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

ID or keywords:

Entry

Database: PDB / ID: 4hgy

Title

Structure of the CcbJ Methyltransferase from Streptomyces caelestis

Components

CcbJ

Keywords

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

Function / homology

Function and homology information

N-methyltransferase activity / methylation
Similarity search - Function

Biological species

Streptomyces caelestis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 3 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	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_ref_seq_dif / 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_ref_seq_dif.details / _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	4hgy.cif.gz	550.1 KB	Display	PDBx/mmCIF format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hg/4hgy ftp://data.pdbj.org/pub/pdb/validation_reports/hg/4hgy	HTTPS FTP

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Related structure data

Related structure data	4hgzC 4hh4C C: citing same article (ref.)
Similar structure data	4hgz-d 4hh4-d 6tlk-d 3mog-d 1wzn-1 1exb-1 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

183 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)	168.180, 245.140, 117.830
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 domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	19 - 30
2	1	1	1	B	19 - 30
3	1	1	1	C	19 - 30
4	1	1	1	D	19 - 30
5	1	1	1	E	19 - 30
6	1	1	1	F	19 - 30
1	2	1	1	A	106 - 116
2	2	1	1	B	106 - 116
3	2	1	1	C	106 - 116
4	2	1	1	D	106 - 116
5	2	1	1	E	106 - 116
6	2	1	1	F	106 - 116
1	3	1	1	A	77 - 80
2	3	1	1	B	77 - 80
3	3	1	1	C	77 - 80
4	3	1	1	D	77 - 80
5	3	1	1	E	77 - 80
6	3	1	1	F	77 - 80
1	4	1	1	A	46 - 50
2	4	1	1	B	46 - 50
3	4	1	1	C	46 - 50
4	4	1	1	D	46 - 50
5	4	1	1	E	46 - 50
6	4	1	1	F	46 - 50
1	5	1	1	A	57 - 60
2	5	1	1	B	57 - 60
3	5	1	1	C	57 - 60
4	5	1	1	D	57 - 60
5	5	1	1	E	57 - 60
6	5	1	1	F	57 - 60
1	6	1	1	A	92 - 95
2	6	1	1	B	92 - 95
3	6	1	1	C	92 - 95
4	6	1	1	D	92 - 95
5	6	1	1	E	92 - 95
6	6	1	1	F	92 - 95
1	7	1	1	A	118 - 134
2	7	1	1	B	118 - 134
3	7	1	1	C	118 - 134
4	7	1	1	D	118 - 134
5	7	1	1	E	118 - 134
6	7	1	1	F	118 - 134
1	8	1	1	A	136 - 196
2	8	1	1	B	136 - 196
3	8	1	1	C	136 - 196
4	8	1	1	D	136 - 196
5	8	1	1	E	136 - 196
6	8	1	1	F	136 - 196
1	9	1	1	A	198 - 201
2	9	1	1	B	198 - 201
3	9	1	1	C	198 - 201
4	9	1	1	D	198 - 201
5	9	1	1	E	198 - 201
6	9	1	1	F	198 - 201
1	10	1	1	A	203 - 235
2	10	1	1	B	203 - 235
3	10	1	1	C	203 - 235
4	10	1	1	D	203 - 235
5	10	1	1	E	203 - 235
6	10	1	1	F	203 - 235
1	11	1	1	A	237
2	11	1	1	B	237
3	11	1	1	C	237
4	11	1	1	D	237
5	11	1	1	E	237
6	11	1	1	F	237
1	12	1	1	A	239 - 252
2	12	1	1	B	239 - 252
3	12	1	1	C	239 - 252
4	12	1	1	D	239 - 252
5	12	1	1	E	239 - 252
6	12	1	1	F	239 - 252
1	1	2	1	A	41 - 45
2	1	2	1	C	41 - 45
3	1	2	1	D	41 - 45
1	1	3	1	A	51 - 53
2	1	3	1	B	51 - 53
3	1	3	1	C	51 - 53
4	1	3	1	E	51 - 53
5	1	3	1	F	51 - 53
1	1	4	1	A	32 - 34
2	1	4	1	C	32 - 34
3	1	4	1	D	32 - 34
4	1	4	1	E	32 - 34
5	1	4	1	F	32 - 34
1	2	4	1	A	36 - 40
2	2	4	1	C	36 - 40
3	2	4	1	D	36 - 40
4	2	4	1	E	36 - 40
5	2	4	1	F	36 - 40
1	3	4	1	A	54 - 56
2	3	4	1	C	54 - 56
3	3	4	1	D	54 - 56
4	3	4	1	E	54 - 56
5	3	4	1	F	54 - 56
1	4	4	1	A	61 - 65
2	4	4	1	C	61 - 65
3	4	4	1	D	61 - 65
4	4	4	1	E	61 - 65
5	4	4	1	F	61 - 65
1	5	4	1	A	117
2	5	4	1	C	117
3	5	4	1	D	117
4	5	4	1	E	117
5	5	4	1	F	117
1	6	4	3	A	135
2	6	4	3	C	135
3	6	4	3	D	135
4	6	4	3	E	135
5	6	4	3	F	135
1	1	5	1	A	238
2	1	5	1	D	238
3	1	5	1	E	238
4	1	5	1	F	238
1	1	6	1	A	35
2	1	6	1	B	35
3	1	6	1	D	35
4	1	6	1	E	35
5	1	6	1	F	35
1	2	6	1	A	236
2	2	6	1	B	236
3	2	6	1	D	236
4	2	6	1	E	236
5	2	6	1	F	236
1	1	7	1	B	81 - 90
2	1	7	1	C	81 - 90
3	1	7	1	D	81 - 90
4	1	7	1	E	81 - 90
5	1	7	1	F	81 - 90
1	1	8	1	A	31
2	1	8	1	C	31
1	1	9	4	B	31
2	1	9	4	D	31
3	1	9	4	E	31
4	1	9	4	F	31
1	1	10	3	D	197
2	1	10	3	E	197
3	1	10	3	F	197
1	2	10	3	D	202
2	2	10	3	E	202
3	2	10	3	F	202

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10

#1: Protein	CcbJ Mass: 30286.164 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces caelestis (bacteria) / Gene: ccbJ / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) / References: UniProt: E9JES0
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 11 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 92 / 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: 3.34 Å³/Da / Density % sol: 63.19 %
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% ethylene glycol, 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: 0.97936, 0.97944, 0.97549

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: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.97936	1
2	0.97944	1
3	0.97549	1

Reflection

Resolution: 3→62.4 Å / Num. all: 49290 / Num. obs: 49290 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 14.6 % / B_iso Wilson estimate: 62.3 Å² / R_merge(I) obs: 0.076 / Net I/σ(I): 25.9

Reflection shell

Resolution: 3→3.16 Å / Redundancy: 14.9 % / R_merge(I) obs: 0.378 / Mean I/σ(I) obs: 7.5 / Num. unique all: 7117 / % possible all: 100

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
BP3		model building
REFMAC	5.5.0109	refinement
MOSFLM		data reduction
SCALA		data scaling
BP3		phasing

Refinement

Method to determine structure:

MAD / Resolution: 3→62.36 Å / Cor.coef. F_o:F_c: 0.912 / Cor.coef. F_o:F_c free: 0.897 / SU B: 31.367 / SU ML: 0.266 / Cross valid method: THROUGHOUT / ESU R: 1.328 / ESU R Free: 0.366 / Stereochemistry target values: Engh & Huber / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.24791	2480	5.1 %	RANDOM
R_work	0.22518	-	-	-
all	0.22633	49069	-	-
obs	0.22633	46589	99.94 %	-

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: 62.292 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.59 Å²	-0 Å²	0 Å²
2-	-	1.52 Å²	0 Å²
3-	-	-	-0.93 Å²

Refinement step

Cycle: LAST / Resolution: 3→62.36 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10753	0	71	92	10916

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.004	0.022	11046
X-RAY DIFFRACTION	r_angle_refined_deg	0.747	1.973	15012
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	4.492	5	1401
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.475	23.169	527
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.807	15	1678
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15	15	102
X-RAY DIFFRACTION	r_chiral_restr	0.051	0.2	1655
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.021	8610
X-RAY DIFFRACTION	r_mcbond_it	0.748	1.5	6987
X-RAY DIFFRACTION	r_mcangle_it	1.464	2	11116
X-RAY DIFFRACTION	r_scbond_it	2.071	3	4059
X-RAY DIFFRACTION	r_scangle_it	3.613	4.5	3896

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	1253	TIGHT POSITIONAL	0.05	0.05
1	2	B	1253	TIGHT POSITIONAL	0.1	0.05
1	3	C	1253	TIGHT POSITIONAL	0.06	0.05
1	4	D	1253	TIGHT POSITIONAL	0.05	0.05
1	5	E	1253	TIGHT POSITIONAL	0.06	0.05
1	6	F	1253	TIGHT POSITIONAL	0.05	0.05
1	1	A	1253	TIGHT THERMAL	0.1	0.5
1	2	B	1253	TIGHT THERMAL	0.12	0.5
1	3	C	1253	TIGHT THERMAL	0.1	0.5
1	4	D	1253	TIGHT THERMAL	0.11	0.5
1	5	E	1253	TIGHT THERMAL	0.09	0.5
1	6	F	1253	TIGHT THERMAL	0.08	0.5
2	1	A	33	TIGHT POSITIONAL	0.03	0.05
2	2	C	33	TIGHT POSITIONAL	0.05	0.05
2	3	D	33	TIGHT POSITIONAL	0.03	0.05
2	1	A	33	TIGHT THERMAL	0.06	0.5
2	2	C	33	TIGHT THERMAL	0.06	0.5
2	3	D	33	TIGHT THERMAL	0.08	0.5
3	1	A	18	TIGHT POSITIONAL	0.02	0.05
3	2	B	18	TIGHT POSITIONAL	0.03	0.05
3	3	C	18	TIGHT POSITIONAL	0.04	0.05
3	4	E	18	TIGHT POSITIONAL	0.03	0.05
3	5	F	18	TIGHT POSITIONAL	0.02	0.05
3	1	A	18	TIGHT THERMAL	0.06	0.5
3	2	B	18	TIGHT THERMAL	0.09	0.5
3	3	C	18	TIGHT THERMAL	0.06	0.5
3	4	E	18	TIGHT THERMAL	0.07	0.5
3	5	F	18	TIGHT THERMAL	0.05	0.5
4	1	A	124	TIGHT POSITIONAL	0.04	0.05
4	2	C	124	TIGHT POSITIONAL	0.04	0.05
4	3	D	124	TIGHT POSITIONAL	0.03	0.05
4	4	E	124	TIGHT POSITIONAL	0.04	0.05
4	5	F	124	TIGHT POSITIONAL	0.03	0.05
4	1	A	5	LOOSE POSITIONAL	0.04	5
4	2	C	5	LOOSE POSITIONAL	0.08	5
4	3	D	5	LOOSE POSITIONAL	0.04	5
4	4	E	5	LOOSE POSITIONAL	0.05	5
4	5	F	5	LOOSE POSITIONAL	0.02	5
4	1	A	124	TIGHT THERMAL	0.1	0.5
4	2	C	124	TIGHT THERMAL	0.1	0.5
4	3	D	124	TIGHT THERMAL	0.12	0.5
4	4	E	124	TIGHT THERMAL	0.09	0.5
4	5	F	124	TIGHT THERMAL	0.08	0.5
4	1	A	5	LOOSE THERMAL	0.08	10
4	2	C	5	LOOSE THERMAL	0.08	10
4	3	D	5	LOOSE THERMAL	0.07	10
4	4	E	5	LOOSE THERMAL	0.03	10
4	5	F	5	LOOSE THERMAL	0.05	10
5	1	A	11	TIGHT POSITIONAL	0.15	0.05
5	2	D	11	TIGHT POSITIONAL	0.16	0.05
5	3	E	11	TIGHT POSITIONAL	0.16	0.05
5	4	F	11	TIGHT POSITIONAL	0.46	0.05
5	1	A	11	TIGHT THERMAL	0.04	0.5
5	2	D	11	TIGHT THERMAL	0.03	0.5
5	3	E	11	TIGHT THERMAL	0.05	0.5
5	4	F	11	TIGHT THERMAL	0.03	0.5
6	1	A	19	TIGHT POSITIONAL	0.03	0.05
6	2	B	19	TIGHT POSITIONAL	0.05	0.05
6	3	D	19	TIGHT POSITIONAL	0.03	0.05
6	4	E	19	TIGHT POSITIONAL	0.06	0.05
6	5	F	19	TIGHT POSITIONAL	0.02	0.05
6	1	A	19	TIGHT THERMAL	0.07	0.5
6	2	B	19	TIGHT THERMAL	0.13	0.5
6	3	D	19	TIGHT THERMAL	0.11	0.5
6	4	E	19	TIGHT THERMAL	0.12	0.5
6	5	F	19	TIGHT THERMAL	0.08	0.5
7	1	B	73	TIGHT POSITIONAL	0.03	0.05
7	2	C	73	TIGHT POSITIONAL	0.04	0.05
7	3	D	73	TIGHT POSITIONAL	0.02	0.05
7	4	E	73	TIGHT POSITIONAL	0.02	0.05
7	5	F	73	TIGHT POSITIONAL	0.02	0.05
7	1	B	73	TIGHT THERMAL	0.03	0.5
7	2	C	73	TIGHT THERMAL	0.06	0.5
7	3	D	73	TIGHT THERMAL	0.04	0.5
7	4	E	73	TIGHT THERMAL	0.03	0.5
7	5	F	73	TIGHT THERMAL	0.03	0.5
8	1	A	11	TIGHT POSITIONAL	0.02	0.05
8	1	A	11	TIGHT THERMAL	0.07	0.5
9	1	B	11	MEDIUM POSITIONAL	0.23	0.5
9	2	D	11	MEDIUM POSITIONAL	0.16	0.5
9	3	E	11	MEDIUM POSITIONAL	0.25	0.5
9	4	F	11	MEDIUM POSITIONAL	0.16	0.5
9	1	B	11	MEDIUM THERMAL	0.33	2
9	2	D	11	MEDIUM THERMAL	0.38	2
9	3	E	11	MEDIUM THERMAL	0.59	2
9	4	F	11	MEDIUM THERMAL	0.31	2
10	1	D	8	TIGHT POSITIONAL	0.02	0.05
10	2	E	8	TIGHT POSITIONAL	0.03	0.05
10	3	F	8	TIGHT POSITIONAL	0.02	0.05
10	1	D	12	LOOSE POSITIONAL	0.04	5
10	2	E	12	LOOSE POSITIONAL	0.04	5
10	3	F	12	LOOSE POSITIONAL	0.05	5
10	1	D	8	TIGHT THERMAL	0.06	0.5
10	2	E	8	TIGHT THERMAL	0.05	0.5
10	3	F	8	TIGHT THERMAL	0.06	0.5
10	1	D	12	LOOSE THERMAL	0.15	10
10	2	E	12	LOOSE THERMAL	0.09	10
10	3	F	12	LOOSE THERMAL	0.12	10

LS refinement shell

Resolution: 3→3.078 Å / R_factor R_free error: 0.022 / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.296	177	-
R_work	0.295	3399	-
obs	-	3576	99.83 %

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	1.6595	0.8118	-0.6068	2.9863	0.2695	-0.0007	-0.0691	0.123	-0.1356	-0.2484	0.0111	0.0385	0.0431	-0.0171	0.058	0.2414	-0.0167	-0.0612	0.0887	-0.1129	0.0232	103.008	15.85	-16.82
2	1.9827	1.5306	2.4832	0.3509	0.48	3.7309	-0.0011	0.6246	0.0087	0.0098	0.1439	0.1487	-0.0644	0.7737	-0.1428	-0.0212	-0.0326	0.0233	0.3724	-0.1482	0.1245	135.486	43.079	3.663
3	0.6121	-0.9291	-0.4433	1.2215	-0.8115	1.635	-0.1623	0.3786	0.1854	0.131	0.1633	-0.0774	0.1779	-0.1764	-0.001	-0.0179	-0.2562	-0.011	0.3163	0.1056	0.1298	101.549	62.347	-22.19
4	0.6854	1.8707	-0.9351	2.6561	-1.7892	2.4553	0.1297	-0.1608	-0.0006	0.6079	-0.1065	0.2682	-0.828	0.3483	-0.0232	0.3928	-0.1185	0.0167	0.1109	-0.083	0.0914	103.079	69.046	15.838
5	2.1483	-1.5501	-0.2328	2.0849	-0.3357	0.4272	-0.0469	0.0403	-0.1476	0.4193	0.1308	-0.0038	0.1011	-0.0767	-0.0839	0.2345	-0.0452	-0.0637	0.0282	-0.149	0.1009	110.383	23.922	25.327
6	1.3116	0.1757	1.3382	1.0909	1.5958	3.586	0.1371	-0.0282	-0.0844	0.0602	-0.3169	0.3975	0.0088	-0.4984	0.1798	0.0368	-0.0054	0.0567	0.1832	-0.0483	0.2399	73.739	36.463	-1.891

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	17 - 254
2	X-RAY DIFFRACTION	2	B	29 - 255
3	X-RAY DIFFRACTION	3	C	20 - 253
4	X-RAY DIFFRACTION	4	D	19 - 253
5	X-RAY DIFFRACTION	5	E	18 - 253
6	X-RAY DIFFRACTION	6	F	19 - 253

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