ukiC C: citing same article (ref.)
Similar structure data	6ukf-d 6ukh-d 5azb-d 5itu-2 3uze-1 1c08-d 1ca1-d 6q3x-2 6teq-1 1ic4-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Experimental dataset #1	Data reference: 10.15785/SBGRID/745 / Data set type: diffraction image data / Details: X-Ray Diffraction data from HhaI/DNA (w-IodineU)

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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

X: HhaI Restriction Endonuclease

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

B: DNA (5'-D(*CP*GP*(5IT)P*TP*GP*CP*GP*CP*TP*(5IT)P*GP*GP*A)-3')

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: gel filtration

Unit cell

Length a, b, c (Å)	60.890, 37.193, 68.744
Angle α, β, γ (deg.)	90.000, 109.796, 90.000
Int Tables number	4
Space group name H-M	P12₁1
Space group name Hall	P2yb
Symmetry operation	#1: x,y,z #2: -x,y+1/2,-z

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Protein , 1 types, 1 molecules X

#1: Protein	HhaI Restriction Endonuclease Mass: 29977.062 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Haemophilus parahaemolyticus (bacteria) Gene: HMPREF1050_0931 / Production host: Escherichia coli (E. coli) / References: UniProt: I3DBY6, Hydrolases

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DNA chain , 2 types, 2 molecules AB

#2: DNA chain	DNA (5'-D(TPCPCPAPAPGPCPGPCPAPAPCPG)-3') Mass: 3945.589 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus parahaemolyticus* (bacteria)
#3: DNA chain	DNA (5'-D(CPGP(5IT)PTPGPCPGPCPTP(5IT)PGPGPA)-3') Mass: 4222.334 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) Haemophilus parahaemolyticus* (bacteria)

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Non-polymers , 5 types, 226 molecules

#4: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#5: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 19 / Source method: obtained synthetically / Formula: C₂H₆O₂
#6: Chemical	ChemComp-ACT / ACETATE ION / Acetate Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₃O₂
#7: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO₄
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 203 / Source method: isolated from a natural source / Formula: H₂O

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Details

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: 1.96 Å³/Da / Density % sol: 37.4 %
Crystal grow	Temperature: 292 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: 35% v/v 2-propanol, 0.1 M sodium phosphate dibasic / citric acid, pH 4.2

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SEALED TUBE / Type: RIGAKU MICROMAX-003 / Wavelength: 1.54 Å
Detector	Type: RIGAKU / Detector: PIXEL / Date: Feb 20, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54 Å / Relative weight: 1
Reflection	Resolution: 1.62→28.65 Å / Num. obs: 69465 / % possible obs: 97.8 % / Redundancy: 17.8 % / B_iso Wilson estimate: 11.17 Å² / R_merge(I) obs: 0.091 / R_pim(I) all: 0.021 / Net I/σ(I): 21.4
Reflection shell	Resolution: 1.62→1.65 Å / R_merge(I) obs: 0.767 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 2133 / CC_1/2: 0.667 / R_pim(I) all: 0.413

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Processing

Software

Name	Version	Classification
JDirector		data collection
PHENIX	1.15.2_3472	refinement
CrysalisPro		data reduction
Aimless		data scaling
PHENIX		phasing

Refinement

Method to determine structure: AB INITIO PHASING / Resolution: 1.62→28.65 Å / SU ML: 0.1599 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 19.7017

	R_factor	Num. reflection	% reflection
R_free	0.2031	3451	4.97 %
R_work	0.1714	-	-
obs	0.173	69465	96.33 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Displacement parameters

B_iso mean: 19.59 Å²

Refinement step

Cycle: LAST / Resolution: 1.62→28.65 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2073	527	90	203	2893

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0068	2824
X-RAY DIFFRACTION	f_angle_d	0.9574	3891
X-RAY DIFFRACTION	f_chiral_restr	0.0551	413
X-RAY DIFFRACTION	f_plane_restr	0.0057	405
X-RAY DIFFRACTION	f_dihedral_angle_d	20.8701	1059

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 (%)
1.62-1.64	0.301	80	0.311	1442	X-RAY DIFFRACTION	54.38
1.64-1.67	0.3069	102	0.2848	2074	X-RAY DIFFRACTION	74.62
1.67-1.69	0.2938	131	0.2553	2473	X-RAY DIFFRACTION	88.84
1.69-1.72	0.2507	138	0.2432	2575	X-RAY DIFFRACTION	95.9
1.72-1.75	0.2573	138	0.2173	2673	X-RAY DIFFRACTION	96.07
1.75-1.78	0.2455	145	0.2074	2754	X-RAY DIFFRACTION	99.35
1.78-1.81	0.2269	143	0.1935	2704	X-RAY DIFFRACTION	99.82
1.81-1.84	0.2277	142	0.1982	2733	X-RAY DIFFRACTION	99.62
1.84-1.88	0.2111	143	0.1814	2723	X-RAY DIFFRACTION	99.86
1.88-1.92	0.1998	144	0.1773	2733	X-RAY DIFFRACTION	99.72
1.92-1.97	0.1939	144	0.1675	2788	X-RAY DIFFRACTION	99.86
1.97-2.01	0.1767	141	0.1659	2673	X-RAY DIFFRACTION	99.79
2.01-2.07	0.2438	149	0.1753	2756	X-RAY DIFFRACTION	99.73
2.07-2.13	0.1979	138	0.1681	2716	X-RAY DIFFRACTION	100
2.13-2.2	0.2301	145	0.1568	2786	X-RAY DIFFRACTION	99.86
2.2-2.28	0.2137	140	0.1557	2700	X-RAY DIFFRACTION	100
2.28-2.37	0.1697	146	0.1628	2782	X-RAY DIFFRACTION	100
2.37-2.48	0.2094	143	0.1635	2727	X-RAY DIFFRACTION	100
2.48-2.61	0.1987	142	0.1645	2747	X-RAY DIFFRACTION	100
2.61-2.77	0.1784	147	0.1596	2734	X-RAY DIFFRACTION	100
2.77-2.98	0.227	143	0.1599	2743	X-RAY DIFFRACTION	100
2.98-3.28	0.1875	144	0.1515	2730	X-RAY DIFFRACTION	100
3.28-3.76	0.164	143	0.1447	2789	X-RAY DIFFRACTION	100
3.76-4.73	0.1594	141	0.1451	2703	X-RAY DIFFRACTION	100
4.73-28.65	0.2306	139	0.1858	2756	X-RAY DIFFRACTION	99.97

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	7.92960159628	7.52481056904	-3.5717892423	8.77936847782	-3.68075672483	1.9657556412	0.12266962241	-0.308803432996	-0.0906907055282	0.136250574708	-0.258786394064	-0.246947097683	-0.0366004126499	0.209970897577	0.134486549356	0.10747512509	0.0147334797709	-0.01467928564	0.105257583944	0.0280200598598	0.0714203204257	27.1216568214	1.67379951924	62.9515091383
2	5.31676696133	-0.506488516729	-0.184578617369	2.92200524074	0.695588158996	4.0659818866	-0.0295085630132	0.344976918563	0.193637303932	-0.313794878133	-0.0146023961556	-0.448847756162	-0.177915412488	0.498027835246	0.0402607212341	0.146943331656	-0.00322900270902	0.0374565978735	0.114684113157	0.0194606481619	0.151416852521	23.3277097804	-4.14872988757	52.0481535041
3	1.06906731439	0.212493376252	-0.61480209776	2.07903225748	-1.78614732252	2.32115076929	0.0157091698782	0.228730111111	-0.00223265552902	-0.117066184812	-0.0144199505856	0.00611084234959	0.0206161800554	-0.0566304662928	0.0107957689568	0.0653966907947	0.000916840043224	0.0019620540791	0.0970606814167	-0.0148489340518	0.0546705598045	24.8157166667	19.3941410603	39.3268326203
4	1.30951425597	0.109817837573	-0.12493856644	0.787440197318	-0.311616760496	0.677155574399	0.022747952772	0.0428882954954	0.0256319052932	0.103620237995	0.00756240480507	-0.00506296652771	-0.0193390730013	0.0231572046071	-0.0300880361718	0.0670897329132	0.00137076498006	-0.000361185621653	0.0406465590238	-0.0148756139104	0.0365795533422	23.6184563603	15.2061280721	49.6057861608
5	1.75972640214	1.22332615239	0.301904455698	3.28348221906	0.388720062221	6.13512009995	0.002703818064	0.101075849968	-0.207984544948	-0.125429692001	0.0867208985625	-0.120540538402	0.195200743625	0.226660988646	-0.0528860205195	0.086443185185	0.0460993120437	-0.024848686572	0.213342898934	-0.0416186388154	0.172204978996	59.934770287	4.99861523146	48.3429595614
6	7.30430097135	-3.69003486315	2.62523116748	3.78128244486	-0.167783839718	1.62394863734	0.111239669499	0.151138046426	-0.0829320980411	0.070679310929	-0.101335816357	-0.207962779395	0.0861959370057	0.340978501992	-0.0597254598668	0.0808479151093	-0.00964639203421	-0.00297480359093	0.159642874735	0.00806384641352	0.168276521039	50.7665651509	10.1243049227	46.4734047988
7	2.18381187515	0.901886478506	-1.42580020512	1.17705652847	-0.403016351	1.46188031105	0.122043517726	-0.0969378374152	0.141575300357	0.183118618864	-0.0477568700056	0.142774353511	-0.0998437210592	-0.0225742459135	-0.0636761266931	0.0402303739035	0.0167541789896	-0.00786815913022	0.0508100232656	0.00483413361329	0.0394867438522	14.884603136	10.5000153753	58.7112917234
8	3.40351743738	-0.209692743254	-0.428851178622	2.6443440076	-0.941441080914	2.37215499518	0.142358959253	0.0560997942839	-0.192752901129	-0.0185403471537	-0.0942940420659	-0.357703724803	0.23002272221	0.481800579041	-0.108013470161	0.0811818898113	0.0250705828573	-0.00195651982853	0.138350866273	0.00896943276741	0.184261721478	38.5179521194	10.728775422	45.3461647887
9	4.74815731782	1.05729877921	-0.130565090258	4.07466700665	-0.314418932244	5.11537397503	0.228639608235	0.394400534971	-0.303889342764	-0.556294549068	-0.300821793493	0.0964474520698	0.209044692799	-0.392006716961	0.0477131844169	0.152565276517	0.034287193804	-0.0861388890498	0.228476695931	0.00547392967031	0.17082333553	37.7031072533	11.5977847603	44.613623856

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'X' and (resid 1 through 18 )
2	X-RAY DIFFRACTION	2	chain 'X' and (resid 19 through 42 )
3	X-RAY DIFFRACTION	3	chain 'X' and (resid 43 through 96 )
4	X-RAY DIFFRACTION	4	chain 'X' and (resid 97 through 165 )
5	X-RAY DIFFRACTION	5	chain 'X' and (resid 166 through 198 )
6	X-RAY DIFFRACTION	6	chain 'X' and (resid 199 through 227 )
7	X-RAY DIFFRACTION	7	chain 'X' and (resid 228 through 258 )
8	X-RAY DIFFRACTION	8	chain 'A' and (resid 1 through 13 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 1 through 13 )

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Protein , 1 types, 1 molecules X

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DNA chain , 2 types, 2 molecules AB

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Non-polymers , 5 types, 226 molecules

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Experiment

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Movie

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Structure viewers

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Open data

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Assembly

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Protein , 1 types, 1 molecules X

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DNA chain , 2 types, 2 molecules AB

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Non-polymers , 5 types, 226 molecules

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Details

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

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About Yorodumi

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Feb 9, 2022. New format data for meta-information of EMDB entries

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi