PDB-3bus: Crystal Structure of RebM

ID or keywords:

Entry

Database: PDB / ID: 3bus

Title

Crystal Structure of RebM

Components

Methyltransferase

Keywords

TRANSFERASE / rebeccamycin synthesis /

Methyltransferase

Function / homology

Function and homology information

demethylrebeccamycin-D-glucose O-methyltransferase / demethylrebeccamycin--D-glucose O-methyltransferase activity /

methyltransferase activity /

Biological species

Lechevalieria aerocolonigenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.65 Å

Authors

McCoy, J.G. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N.

Citation

Journal: J.Biol.Chem. / Year: 2008
Title: Structure and mechanism of the rebeccamycin sugar 4'-O-methyltransferase RebM.
Authors: Singh, S. / McCoy, J.G. / Zhang, C. / Bingman, C.A. / Phillips Jr., G.N. / Thorson, J.S.

History

Deposition	Jan 3, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 25, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Jan 30, 2013	Group: Database references / Structure summary
Revision 1.3	Oct 25, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3bus.cif.gz	102.3 KB	Display	PDBx/mmCIF format
PDB format	pdb3bus.ent.gz	85 KB	Display	PDB format
PDBx/mmJSON format	3bus.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/bu/3bus ftp://data.pdbj.org/pub/pdb/validation_reports/bu/3bus	HTTPS FTP

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Related structure data

Similar structure data	1ja9-d 1ese-d 1qfj-2 1qca-d 4oq0-d 6k94-3 5i9l-d 5xtg-d 6u0a-d 3o1t-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) 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: Methyltransferase

B: Methyltransferase

hetero molecules

60.3 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Methyltransferase

hetero molecules

defined by author&software
30.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Methyltransferase

hetero molecules

defined by author&software
30.2 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	119.153, 119.153, 84.412
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Methyltransferase / / RebM Mass: 29790.209 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Lechevalieria aerocolonigenes (bacteria) Gene: rbmF, rebM / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS / References: UniProt: Q8KI52, UniProt: Q8KZ94*PLUS
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE / S-Adenosyl-L-homocysteine Type: L-peptide linking / Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 6 / 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: 2.51 Å³/Da / Density % sol: 51.08 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5 Details: MEPEG 5000, NH4SO4, Na Acetate, pH 5.0, vapor diffusion, hanging drop, temperature 293K

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Data collection

Diffraction

Mean temperature: 93 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 0.9804 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 10, 2007

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9804 Å / Relative weight: 1

Reflection

Resolution: 2.65→50 Å / Num. obs: 17746 / % possible obs: 97.2 % / Redundancy: 25.9 % / R_merge(I) obs: 0.074 / Χ²: 1.11 / Net I/σ(I): 13.6

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.65-2.74	14.5	0.382	1444	0.946	1	81.3
2.74-2.85	17.5	0.332	1665	0.95	1	93.2
2.85-2.98	23.4	0.304	1773	0.974	1	99.2
2.98-3.14	28.4	0.238	1801	1.006	1	99.5
3.14-3.34	29.3	0.148	1771	1.093	1	99.8
3.34-3.6	29.3	0.096	1794	1.108	1	99.7
3.6-3.96	29.1	0.073	1826	1.116	1	99.8
3.96-4.53	28.9	0.06	1832	1.123	1	99.8
4.53-5.71	28.5	0.063	1866	1.128	1	99.9
5.71-50	26.6	0.053	1974	1.452	1	99.2

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Phasing

Phasing

Method:

SAD

Phasing MAD set

ID	Highest resolution (Å)	Lowest resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	2.65	39.78	0	0	15150	2547
ANO_1	2.65	39.78	1.823	0	14667	0

Phasing MAD set shell

ID	Resolution (Å)	Power acentric	Reflection acentric	Reflection centric
ISO_1	11.38-39.78	0	144	126
ISO_1	8.22-11.38	0	286	128
ISO_1	6.76-8.22	0	389	130
ISO_1	5.87-6.76	0	463	137
ISO_1	5.27-5.87	0	530	126
ISO_1	4.81-5.27	0	607	139
ISO_1	4.46-4.81	0	657	126
ISO_1	4.18-4.46	0	695	135
ISO_1	3.94-4.18	0	755	137
ISO_1	3.74-3.94	0	810	128
ISO_1	3.57-3.74	0	857	132
ISO_1	3.42-3.57	0	877	129
ISO_1	3.28-3.42	0	932	139
ISO_1	3.16-3.28	0	973	131
ISO_1	3.06-3.16	0	1001	127
ISO_1	2.96-3.06	0	1055	136
ISO_1	2.87-2.96	0	1063	126
ISO_1	2.79-2.87	0	1077	116
ISO_1	2.72-2.79	0	1029	95
ISO_1	2.65-2.72	0	950	104
ANO_1	11.38-39.78	4.261	144	0
ANO_1	8.22-11.38	4.129	286	0
ANO_1	6.76-8.22	4.91	389	0
ANO_1	5.87-6.76	5.102	463	0
ANO_1	5.27-5.87	4.485	530	0
ANO_1	4.81-5.27	3.513	607	0
ANO_1	4.46-4.81	3.119	657	0
ANO_1	4.18-4.46	3.234	695	0
ANO_1	3.94-4.18	2.785	755	0
ANO_1	3.74-3.94	2.631	810	0
ANO_1	3.57-3.74	2.204	857	0
ANO_1	3.42-3.57	1.771	877	0
ANO_1	3.28-3.42	1.522	932	0
ANO_1	3.16-3.28	1.111	973	0
ANO_1	3.06-3.16	0.939	1000	0
ANO_1	2.96-3.06	0.68	1055	0
ANO_1	2.87-2.96	0.493	1042	0
ANO_1	2.79-2.87	0.416	976	0
ANO_1	2.72-2.79	0.342	870	0
ANO_1	2.65-2.72	0.285	749	0

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 17696

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
9.08-100	69.2	0.688	515
7.16-9.08	57	0.846	505
6.21-7.16	58.9	0.827	510
5.62-6.21	60.2	0.859	502
5.21-5.62	54.8	0.88	507
4.89-5.21	51.2	0.907	508
4.63-4.89	55.1	0.916	535
4.41-4.63	52.8	0.933	542
4.21-4.41	56	0.914	568
4.04-4.21	57.9	0.911	604
3.89-4.04	56.8	0.916	628
3.76-3.89	62.4	0.904	632
3.63-3.76	64.4	0.884	661
3.52-3.63	60.1	0.905	685
3.42-3.52	64.2	0.889	706
3.33-3.42	63.7	0.873	710
3.24-3.33	66.3	0.869	737
3.16-3.24	68.5	0.834	768
3.09-3.16	72.7	0.83	767
3.02-3.09	73.7	0.816	799
2.96-3.02	79.1	0.805	814
2.9-2.96	71.3	0.762	809
2.84-2.9	78.8	0.728	827
2.78-2.84	84.7	0.746	812
2.73-2.78	82.2	0.691	782
2.65-2.73	81.5	0.664	1263

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	3.004	data extraction

Refinement

Method to determine structure:

SAD / Resolution: 2.65→45.04 Å / Cor.coef. F_o:F_c: 0.946 / Cor.coef. F_o:F_c free: 0.916 / SU B: 33.609 / SU ML: 0.308 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.857 / ESU R Free: 0.335 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.26	901	5.1 %	RANDOM
R_work	0.214	-	-	-
obs	0.217	17714	97.26 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 59.516 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.38 Å²	0 Å²	0 Å²
2-	-	1.38 Å²	0 Å²
3-	-	-	-2.76 Å²

Refinement step

Cycle: LAST / Resolution: 2.65→45.04 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3709	0	52	6	3767

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	3824
X-RAY DIFFRACTION	r_angle_refined_deg	1.33	1.979	5191
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.866	5	490
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.293	23.006	173
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	20.311	15	598
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.836	15	42
X-RAY DIFFRACTION	r_chiral_restr	0.094	0.2	591
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	2940
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	1484
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	2571
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.14	0.2	94
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.219	0.2	25
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.147	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	0.405	1.5	2508
X-RAY DIFFRACTION	r_mcangle_it	0.7	2	3897
X-RAY DIFFRACTION	r_scbond_it	0.978	3	1478
X-RAY DIFFRACTION	r_scangle_it	1.569	4.5	1294

LS refinement shell

Resolution: 2.65→2.718 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.394	52	-
R_work	0.377	1005	-
all	-	1057	-
obs	-	-	79.41 %

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	5.9316	0.5145	-1.0275	6.4537	2.2025	12.4799	-0.3427	-0.3067	0.2091	0.3473	0.1798	0.0091	-0.3018	-0.5362	0.1628	0.0623	0.0987	0.0863	-0.2797	0.0398	-0.1008	10.0439	41.3233	25.3909
2	7.1944	0.0857	-2.7422	3.409	-0.1012	5.0779	-0.6684	0.2294	-0.2533	-0.2123	0.3536	0.1184	0.8896	-1.3808	0.3148	0.1863	-0.0893	0.1497	-0.1532	0.0071	-0.0993	3.3933	30.0924	25.5115
3	7.6843	-1.5293	-3.3994	3.0557	0.4825	12.1355	-1.0568	0.5877	-1.2766	-0.2149	0.4257	0.2816	2.2409	-1.0563	0.6311	0.5216	-0.2366	0.2243	-0.5041	-0.0562	-0.0063	7.5751	23.1558	20.3879
4	6.8846	-1.6009	1.1083	5.498	-3.0723	8.3517	-0.4209	0.3383	-0.0485	-0.1195	0.1008	-0.4428	1.3939	0.5014	0.3202	0.291	0.0468	0.2946	-0.4743	0.0237	-0.1002	18.8491	28.9776	20.4269
5	1.7821	1.3728	-0.8586	4.1565	1.9154	5.7738	-0.2942	0.1022	-0.4875	0.0985	0.3017	-0.6249	0.2785	1.2737	-0.0074	0.1818	0.0961	0.113	-0.1429	0.1335	-0.0149	24.8927	36.6769	24.1251
6	2.833	0.0307	-0.4791	2.0449	-0.7935	7.7478	-0.4474	-0.2165	0.0501	0.2233	0.2202	-0.2313	-0.1096	1.1654	0.2271	0.0784	0.028	0.0671	-0.3124	0.05	-0.0897	21.6829	40.0472	29.0877
7	2.8202	1.5289	0.1388	3.3465	0.6356	5.7627	-0.0452	-0.4545	-0.0058	0.5271	0.0293	-0.2444	-0.2718	0.6208	0.0159	0.126	0.1858	0.0392	-0.3295	0.0771	-0.0735	19.9065	39.7744	36.335
8	4.0961	1.0894	0.1299	6.3501	-0.5475	4.8413	0.5331	0.401	0.6553	0.7418	0.2497	0.6835	-0.6847	-1.5117	-0.7828	0.3453	-0.0242	0.3046	-0.0477	0.2163	0.0505	22.2071	61.3923	5.0117
9	10.5248	1.4159	-0.2037	6.7628	-4.7317	6.4212	0.3691	0.133	0.2317	1.7191	-0.2429	0.4699	-1.7868	-0.5398	-0.1262	0.5407	-0.1225	0.3186	-0.4671	0.0331	-0.0817	29.2847	72.1783	3.8155
10	3.2008	3.2438	-2.1371	9.8868	-5.7022	8.4548	0.7638	0.0304	0.364	1.7211	-0.9137	-0.945	-1.1424	0.859	0.1498	0.3104	-0.3299	-0.0583	-0.346	0.1146	-0.003	36.319	62.8659	9.1855
11	12.7811	1.0296	-7.0699	10.2747	-3.3977	13.5517	0.3542	-1.2173	-0.2089	1.2706	-0.9856	-1.6416	-1.0723	3.4269	0.6315	0.1394	-0.3813	-0.3026	0.2049	0.4098	0.1747	40.8209	57.4703	11.069
12	3.8749	2.0078	-3.582	11.0603	3.1525	9.8162	-0.6007	0.4525	-0.7833	-0.0389	0.1577	-0.952	2.6179	0.5475	0.443	0.5897	-0.0518	0.1409	-0.2323	0.0086	0.132	32.342	47.3129	-2.2427
13	0.6384	0.6582	-1.3561	5.2497	-6.1681	17.0076	-0.1453	0.5929	-0.2096	-0.5394	0.046	-0.1186	1.4502	-0.1775	0.0992	0.086	-0.2743	0.0471	-0.1019	0.0624	-0.0077	26.0887	52.8996	-5.2384
14	5.2295	-0.9466	-1.1509	6.9449	-3.9234	9.4552	-0.6857	-0.2673	-0.1892	-0.0347	-0.0824	0.3829	0.8394	-0.4842	0.7681	0.1698	-0.4209	0.2165	-0.4756	0.0699	0.0189	26.1841	48.432	2.8964

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	24 - 72	24 - 72
2	X-RAY DIFFRACTION	2	A	A	73 - 106	73 - 106
3	X-RAY DIFFRACTION	3	A	A	107 - 128	107 - 128
4	X-RAY DIFFRACTION	4	A	A	129 - 152	129 - 152
5	X-RAY DIFFRACTION	5	A	A	153 - 181	153 - 181
6	X-RAY DIFFRACTION	6	A	A	182 - 237	182 - 237
7	X-RAY DIFFRACTION	7	A	A	238 - 273	238 - 273
8	X-RAY DIFFRACTION	8	B	B	26 - 72	26 - 72
9	X-RAY DIFFRACTION	9	B	B	73 - 120	73 - 120
10	X-RAY DIFFRACTION	10	B	B	121 - 141	121 - 141
11	X-RAY DIFFRACTION	11	B	B	142 - 157	142 - 157
12	X-RAY DIFFRACTION	12	B	B	158 - 194	158 - 194
13	X-RAY DIFFRACTION	13	B	B	195 - 254	195 - 254
14	X-RAY DIFFRACTION	14	B	B	255 - 273	255 - 273

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