PDB-4hh4: Structure of the CcbJ Methyltransferase from Streptomyces caelestis

ID or keywords:

Entry

Database: PDB / ID: 4hh4

Title

Structure of the CcbJ Methyltransferase from Streptomyces caelestis

Components

CcbJ

Keywords

TRANSFERASE / S-adenosyl-L-methionine-dependent methyltransferase / Methyltransferase

Function / homology

Function and homology information

N-methyltransferase activity / biosynthetic process / methylation
Similarity search - Function

Biological species

Streptomyces caelestis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Bauer, J.A. / Ondrovicova, G. / Kutejova, E. / Janata, J.

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2014
Title: Structure and possible mechanism of the CcbJ methyltransferase from Streptomyces caelestis.
Authors: Bauer, J. / Ondrovicova, G. / Najmanova, L. / Pevala, V. / Kamenik, Z. / Kostan, J. / Janata, J. / Kutejova, E.

History

Deposition	Oct 9, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 30, 2013	Provider: repository / Type: Initial release
Revision 1.1	Apr 16, 2014	Group: Database references
Revision 1.2	Feb 26, 2020	Group: Data collection / Database references / Category: reflns / reflns_shell / struct_ref_seq_dif Item: _reflns.pdbx_Rmerge_I_obs / _reflns_shell.Rmerge_I_obs / _struct_ref_seq_dif.details
Revision 1.3	Feb 28, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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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Download

PDBx/mmCIF format	4hh4.cif.gz	611.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4hh4.ent.gz	506 KB	Display	PDB format
PDBx/mmJSON format	4hh4.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4hh4_validation.pdf.gz	1.9 MB	Display	wwPDB validaton report
Full document	4hh4_full_validation.pdf.gz	1.9 MB	Display
Data in XML	4hh4_validation.xml.gz	57 KB	Display
Data in CIF	4hh4_validation.cif.gz	76.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hh/4hh4 ftp://data.pdbj.org/pub/pdb/validation_reports/hh/4hh4	HTTPS FTP

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Related structure data

Related structure data	4hgyC 4hgzC C: citing same article (ref.)
Similar structure data	1wzn-1 5y5v-d 4hgz-d 5y51-d 1v1a-1 1v1s-2 4hgy-d 1v1b-2 Search similar-shape structures by Omokage search (details) 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

Deposited unit

A: CcbJ

B: CcbJ

C: CcbJ

D: CcbJ

E: CcbJ

F: CcbJ

hetero molecules

185 kDa, 6 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)	169.950, 244.000, 118.070
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

ID
1
2
3
4
5

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Protein , 1 types, 6 molecules ABCDEF

#1: Protein	CcbJ Mass: 30051.688 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces caelestis (bacteria) / Gene: ccbJ / Plasmid: pET 28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: E9JES0

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Non-polymers , 5 types, 140 molecules

#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 20 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₈H₁₈N₂O₄S / Comment: pH buffer*YM
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 107 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 3.39 Å³/Da / Density % sol: 63.76 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 0.1 M Na HEPES pH 7.5, 1.3 M Li2SO4.H2O, 10% Glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.97549 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 22, 2009 / Details: Pd-coated toroidal mirror (Seso, France)
Radiation	Monochromator: 2 x channel-cut double-crystal silicon [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97549 Å / Relative weight: 1
Reflection	Resolution: 2.9→69.73 Å / Num. all: 52391 / Num. obs: 52391 / % possible obs: 96 % / Observed criterion σ(I): 2 / Redundancy: 4.2 % / B_iso Wilson estimate: 48.71 Å² / R_merge(I) obs: 0.079 / Net I/σ(I): 15.8
Reflection shell	Resolution: 2.9→3.06 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.472 / Mean I/σ(I) obs: 3 / Num. unique all: 6436 / % possible all: 81.6

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.9→69.73 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.89 / SU B: 28.859 / SU ML: 0.243 / Cross valid method: THROUGHOUT / ESU R: 1.586 / ESU R Free: 0.327 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22138	2647	5.1 %	RANDOM
R_work	0.1827	-	-	-
all	0.18466	49744	-	-
obs	0.18466	49744	95.77 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 43.682 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.24 Å²	0 Å²	0 Å²
2-	-	2.28 Å²	0 Å²
3-	-	-	-3.51 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→69.73 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11663	0	307	107	12077

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.021	12216
X-RAY DIFFRACTION	r_angle_refined_deg	1.499	1.989	16629
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.523	5	1513
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.511	23.458	590
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.971	15	1801
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.499	15	105
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	1813
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.021	9493
X-RAY DIFFRACTION	r_mcbond_it	0.938	1.5	7571
X-RAY DIFFRACTION	r_mcangle_it	1.873	2	12050
X-RAY DIFFRACTION	r_scbond_it	3.438	3	4645
X-RAY DIFFRACTION	r_scangle_it	5.868	4.5	4579

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	1842	TIGHT POSITIONAL	0.12	0.05
1	2	B	1842	TIGHT POSITIONAL	0.15	0.05
1	3	C	1842	TIGHT POSITIONAL	0.12	0.05
1	4	D	1842	TIGHT POSITIONAL	0.11	0.05
1	5	E	1842	TIGHT POSITIONAL	0.12	0.05
1	6	F	1842	TIGHT POSITIONAL	0.11	0.05
1	1	A	1842	TIGHT THERMAL	0.28	0.5
1	2	B	1842	TIGHT THERMAL	0.28	0.5
1	3	C	1842	TIGHT THERMAL	0.29	0.5
1	4	D	1842	TIGHT THERMAL	0.24	0.5
1	5	E	1842	TIGHT THERMAL	0.29	0.5
1	6	F	1842	TIGHT THERMAL	0.24	0.5
2	1	A	51	TIGHT POSITIONAL	0.13	0.05
2	2	B	51	TIGHT POSITIONAL	0.23	0.05
2	3	D	51	TIGHT POSITIONAL	0.08	0.05
2	4	E	51	TIGHT POSITIONAL	0.22	0.05
2	5	F	51	TIGHT POSITIONAL	0.08	0.05
2	1	A	51	TIGHT THERMAL	0.33	0.5
2	2	B	51	TIGHT THERMAL	0.36	0.5
2	3	D	51	TIGHT THERMAL	0.22	0.5
2	4	E	51	TIGHT THERMAL	0.34	0.5
2	5	F	51	TIGHT THERMAL	0.19	0.5
3	1	A	17	TIGHT POSITIONAL	0.08	0.05
3	2	C	17	TIGHT POSITIONAL	0.09	0.05
3	3	D	17	TIGHT POSITIONAL	0.05	0.05
3	4	E	17	TIGHT POSITIONAL	0.08	0.05
3	5	F	17	TIGHT POSITIONAL	0.08	0.05
3	1	A	17	TIGHT THERMAL	0.2	0.5
3	2	C	17	TIGHT THERMAL	0.26	0.5
3	3	D	17	TIGHT THERMAL	0.23	0.5
3	4	E	17	TIGHT THERMAL	0.26	0.5
3	5	F	17	TIGHT THERMAL	0.3	0.5
4	1	B	19	TIGHT POSITIONAL	0.11	0.05
4	2	C	19	TIGHT POSITIONAL	0.13	0.05
4	3	D	19	TIGHT POSITIONAL	0.08	0.05
4	4	E	19	TIGHT POSITIONAL	0.08	0.05
4	5	F	19	TIGHT POSITIONAL	0.1	0.05
4	1	B	19	TIGHT THERMAL	0.22	0.5
4	2	C	19	TIGHT THERMAL	0.34	0.5
4	3	D	19	TIGHT THERMAL	0.27	0.5
4	4	E	19	TIGHT THERMAL	0.22	0.5
4	5	F	19	TIGHT THERMAL	0.22	0.5
5	1	A	11	TIGHT POSITIONAL	0.13	0.05
5	2	B	11	TIGHT POSITIONAL	0.14	0.05
5	3	C	11	TIGHT POSITIONAL	0.15	0.05
5	4	E	11	TIGHT POSITIONAL	0.11	0.05
5	5	F	11	TIGHT POSITIONAL	0.18	0.05
5	1	A	11	TIGHT THERMAL	0.16	0.5
5	2	B	11	TIGHT THERMAL	0.31	0.5
5	3	C	11	TIGHT THERMAL	0.24	0.5
5	4	E	11	TIGHT THERMAL	0.26	0.5
5	5	F	11	TIGHT THERMAL	0.16	0.5

LS refinement shell

Resolution: 2.9→2.975 Å / R_factor R_free error: 0.031 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.372	145	-
R_work	0.329	2699	-
obs	-	2844	70.75 %

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	6.1266	-0.728	0.4396	2.1901	1.1314	4.4317	-0.1697	-1.0401	-0.3116	0.4141	0.2277	0.1951	0.2218	-0.7024	-0.0579	0.1488	0.0354	-0.0418	0.5244	0.1683	0.3755	-58.8272	-76.52	0.0195
2	0.6291	1.0108	2.5957	3.4931	2.9157	11.6223	-0.0084	-0.0137	0.0199	-0.0986	0.0959	0.4006	0.1184	-0.0286	-0.0875	0.0221	0.0535	-0.0087	0.2555	0.1187	0.2585	-38.7194	-82.5366	7.3852
3	7.1772	-1.1731	-0.0042	3.1257	0.8879	4.3411	0.037	0.0731	0.2296	-0.334	0.0837	0.1028	0.0656	-0.2133	-0.1207	0.1414	0.0039	-0.0451	0.1779	0.1287	0.1713	-49.3617	-80.0606	-13.9159
4	4.9321	1.0988	-0.6462	5.5472	-1.9302	3.9484	0.0347	-0.5619	0.1358	0.5376	-0.2301	0.052	-0.0796	0.2024	0.1953	0.4048	0.0839	0.0166	0.1925	0.0691	0.172	-22.2668	-110.9856	22.0762
5	11.0441	-3.6363	-1.7366	1.924	0.6386	2.3525	0.2879	-0.0676	0.4769	-0.1087	-0.027	-0.1472	0.1163	-0.0857	-0.2609	0.1954	0.0297	-0.0002	0.1126	0.0517	0.1095	-24.7869	-90.3092	16.1379
6	6.0097	1.5045	0.5538	5.7171	-0.8961	2.3985	-0.1781	-0.0444	-0.3475	-0.3923	-0.021	-0.4619	0.5964	0.3608	0.199	0.3367	0.1558	0.1005	0.2119	0.0721	0.1738	-9.4014	-108.0878	11.0037
7	2.0558	0.4561	0.1035	4.1814	0.2888	7.0658	0.1337	-0.4112	0.12	0.0304	-0.1711	0.4216	0.1992	-0.0782	0.0374	0.1011	0.1306	-0.0157	0.4427	-0.1755	0.2804	-18.5081	-57.9103	30.1615
8	2.6083	2.467	-1.833	9.3567	-4.743	3.4489	-0.1978	-0.0875	0.0495	-0.151	0.2609	-0.0695	0.0263	-0.3086	-0.063	0.0922	0.0706	-0.0328	0.2513	-0.0738	0.1173	-26.9274	-72.2401	16.4551
9	5.1847	0.2475	0.3376	3.2193	0.5285	5.8887	0.0554	-0.1024	0.3854	-0.1221	0.2151	-0.2341	-0.2345	0.6538	-0.2704	0.0899	0.041	0.0397	0.3024	-0.108	0.2123	-12.1024	-53.3732	14.7993
10	7.4778	1.2473	-0.8481	4.3614	-2.9633	4.5388	-0.0289	0.2008	-0.3719	-0.6536	-0.2577	-0.7738	0.1847	1.118	0.2866	0.2935	0.1112	0.1204	0.6937	0.0328	0.6141	18.1499	-83.6367	-0.8951
11	1.0336	-0.6355	-0.2057	5.5366	-4.7299	9.1998	-0.1213	-0.0986	0.0531	-0.1712	0.1019	-0.3303	0.0661	0.0266	0.0194	0.078	0.0031	0.0656	0.2656	-0.0164	0.3037	-2.4622	-82.8669	-9.1972
12	6.8268	1.4557	-0.865	6.7088	-0.5527	5.3994	0.1243	-0.8243	-0.0514	0.2513	-0.2905	-0.3504	0.2846	0.7607	0.1662	0.158	0.0622	0.014	0.4898	0.1085	0.2668	7.882	-90.0546	11.3701
13	4.3805	1.3092	-0.089	5.6292	1.3996	3.3449	-0.0855	0.4828	0.0061	-1.2426	0.1468	-0.6832	-0.0816	0.2711	-0.0612	0.6659	0.0198	0.0955	0.1926	0.0348	0.2582	-23.4351	-101.8255	-31.8253
14	12.9383	2.4859	-0.9735	1.906	-1.1881	1.9494	0.1844	-0.1757	0.0097	-0.1917	0.0219	0.0866	0.118	0.1299	-0.2062	0.2704	-0.028	0.0425	0.0565	-0.0185	0.0947	-17.1359	-84.966	-19.6668
15	3.6417	-0.6878	-0.4201	7.1085	1.0879	3.7438	-0.1872	-0.0329	-0.0933	-0.1522	0.213	0.3103	0.3968	-0.3298	-0.0258	0.3118	-0.0448	0.0184	0.1042	0.1076	0.1537	-35.9888	-100.0106	-20.2805
16	2.3046	-0.0738	-0.4777	6.4253	0.7008	7.3356	0.0134	0.4336	0.4311	-1.4049	0.038	-0.6849	-1.1304	0.2329	-0.0514	0.924	-0.0122	0.0629	0.2533	0.1148	0.3957	-18.2358	-48.6344	-23.0556
17	2.849	-1.2615	-2.1642	5.1005	5.0746	6.9923	-0.1814	-0.0935	0.0609	-0.0324	0.1389	0.0752	-0.0854	0.2586	0.0425	0.2097	0.0029	0.0635	0.1216	0.0702	0.2184	-12.0501	-68.2915	-14.5761
18	4.9481	1.1442	0.8316	6.9206	-0.0127	8.5729	-0.0006	0.0081	0.4251	-0.4566	0.1547	0.213	-0.9081	-0.6397	-0.1541	0.3916	0.1189	0.0266	0.2032	-0.0161	0.2764	-23.7884	-48.7292	-6.717

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	B	4 - 122
2	X-RAY DIFFRACTION	1	B	301
3	X-RAY DIFFRACTION	2	B	152 - 210
4	X-RAY DIFFRACTION	3	B	123 - 151
5	X-RAY DIFFRACTION	3	B	211 - 254
6	X-RAY DIFFRACTION	4	A	1 - 122
7	X-RAY DIFFRACTION	4	A	301
8	X-RAY DIFFRACTION	5	A	152 - 210
9	X-RAY DIFFRACTION	6	A	123 - 151
10	X-RAY DIFFRACTION	6	A	211 - 254
11	X-RAY DIFFRACTION	7	C	1 - 122
12	X-RAY DIFFRACTION	7	C	301
13	X-RAY DIFFRACTION	8	C	152 - 210
14	X-RAY DIFFRACTION	9	C	123 - 151
15	X-RAY DIFFRACTION	9	C	211 - 254
16	X-RAY DIFFRACTION	10	F	4 - 122
17	X-RAY DIFFRACTION	10	F	301
18	X-RAY DIFFRACTION	11	F	152 - 210
19	X-RAY DIFFRACTION	12	F	123 - 151
20	X-RAY DIFFRACTION	12	F	211 - 254
21	X-RAY DIFFRACTION	13	E	1 - 122
22	X-RAY DIFFRACTION	13	E	301
23	X-RAY DIFFRACTION	14	E	152 - 210
24	X-RAY DIFFRACTION	15	E	123 - 151
25	X-RAY DIFFRACTION	15	E	211 - 254
26	X-RAY DIFFRACTION	16	D	4 - 122
27	X-RAY DIFFRACTION	16	D	301
28	X-RAY DIFFRACTION	17	D	152 - 210
29	X-RAY DIFFRACTION	18	D	123 - 151
30	X-RAY DIFFRACTION	18	D	211 - 254

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Protein , 1 types, 6 molecules ABCDEF

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Non-polymers , 5 types, 140 molecules

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-Yorodumi

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Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Protein , 1 types, 6 molecules ABCDEF

-
Non-polymers , 5 types, 140 molecules

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

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

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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

+
Jul 12, 2017. Major update of PDB

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Yorodumi