PDB-3lst: Crystal Structure of CalO1, Methyltransferase in Calicheamicin Bi...

ID or keywords:

Entry

Database: PDB / ID: 3lst

Title

Crystal Structure of CalO1, Methyltransferase in Calicheamicin Biosynthesis, SAH bound form

Components

CalO1 Methyltransferase

Keywords

TRANSFERASE / Calicheamicin / Methyltransferase / CalO1 / enediyne / SAH / Structural Genomics / PSI-2 / Protein Structure Initiative / Center for Eukaryotic Structural Genomics / CESG

Function / homology

Function and homology information

O-methyltransferase activity / protein dimerization activity
Similarity search - Function

Biological species

Micromonospora echinospora (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 2.4 Å

Authors

Chang, A. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips Jr., G.N. / Center for Eukaryotic Structural Genomics (CESG)

Citation

Journal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structural characterization of CalO1: a putative orsellinic acid methyltransferase in the calicheamicin-biosynthetic pathway.
Authors: Chang, A. / Singh, S. / Bingman, C.A. / Thorson, J.S. / Phillips, G.N.

History

Deposition	Feb 12, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Mar 2, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 1, 2017	Group: Refinement description / Category: software
Revision 1.3	Oct 16, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _chem_comp.mon_nstd_flag / _chem_comp.type ..._chem_comp.mon_nstd_flag / _chem_comp.type / _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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Download

PDBx/mmCIF format	3lst.cif.gz	275.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3lst.ent.gz	223.4 KB	Display	PDB format
PDBx/mmJSON format	3lst.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/ls/3lst ftp://data.pdbj.org/pub/pdb/validation_reports/ls/3lst	HTTPS FTP

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Related structure data

Similar structure data	4u1q-1 3pzr-1 4x3q-2 6nej-d 4x3q-1 1brm-1 1mb4-d 3fg1-2 1f4l-d 4nu5-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: CalO1 Methyltransferase

B: CalO1 Methyltransferase

hetero molecules

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

1

A: CalO1 Methyltransferase

hetero molecules

A: CalO1 Methyltransferase

hetero molecules

defined by author&software
76.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: CalO1 Methyltransferase

hetero molecules

B: CalO1 Methyltransferase

hetero molecules

defined by author&software
76.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.515, 93.603, 240.971
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	B-398- HOH
2	1	B-429- HOH

Details

The biological unit is a dimer. There are half of 2 biological units in the asymmetric unit. The dimer generated from the monomer in the asymmetric unit by the operations: x, -y,-z and -x, y,-z+1/2

#1: Protein	CalO1 Methyltransferase Mass: 37936.082 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calO1 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q8KNE5
#2: Chemical	ChemComp-SAH / S-ADENOSYL-L-HOMOCYSTEINE Mass: 384.411 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₄H₂₀N₆O₅S
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 181 / 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: 2.36 Å³/Da / Density % sol: 47.89 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7 Details: Protein Solution 20mg/ml CalO1 protein, 20mM Tris pH 8, mixed in a 1:1 ratio with the well solution 20% MEPEG 5K, 0.2M Glycine, 0.1M BTP pH 7.0. Cryoprotected with 20% ethylene glycol, 20% ...Details: Protein Solution 20mg/ml CalO1 protein, 20mM Tris pH 8, mixed in a 1:1 ratio with the well solution 20% MEPEG 5K, 0.2M Glycine, 0.1M BTP pH 7.0. Cryoprotected with 20% ethylene glycol, 20% MEPEG 5K, 0.2M Glycine, 0.1M BTP pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal

Density Matthews: 2.36 Å³/Da / Density % sol: 47.89 %

Crystal grow

Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: Protein Solution 20mg/ml CalO1 protein, 20mM Tris pH 8, mixed in a 1:1 ratio with the well solution 20% MEPEG 5K, 0.2M Glycine, 0.1M BTP pH 7.0. Cryoprotected with 20% ethylene glycol, 20% ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.9794, 0.9641

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 6, 2009 / Details: Adjustable focusing mirrors in K-B geometry

Radiation

Monochromator: Si(111) Double Crystal Monochromater / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

ID	Wavelength (Å)	Relative weight
1	0.9794	1
2	0.9641	1

Reflection

Redundancy: 12.3 % / Av σ(I) over netI: 22.53 / Number: 344828 / R_merge(I) obs: 0.12 / Χ²: 1.39 / D res high: 2.4 Å / D res low: 50 Å / Num. obs: 28057 / % possible obs: 97.7

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
6.51	50	99.8	1	0.072	3.337	13.4
5.17	6.51	100	1	0.088	2.035	13.8
4.52	5.17	100	1	0.084	1.571	13.5
4.1	4.52	100	1	0.088	1.314	13.1
3.81	4.1	99.9	1	0.085	1.279	13
3.58	3.81	100	1	0.093	1.236	13.1
3.41	3.58	100	1	0.111	1.192	13
3.26	3.41	100	1	0.13	1.104	12.9
3.13	3.26	100	1	0.156	1.172	13.1
3.02	3.13	100	1	0.191	1.185	12.8
2.93	3.02	100	1	0.208	1.26	13
2.85	2.93	100	1	0.243	1.151	12.9
2.77	2.85	100	1	0.292	1.204	12.6
2.7	2.77	100	1	0.333	1.183	12.4
2.64	2.7	99.2	1	0.369	1.092	11.5
2.59	2.64	97.6	1	0.404	1.128	11.1
2.53	2.59	95.2	1	0.404	1.155	10.3
2.49	2.53	91.2	1	0.437	1.134	10.1
2.44	2.49	87.7	1	0.513	1.107	9.5
2.4	2.44	83.4	1	0.525	1.051	9

Reflection

Resolution: 2.4→50 Å / Num. obs: 28057 / % possible obs: 97.7 % / Redundancy: 12.3 % / R_merge(I) obs: 0.12 / Χ²: 1.387 / Net I/σ(I): 9.7

Reflection shell

Resolution: 2.4→2.44 Å / Redundancy: 9 % / R_merge(I) obs: 0.525 / Num. unique all: 1182 / Χ²: 1.051 / % possible all: 83.4

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Phasing

Phasing

Method:

MAD

Phasing MAD

D res high: 2.4 Å / D res low: 48.17 Å / FOM acentric: 0.462 / FOM centric: 0.305 / Reflection acentric: 25104 / Reflection centric: 2856

Phasing MAD set

ID	R cullis acentric	R cullis centric	Highest resolution (Å)	Lowest resolution (Å)	Reflection acentric	Reflection centric
ISO_1	0	0	2.4	48.17	25104	2856
ISO_2	0.873	0.865	2.4	48.17	24468	2820
ANO_1	0.648	0	2.4	48.17	24680	0
ANO_2	0.865	0	2.4	48.17	23912	0

Phasing MAD set shell

ID	Resolution (Å)	R cullis acentric	R cullis centric	Reflection acentric	Reflection centric
ISO_1	10.49-48.17	0	0	253	142
ISO_1	7.51-10.49	0	0	492	149
ISO_1	6.15-7.51	0	0	650	142
ISO_1	5.34-6.15	0	0	787	136
ISO_1	4.78-5.34	0	0	884	152
ISO_1	4.37-4.78	0	0	986	148
ISO_1	4.05-4.37	0	0	1085	141
ISO_1	3.79-4.05	0	0	1170	154
ISO_1	3.57-3.79	0	0	1274	141
ISO_1	3.39-3.57	0	0	1328	151
ISO_1	3.23-3.39	0	0	1404	144
ISO_1	3.1-3.23	0	0	1456	156
ISO_1	2.97-3.1	0	0	1523	137
ISO_1	2.87-2.97	0	0	1590	153
ISO_1	2.77-2.87	0	0	1666	144
ISO_1	2.68-2.77	0	0	1704	146
ISO_1	2.6-2.68	0	0	1762	147
ISO_1	2.53-2.6	0	0	1725	142
ISO_1	2.46-2.53	0	0	1694	109
ISO_1	2.4-2.46	0	0	1671	122
ANO_1	10.49-48.17	0.208	0	253	0
ANO_1	7.51-10.49	0.191	0	492	0
ANO_1	6.15-7.51	0.2	0	650	0
ANO_1	5.34-6.15	0.263	0	787	0
ANO_1	4.78-5.34	0.311	0	884	0
ANO_1	4.37-4.78	0.409	0	986	0
ANO_1	4.05-4.37	0.453	0	1084	0
ANO_1	3.79-4.05	0.466	0	1170	0
ANO_1	3.57-3.79	0.546	0	1274	0
ANO_1	3.39-3.57	0.6	0	1328	0
ANO_1	3.23-3.39	0.696	0	1404	0
ANO_1	3.1-3.23	0.733	0	1456	0
ANO_1	2.97-3.1	0.782	0	1523	0
ANO_1	2.87-2.97	0.845	0	1590	0
ANO_1	2.77-2.87	0.879	0	1664	0
ANO_1	2.68-2.77	0.91	0	1688	0
ANO_1	2.6-2.68	0.942	0	1722	0
ANO_1	2.53-2.6	0.959	0	1656	0
ANO_1	2.46-2.53	0.965	0	1577	0
ANO_1	2.4-2.46	0.975	0	1492	0
ISO_2	10.49-48.17	0.59	0.676	253	142
ISO_2	7.51-10.49	0.667	0.849	492	149
ISO_2	6.15-7.51	0.707	0.69	650	142
ISO_2	5.34-6.15	0.757	0.793	787	136
ISO_2	4.78-5.34	0.756	0.773	884	152
ISO_2	4.37-4.78	0.787	0.808	986	148
ISO_2	4.05-4.37	0.807	0.833	1085	141
ISO_2	3.79-4.05	0.846	0.879	1169	154
ISO_2	3.57-3.79	0.855	0.831	1274	141
ISO_2	3.39-3.57	0.853	0.876	1327	151
ISO_2	3.23-3.39	0.861	0.836	1404	144
ISO_2	3.1-3.23	0.865	0.9	1456	156
ISO_2	2.97-3.1	0.877	0.861	1520	137
ISO_2	2.87-2.97	0.898	0.943	1587	153
ISO_2	2.77-2.87	0.897	0.93	1665	143
ISO_2	2.68-2.77	0.923	0.94	1687	146
ISO_2	2.6-2.68	0.954	0.971	1706	137
ISO_2	2.53-2.6	0.967	1.023	1603	135
ISO_2	2.46-2.53	0.988	1.026	1506	100
ISO_2	2.4-2.46	0.942	0.985	1427	113
ANO_2	10.49-48.17	0.242	0	253	0
ANO_2	7.51-10.49	0.253	0	492	0
ANO_2	6.15-7.51	0.283	0	650	0
ANO_2	5.34-6.15	0.378	0	787	0
ANO_2	4.78-5.34	0.426	0	884	0
ANO_2	4.37-4.78	0.561	0	986	0
ANO_2	4.05-4.37	0.605	0	1085	0
ANO_2	3.79-4.05	0.675	0	1169	0
ANO_2	3.57-3.79	0.775	0	1274	0
ANO_2	3.39-3.57	0.809	0	1327	0
ANO_2	3.23-3.39	0.893	0	1404	0
ANO_2	3.1-3.23	0.918	0	1456	0
ANO_2	2.97-3.1	0.939	0	1520	0
ANO_2	2.87-2.97	0.959	0	1587	0
ANO_2	2.77-2.87	0.976	0	1655	0
ANO_2	2.68-2.77	0.981	0	1680	0
ANO_2	2.6-2.68	0.986	0	1630	0
ANO_2	2.53-2.6	0.99	0	1463	0
ANO_2	2.46-2.53	0.994	0	1357	0
ANO_2	2.4-2.46	0.995	0	1253	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	11.584	-10.507	-109.343	SE	31.73	0.8
2	20.946	-14.61	-121.932	SE	45.76	0.86
3	6.052	-6.327	-113.361	SE	60.46	0.96
4	29.513	-31.974	-234.832	SE	49.1	0.93
5	13.234	-15.18	-106.682	SE	57.08	0.87
6	9.9	-8.256	-113.346	SE	45.07	0.95
7	12.072	-0.981	-25.832	SE	39.4	0.87
8	29.118	-39.933	-129.084	SE	70.02	0.88
9	27.999	-12.541	-51.622	SE	82.19	0.98
10	28.837	-8.642	-49.804	SE	43.56	0.84
11	14.908	-23.274	-87.555	SE	69.29	0.91
12	25.496	-5.275	-40.249	SE	71.8	0.81
13	26.902	-20.95	-50.362	SE	58.68	0.8
14	21.364	-12.286	-45.572	SE	60.32	0.86
15	30.704	-16.175	-76.251	SE	44.4	0.71
16	26.112	-37.974	-225.473	SE	79	1.01
17	24.143	-2.438	-167.756	SE	43.81	0.63
18	30.69	-29.678	-230.421	SE	67.33	0.72
19	23.911	-23.059	-54.566	SE	62.3	0.71
20	4.751	-1.959	-9.237	SE	76.43	0.87
21	29.967	-17.543	-40.136	SE	98.66	0.64
22	26.151	-6.473	-46.189	SE	40.51	0.42
23	26.827	9.716	46.509	SE	64.36	0.45
24	1.004	9.473	169.403	SE	1	0.05

Phasing MAD shell

Resolution (Å)	FOM acentric	FOM centric	Reflection acentric	Reflection centric
10.49-48.17	0.889	0.652	253	142
7.51-10.49	0.872	0.632	492	149
6.15-7.51	0.853	0.568	650	142
5.34-6.15	0.804	0.508	787	136
4.78-5.34	0.76	0.456	884	152
4.37-4.78	0.693	0.411	986	148
4.05-4.37	0.668	0.36	1085	141
3.79-4.05	0.658	0.311	1170	154
3.57-3.79	0.605	0.311	1274	141
3.39-3.57	0.571	0.282	1328	151
3.23-3.39	0.512	0.259	1404	144
3.1-3.23	0.493	0.209	1456	156
2.97-3.1	0.446	0.182	1523	137
2.87-2.97	0.405	0.16	1590	153
2.77-2.87	0.353	0.142	1666	144
2.68-2.77	0.313	0.135	1704	146
2.6-2.68	0.258	0.137	1762	147
2.53-2.6	0.232	0.106	1725	142
2.46-2.53	0.208	0.098	1694	109
2.4-2.46	0.177	0.116	1671	122

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
PHENIX	1.5_2	refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MAD / Resolution: 2.4→48.174 Å / Occupancy max: 1 / Occupancy min: 0.46 / SU ML: 0.38 / σ(F): 1.32 / Stereochemistry target values: MLHL

	R_factor	Num. reflection	% reflection
R_free	0.251	1411	5.05 %
R_work	0.2	-	-
obs	0.203	27959	97.75 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 40 Å² / k_sol: 0.334 e/Å³

Displacement parameters

B_iso max: 210.78 Å² / B_iso mean: 51.029 Å² / B_iso min: 13.71 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.508 Å²	-0 Å²	0 Å²
2-	-	-2.326 Å²	-0 Å²
3-	-	-	1.891 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→48.174 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5020	0	60	181	5261

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.004	5222
X-RAY DIFFRACTION	f_angle_d	0.717	7098
X-RAY DIFFRACTION	f_chiral_restr	0.049	808
X-RAY DIFFRACTION	f_plane_restr	0.002	938
X-RAY DIFFRACTION	f_dihedral_angle_d	14.893	1882

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.4-2.486	0.303	122	0.259	2280	2402	86
2.486-2.585	0.33	144	0.245	2503	2647	93
2.585-2.703	0.331	126	0.25	2639	2765	99
2.703-2.845	0.28	159	0.229	2671	2830	100
2.845-3.024	0.285	130	0.222	2708	2838	100
3.024-3.257	0.29	152	0.228	2665	2817	100
3.257-3.585	0.237	131	0.217	2743	2874	100
3.585-4.103	0.235	138	0.169	2721	2859	100
4.103-5.169	0.205	142	0.145	2771	2913	100
5.169-48.183	0.204	167	0.173	2847	3014	100

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