PDB-3d0q: Crystal structure of calG3 from Micromonospora echinospora determ...

ID or keywords:

Entry

Database: PDB / ID: 3d0q

Title

Crystal structure of calG3 from Micromonospora echinospora determined in space group I222

Components

Protein CalG3

Keywords

TRANSFERASE / Calicheamicin synthesis /

glycosyltransferase / enediyne antibiotic

Function / homology

Function and homology information

UDP-glycosyltransferase activity /

glucosyltransferase activity / antibiotic biosynthetic process
Similarity search - Function

Biological species

Micromonospora echinospora (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 2.79 Å

Authors

Bitto, E. / Singh, S. / Bingman, C.A. / Wesenberg, G.E. / Phillips Jr., G.N.

Citation

Journal: Chem.Biol. / Year: 2008
Title: Biochemical and structural insights of the early glycosylation steps in calicheamicin biosynthesis.
Authors: Zhang, C. / Bitto, E. / Goff, R.D. / Singh, S. / Bingman, C.A. / Griffith, B.R. / Albermann, C. / Phillips, G.N. / Thorson, J.S.

History

Deposition	May 2, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 24, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Oct 25, 2017	Group: Refinement description / Category: software

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3d0q.cif.gz	151.2 KB	Display	PDBx/mmCIF format
PDB format	pdb3d0q.ent.gz	125.3 KB	Display	PDB format
PDBx/mmJSON format	3d0q.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/d0/3d0q ftp://data.pdbj.org/pub/pdb/validation_reports/d0/3d0q	HTTPS FTP

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Related structure data

Related structure data	3d0rC C: citing same article (ref.)
Similar structure data	2a1h-d 2hgx-d 2hg8-d 5cr5-d 3d0r-d 5i5s-d 5i60-d 5mpr-1 1ekf-d 3uyl-d 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: Protein CalG3

B: Protein CalG3

hetero molecules

87.2 kDa, 2 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)	106.654, 119.267, 155.942
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	23
Space group name H-M	I222

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B
1	3	A
2	3	B

NCS domain segments:

Component-ID: 1 / Refine code: 2

Dom-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	HIS	SER	A	A	-2 - 55	20 - 77
2	1	HIS	SER	B	B	-2 - 55	20 - 77
1	2	THR	ARG	A	A	76 - 210	98 - 232
2	2	THR	ARG	B	B	76 - 210	98 - 232
1	3	LEU	ILE	A	A	259 - 374	281 - 396
2	3	LEU	ILE	B	B	259 - 374	281 - 396

NCS ensembles :

ID
1
2
3

#1: Protein	Protein CalG3 Mass: 43387.977 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora echinospora (bacteria) / Strain: LL6600 / Gene: calG3 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8KND7
#2: Chemical	ChemComp-MPO / 3[N-MORPHOLINO]PROPANE SULFONIC ACID / MOPS Mass: 209.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₅NO₄S / Comment: pH buffer*YM
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 45 / 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: 2.86 Å³/Da / Density % sol: 56.95 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.010 M Tris-HCl pH 7.5) mixed in a 1:1 ratio with the Well solution (16% PEG 4000, 0.20 M Tri-ammonium citrate, 0.10 M ...Details: Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.010 M Tris-HCl pH 7.5) mixed in a 1:1 ratio with the Well solution (16% PEG 4000, 0.20 M Tri-ammonium citrate, 0.10 M MOPS pH 7.0). Cryoprotected in well solution containing up to 20% (v/v) Ethylene glycol, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal

Density Matthews: 2.86 Å³/Da / Density % sol: 56.95 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein solution (10 mg/mL Se-Met protein, 0.050 M Sodium chloride, 0.010 M Tris-HCl pH 7.5) mixed in a 1:1 ratio with the Well solution (16% PEG 4000, 0.20 M Tri-ammonium citrate, 0.10 M ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97918 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 26, 2006 / Details: Adjustable focusing mirrors in K-B geometry

Radiation

Monochromator: Si(111) Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97918 Å / Relative weight: 1

Reflection

Resolution: 2.79→27 Å / Num. obs: 24883 / % possible obs: 99.2 % / Redundancy: 7.3 % / R_merge(I) obs: 0.121 / Χ²: 1.125 / Net I/σ(I): 9.819

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
2.79-2.9	6.3	0.426	4.046	2342	0.952	94.9
2.9-3.02	7	0.354		2423	0.925	98.2
3.02-3.15	7.4	0.274		2449	1.001	99.2
3.15-3.32	7.5	0.215		2493	0.986	99.9
3.32-3.53	7.5	0.173		2475	1.101	99.9
3.53-3.8	7.5	0.127		2488	1.167	100
3.8-4.18	7.5	0.096		2507	1.08	100
4.18-4.78	7.4	0.081		2516	1.282	100
4.78-6.01	7.4	0.077		2541	1.277	100
6.01-27	7.1	0.059		2649	1.414	100

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Phasing

Phasing

Method:

SAD

Phasing MAD set

R cullis centric: 0 / Highest resolution: 3.2 Å / Lowest resolution: 26.66 Å / Power centric: 0

ID	R cullis acentric	Power acentric	Reflection acentric	Reflection centric
ISO_1	0	0	14922	1808
ANO_1	0.789	1.165	14921	0

Phasing MAD set shell

R cullis centric: 0 / Power centric: 0

ID	Resolution (Å)	R cullis acentric	Power acentric	Reflection acentric	Reflection centric
ISO_1	12.68-26.66	0	0	183	94
ISO_1	9.52-12.68	0	0	306	91
ISO_1	7.94-9.52	0	0	383	88
ISO_1	6.96-7.94	0	0	457	94
ISO_1	6.27-6.96	0	0	529	87
ISO_1	5.75-6.27	0	0	591	90
ISO_1	5.34-5.75	0	0	620	89
ISO_1	5.01-5.34	0	0	696	90
ISO_1	4.73-5.01	0	0	724	90
ISO_1	4.49-4.73	0	0	760	92
ISO_1	4.29-4.49	0	0	803	87
ISO_1	4.11-4.29	0	0	854	93
ISO_1	3.95-4.11	0	0	892	93
ISO_1	3.81-3.95	0	0	919	87
ISO_1	3.69-3.81	0	0	959	97
ISO_1	3.57-3.69	0	0	992	90
ISO_1	3.47-3.57	0	0	1018	93
ISO_1	3.37-3.47	0	0	1039	85
ISO_1	3.28-3.37	0	0	1089	90
ISO_1	3.2-3.28	0	0	1108	88
ANO_1	12.68-26.66	0.478	2.753	183	0
ANO_1	9.52-12.68	0.633	2.1	306	0
ANO_1	7.94-9.52	0.543	2.348	383	0
ANO_1	6.96-7.94	0.526	2.493	457	0
ANO_1	6.27-6.96	0.522	2.328	529	0
ANO_1	5.75-6.27	0.536	2.27	591	0
ANO_1	5.34-5.75	0.584	2.091	620	0
ANO_1	5.01-5.34	0.654	1.782	696	0
ANO_1	4.73-5.01	0.694	1.587	724	0
ANO_1	4.49-4.73	0.717	1.477	760	0
ANO_1	4.29-4.49	0.706	1.371	803	0
ANO_1	4.11-4.29	0.789	1.159	854	0
ANO_1	3.95-4.11	0.835	1.027	892	0
ANO_1	3.81-3.95	0.872	0.854	918	0
ANO_1	3.69-3.81	0.875	0.817	959	0
ANO_1	3.57-3.69	0.883	0.739	992	0
ANO_1	3.47-3.57	0.924	0.672	1018	0
ANO_1	3.37-3.47	0.924	0.583	1039	0
ANO_1	3.28-3.37	0.938	0.528	1089	0
ANO_1	3.2-3.28	0.948	0.474	1108	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	-83.921	-4.388	-9.593	SE	57.28	1.86
2	-75.384	-16.946	-19.986	SE	62.28	2.36
3	-83.251	-23.945	-47.163	SE	45.24	2.05
4	-88.811	-34.604	-61.42	SE	36.71	1.66
5	-85.026	-9.618	-58.701	SE	66.62	2.1
6	-70.754	-10.614	3.104	SE	92.92	2.17
7	-68.768	-24.159	-4.106	SE	38.55	1.6
8	-82.293	-41.125	-53.613	SE	60.55	1.76
9	-95.763	-22.412	-67.923	SE	78.58	1.8
10	-66.548	-33.661	-7.477	SE	102.58	1.8

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 16729

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
10.43-100	75.7	0.631	508
8.31-10.43	64.8	0.838	501
7.24-8.31	66.1	0.847	501
6.56-7.24	66	0.834	519
6.08-6.56	66.2	0.814	511
5.71-6.08	67	0.842	515
5.41-5.71	66.1	0.868	512
5.17-5.41	65.5	0.862	510
4.95-5.17	59.1	0.887	553
4.76-4.95	60.2	0.88	567
4.59-4.76	61.3	0.887	571
4.44-4.59	61.3	0.892	604
4.3-4.44	61.8	0.906	631
4.17-4.3	62.7	0.88	651
4.06-4.17	62.6	0.895	663
3.95-4.06	69.4	0.889	669
3.85-3.95	67.7	0.872	683
3.76-3.85	70.1	0.86	728
3.68-3.76	70	0.864	734
3.6-3.68	72.3	0.843	731
3.52-3.6	72.5	0.856	766
3.45-3.52	76.8	0.836	770
3.38-3.45	77.8	0.823	776
3.32-3.38	77.6	0.755	824
3.26-3.32	76.6	0.746	796
3.2-3.26	80.7	0.692	935

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC	5.2.0019	refinement
PDB_EXTRACT	3	data extraction
MAR345	CCD	data collection

Refinement

Method to determine structure:

SAD / Resolution: 2.79→26.75 Å / Cor.coef. F_o:F_c: 0.939 / Cor.coef. F_o:F_c free: 0.893 / WR_factor R_free: 0.239 / WR_factor R_work: 0.184 / SU B: 28.63 / SU ML: 0.259 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.881 / ESU R Free: 0.342 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.243	1270	5.104 %	RANDOM
R_work	0.187	-	-	-
obs	0.19	24883	98.883 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 11.99 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	5.326 Å²	0 Å²	0 Å²
2-	-	-2.249 Å²	0 Å²
3-	-	-	-3.077 Å²

Refinement step

Cycle: LAST / Resolution: 2.79→26.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5716	0	26	45	5787

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	5868
X-RAY DIFFRACTION	r_angle_refined_deg	1.337	1.971	8018
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.578	5	752
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.542	22.661	248
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.304	15	896
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.492	15	60
X-RAY DIFFRACTION	r_chiral_restr	0.091	0.2	934
X-RAY DIFFRACTION	r_gen_planes_refined	0.004	0.02	4486
X-RAY DIFFRACTION	r_nbd_refined	0.219	0.2	2529
X-RAY DIFFRACTION	r_nbtor_refined	0.314	0.2	4029
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.13	0.2	191
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.128	0.2	20
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.073	0.2	6
X-RAY DIFFRACTION	r_mcbond_it	1.44	3	3843
X-RAY DIFFRACTION	r_mcangle_it	2.7	6	6068
X-RAY DIFFRACTION	r_scbond_it	5.453	10	2242
X-RAY DIFFRACTION	r_scangle_it	8.431	13	1950

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-ID	Number	Type	Rms dev position (Å)	Weight position
1	232	TIGHT POSITIONAL	0.03	0.05
1	204	MEDIUM POSITIONAL	0.3	0.5
1	232	TIGHT THERMAL	0.1	0.5
1	204	MEDIUM THERMAL	0.88	2
2	540	TIGHT POSITIONAL	0.05	0.05
2	502	MEDIUM POSITIONAL	0.46	0.5
2	540	TIGHT THERMAL	0.1	0.5
2	502	MEDIUM THERMAL	0.91	2
3	464	TIGHT POSITIONAL	0.04	0.05
3	425	MEDIUM POSITIONAL	0.63	0.5
3	464	TIGHT THERMAL	0.09	0.5
3	425	MEDIUM THERMAL	0.85	2

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
2.79-2.861	0.373	88	0.31	1595	1821	92.422
2.861-2.939	0.332	92	0.274	1653	1797	97.106
2.939-3.024	0.257	83	0.215	1633	1744	98.394
3.024-3.117	0.273	90	0.205	1581	1685	99.169
3.117-3.219	0.303	101	0.197	1528	1633	99.755
3.219-3.332	0.223	65	0.197	1519	1587	99.811
3.332-3.458	0.256	96	0.186	1426	1523	99.934
3.458-3.599	0.214	63	0.181	1435	1499	99.933
3.599-3.759	0.221	60	0.18	1349	1410	99.929
3.759-3.942	0.224	77	0.176	1298	1375	100
3.942-4.155	0.23	65	0.156	1227	1292	100
4.155-4.406	0.198	64	0.153	1163	1227	100
4.406-4.71	0.174	56	0.156	1109	1165	100
4.71-5.086	0.218	61	0.156	1038	1099	100
5.086-5.57	0.15	51	0.166	949	1000	100
5.57-6.225	0.208	39	0.189	863	902	100
6.225-7.182	0.316	47	0.209	763	810	100
7.182-8.784	0.262	40	0.168	660	700	100
8.784-12.37	0.283	16	0.163	545	561	100
12.37-94.916	0.36	16	0.281	279	334	88.323

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	1.0448	-0.8785	0.3061	4.8879	-1.933	6.535	0.0481	0.0136	0.076	-0.2794	0.0051	0.3019	-0.1198	-0.7916	-0.0532	-0.1667	-0.0246	0.0318	-0.1268	-0.0244	-0.1864	-28.8901	-21.6762	-15.4736
2	1.0592	0.646	-0.157	3.0554	-0.8679	2.2705	0.0209	0.2073	0.0017	-0.2627	-0.0772	-0.0402	-0.1865	-0.0479	0.0563	-0.1761	0.0033	0.0363	-0.1301	-0.0219	-0.2065	-24.3714	-24.0785	-24.2159
3	7.1082	0.3227	1.0187	0.0162	-0.04	4.9364	0.0876	0.0292	0.7375	-0.2222	0.1567	0.246	-0.689	-0.4071	-0.2443	-0.0213	0.0018	0.0229	0.0146	0.0121	0.0085	-45.6463	-44.3384	-20.7338
4	5.404	1.5225	-0.2748	6.361	-0.6561	2.8063	-0.1978	0.5482	0.3649	-0.5347	0.338	0.3354	-0.4214	-0.128	-0.1402	-0.0834	0.0023	0.0235	-0.02	-0.0642	-0.1333	-34.7722	-43.5582	-29.8317
5	1.4953	1.784	2.3471	5.9784	3.5337	4.1846	0.1461	0.3201	-0.5117	0.3516	0.2765	-0.5244	0.4809	0.3489	-0.4226	0.0212	0.0602	0.1391	-0.0293	-0.0409	-0.1035	-19.2546	-44.2649	-21.4043
6	1.0612	0.5578	-1.3617	1.4222	-0.7465	4.3776	-0.0495	-0.0156	-0.0426	0.1257	-0.083	-0.1297	0.1133	-0.0372	0.1326	-0.1713	0.0214	-0.0241	-0.2052	0.0004	-0.1602	-28.8905	-44.662	12.4666
7	1.6787	0.2246	0.6629	2.1057	-0.4366	3.9598	-0.1306	-0.1742	0.0707	0.4188	-0.0769	-0.4289	-0.4687	0.3854	0.2075	-0.1433	-0.0447	-0.0269	-0.1015	-0.0482	-0.1238	-17.9211	-29.108	8.1777
8	2.7783	-0.3244	1.8312	7.1773	5.7399	12.9404	0.1491	-0.3733	-0.2753	0.739	-0.6745	1.3069	-0.394	-1.9474	0.5254	0.341	0.1541	-0.0069	0.1485	-0.0533	0.1312	-32.3556	-12.751	14.2047
9	2.5268	0.169	1.0088	6.6448	0.2496	9.1157	0.0965	-0.268	-0.3255	0.7962	0.0685	0.3655	0.0206	-0.3375	-0.165	0.0773	-0.0209	-0.0835	-0.1415	0.005	-0.0896	-21.671	-19.8426	20.3608
10	0.7028	0.8009	0.0429	4.5075	3.983	6.7789	-0.1568	0.0838	0.0645	-0.144	0.7723	-1.1256	-0.6147	1.0837	-0.6155	-0.0789	-0.0722	-0.1105	0.0535	0.0201	0.0154	-10.4552	-26.6746	8.5543

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	-2 - 68	20 - 90
2	X-RAY DIFFRACTION	2	A	A	69 - 210	91 - 232
3	X-RAY DIFFRACTION	3	A	A	211 - 275	233 - 297
4	X-RAY DIFFRACTION	4	A	A	276 - 338	298 - 360
5	X-RAY DIFFRACTION	5	A	A	339 - 374	361 - 396
6	X-RAY DIFFRACTION	6	B	B	-2 - 164	20 - 186
7	X-RAY DIFFRACTION	7	B	B	165 - 210	187 - 232
8	X-RAY DIFFRACTION	8	B	B	211 - 275	233 - 297
9	X-RAY DIFFRACTION	9	B	B	276 - 338	298 - 360
10	X-RAY DIFFRACTION	10	B	B	339 - 374	361 - 396

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