PDB-3k0b: Crystal structure of a predicted N6-adenine-specific DNA methylas...

ID or keywords:

Entry

Database: PDB / ID: 3k0b

Title

Crystal structure of a predicted N6-adenine-specific DNA methylase from Listeria monocytogenes str. 4b F2365

Components

predicted N6-adenine-specific DNA methylase

Keywords

structural genomics / unknown function / methylase / PF01170 / putative RNA methylase / PSI / MCSG / Protein Structure Initiative / Midwest Center for Structural Genomics / Methyltransferase / Transferase

Function / homology

VC0802-like - #30 / VC0802-like / Vaccinia Virus protein VP39 / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / :

Function and homology information

Biological species

Listeria monocytogenes str. 4b (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.5 Å

Authors

Nocek, B. / Xu, X. / Cui, H. / Savchenko, A. / Edwards, A. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)

Citation

Journal: To be Published
Title: Crystal structure of a predicted N6-adenine-specific DNA methylase from Listeria monocytogenes str. 4b F2365
Authors: Nocek, B. / Xu, X. / Cui, H. / Ng, J. / Savchenko, A. / Edwards, A. / Joachimiak, A.

History

Deposition	Sep 24, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 13, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.2	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	3k0b.cif.gz	103.4 KB	Display	PDBx/mmCIF format
PDB format	pdb3k0b.ent.gz	77.1 KB	Display	PDB format
PDBx/mmJSON format	3k0b.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3k0b_validation.pdf.gz	448 KB	Display	wwPDB validaton report
Full document	3k0b_full_validation.pdf.gz	451.3 KB	Display
Data in XML	3k0b_validation.xml.gz	24.8 KB	Display
Data in CIF	3k0b_validation.cif.gz	36.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/k0/3k0b ftp://data.pdbj.org/pub/pdb/validation_reports/k0/3k0b	HTTPS FTP

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Related structure data

Similar structure data	1lqw-d 2pof-d 5z7b-d 3tm5-1 4crq-d 3ldu-d 4w9d-2 6zmp-d 3le7-d 3qek-1 Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: apc64818

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: predicted N6-adenine-specific DNA methylase

hetero molecules

44.8 kDa, 1 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)	125.949, 46.156, 91.376
Angle α, β, γ (deg.)	90.00, 131.09, 90.00
Int Tables number	5
Space group name H-M	C121

Details

likely monomer

#1: Protein	predicted N6-adenine-specific DNA methylase Mass: 44612.797 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes str. 4b (bacteria) Strain: F2365 / Gene: LMOf2365_1916 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21magic / References: UniProt: Q71YC9
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 520 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	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: 2.24 Å³/Da / Density % sol: 45.17 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.2 M Ammonium sulfate 25 % PEG3350 0.1 M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Aug 7, 2009 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.5→40 Å / Num. all: 63435 / Num. obs: 62193 / % possible obs: 98 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 3 % / B_iso Wilson estimate: 29 Å² / R_merge(I) obs: 0.058 / Net I/σ(I): 32
Reflection shell	Resolution: 1.5→1.53 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.52 / Mean I/σ(I) obs: 2.1 / Num. unique all: 3036 / % possible all: 95.6

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
SHELX		model building
DM		model building
ARP/wARP		model building
Coot		model building
CCP4		model building
MLPHARE		phasing
REFMAC	5.5.0102	refinement
HKL-3000		data reduction
HKL-3000		data scaling
SHELX		phasing
DM		phasing
CCP4		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.5→40 Å / Cor.coef. F_o:F_c: 0.97 / Cor.coef. F_o:F_c free: 0.957 / SU B: 2.778 / SU ML: 0.047 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.071 / ESU R Free: 0.074 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19771	3160	5.1 %	RANDOM
R_work	0.16417	-	-	-
all	0.17	62195	-	-
obs	0.16591	59033	97.74 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 9.691 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.24 Å²	0 Å²	0.92 Å²
2-	-	-0.89 Å²	0 Å²
3-	-	-	0.86 Å²

Refinement step

Cycle: LAST / Resolution: 1.5→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2998	0	10	520	3528

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	3080
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2109
X-RAY DIFFRACTION	r_angle_refined_deg	1.625	1.966	4176
X-RAY DIFFRACTION	r_angle_other_deg	0.984	3	5125
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.859	5	380
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.363	23.929	140
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.684	15	520
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.737	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.104	0.2	459
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	3421
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	636
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.026	1.5	1890
X-RAY DIFFRACTION	r_mcbond_other	0.318	1.5	771
X-RAY DIFFRACTION	r_mcangle_it	1.779	2	3038
X-RAY DIFFRACTION	r_scbond_it	2.961	3	1190
X-RAY DIFFRACTION	r_scangle_it	4.638	4.5	1137
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.5→1.539 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.296	231	-
R_work	0.288	4159	-
obs	-	-	93.05 %

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	0.6009	0.0504	-1.2004	0.0044	-0.1006	2.4012	0.0726	0.0922	0.0529	0.0061	0.0256	0.0008	-0.0919	-0.1822	-0.0982	0.2039	0.0234	-0.0378	0.1272	-0.0701	0.0992	-5.5743	35.6811	37.2008
2	1.9455	-0.4819	-0.5463	0.8872	-0.063	1.4749	-0.0917	-0.0082	-0.2414	0.051	0.0885	0.1502	0.0962	-0.0127	0.0032	0.1006	-0.016	0.0029	0.0704	0.011	0.0798	-1.6176	22.4228	23.604
3	4.9146	0.3556	-0.9622	4.8996	2.0485	1.7814	-0.1475	0.1021	-0.2934	0.1621	0.0378	0.0974	0.1658	-0.2325	0.1098	0.0932	-0.0232	0.0091	0.0854	0.0186	0.0984	-8.277	25.2796	23.233
4	1.4818	-0.4571	0.0847	0.5032	-0.1366	0.2922	-0.0155	0.0086	0.0321	0.0394	0.0438	-0.0248	0.0901	-0.0394	-0.0284	0.0859	-0.0057	0	0.0882	0.006	0.0609	-2.9315	31.4421	22.0751
5	1.9937	0.5413	-0.0395	1.5659	-0.3226	1.8521	-0.067	-0.074	0.0725	-0.0906	-0.0022	0.0721	0.1243	-0.1691	0.0692	0.062	-0.0175	0.0014	0.0766	-0.0128	0.0494	-17.9524	41.9544	12.9045
6	2.0771	0.4516	-0.2154	0.8015	0.1871	1.4799	-0.0724	-0.0817	0.0076	-0.0983	-0.0349	-0.1161	0.1559	-0.0189	0.1073	0.0891	-0.0144	-0.0012	0.0676	0.0116	0.056	-11.8698	41.6562	14.2899
7	2.8993	-1.7957	-0.3344	1.9422	-0.2355	0.4578	0.161	0.2032	0.1122	-0.3159	-0.1505	-0.1727	0.0486	-0.045	-0.0104	0.1333	0.0115	0.0258	0.0834	0.0163	0.1064	9.417	31.3639	11.9371
8	2.4325	-1.1306	0.0015	1.6959	-0.2032	1.4762	-0.0727	0.0041	-0.1663	-0.0404	0.0659	0.0465	0.0368	-0.0818	0.0068	0.0868	-0.011	0.0066	0.0506	-0.0059	0.0735	11.5724	16.9958	17.0822
9	0.9115	-0.7705	-0.3484	1.1131	0.3371	0.1769	-0.0313	-0.0566	0.0901	0.0162	0.0576	-0.1531	0.0054	0.0087	-0.0263	0.0859	-0.0014	-0.0097	0.0796	-0.0051	0.0779	13.8736	25.8969	18.501
10	2.025	-2.6902	-0.303	3.7452	0.5459	1.3078	-0.0313	-0.0539	0.0446	0.1687	0.1402	-0.104	0.0343	0.0751	-0.109	0.1105	0.0142	-0.0276	0.0978	-0.0382	0.0816	7.8641	38.0242	30.1574
11	1.3349	-0.7515	-0.2762	1.2237	0.2416	0.842	0.0054	-0.0148	0.0764	-0.0505	0.0669	-0.2	0.0207	0.0488	-0.0723	0.0626	-0.0117	0.0054	0.0551	-0.0026	0.0948	24.0222	17.3722	12.7699
12	2.1122	-0.9539	3.0346	1.5853	-0.9032	7.3286	-0.201	0.1021	0.1404	0.0444	-0.1018	-0.0107	-0.1143	0.058	0.3028	0.0567	-0.012	0.0092	0.0818	-0.0156	0.1034	17.4352	5.7994	-0.8119
13	0.8622	-0.3268	0.3855	1.0919	0.5404	1.702	-0.021	0.097	-0.0958	0.0134	-0.0664	-0.0488	0.157	0.0024	0.0873	0.0988	-0.0103	0.0351	0.064	-0.0023	0.1015	14.5649	4.499	9.701
14	5.9537	-0.1546	-5.0912	0.5241	0.5492	8.215	-0.1957	0.0403	-0.1406	-0.0598	0.024	0.0191	0.4568	-0.008	0.1717	0.1066	-0.023	0.0428	0.0247	-0.0109	0.1136	10.5392	-1.0959	8.3171
15	3.1339	-0.1054	-1.0291	3.0848	-1.2945	3.0904	0.0503	0.1212	0.0068	-0.0299	0.054	0.158	-0.1393	-0.2717	-0.1043	0.0864	-0.0145	0.0268	0.0613	-0.0109	0.1069	6.0146	6.5278	12.2102

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-10 - 5
2	X-RAY DIFFRACTION	2	A	6 - 29
3	X-RAY DIFFRACTION	3	A	30 - 41
4	X-RAY DIFFRACTION	4	A	42 - 66
5	X-RAY DIFFRACTION	5	A	67 - 126
6	X-RAY DIFFRACTION	6	A	127 - 154
7	X-RAY DIFFRACTION	7	A	155 - 171
8	X-RAY DIFFRACTION	8	A	172 - 191
9	X-RAY DIFFRACTION	9	A	192 - 228
10	X-RAY DIFFRACTION	10	A	229 - 248
11	X-RAY DIFFRACTION	11	A	249 - 307
12	X-RAY DIFFRACTION	12	A	308 - 328
13	X-RAY DIFFRACTION	13	A	329 - 344
14	X-RAY DIFFRACTION	14	A	345 - 354
15	X-RAY DIFFRACTION	15	A	355 - 372

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