PDB-3d0r: Crystal structure of calG3 from Micromonospora echinospora determ...

ID or keywords:

Entry

Database: PDB / ID: 3d0r

Title

Crystal structure of calG3 from Micromonospora echinospora determined in space group P2(1)

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 /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.9 Å

Authors

Bitto, E. / 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
Revision 1.3	Aug 30, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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_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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PDBx/mmCIF format	3d0r.cif.gz	170.9 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	3d0r_validation.pdf.gz	652 KB	Display	wwPDB validaton report
Full document	3d0r_full_validation.pdf.gz	656.8 KB	Display
Data in XML	3d0r_validation.xml.gz	16.9 KB	Display
Data in CIF	3d0r_validation.cif.gz	28.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/d0/3d0r ftp://data.pdbj.org/pub/pdb/validation_reports/d0/3d0r	HTTPS FTP

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Related structure data

Related structure data	3d0qSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5f7s-1 3d0q-d 3a6o-1 5bwr-d 7jj0-2 3weo-d 5teq-1 1kt8-d 2p6p-d 2a1h-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

86.4 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)	57.440, 97.677, 63.046
Angle α, β, γ (deg.)	90.000, 90.620, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Protein CalG3 Mass: 43012.824 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-PE4 / 2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL / POLYETHYLENE GLYCOL PEG4000 Mass: 354.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₃₄O₈ / Comment: precipitant*YM
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 579 / Source method: isolated from a natural source / Formula: H₂O
Sequence details	THIS STRUCTURE WAS SUBMITTED AS CASP7 TARGET T0333.

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.06 Å³/Da / Density % sol: 40.17 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Protein solution (10 mg/mL protein, 0.050 M Sodium chloride, 0.010 M Tris-HCl pH 7.5) mixed in a 1:1 ratio with the Well solution (25% PEG 1500). Cryoprotected in FOMBLIN MW2500, VAPOR ...Details: Protein solution (10 mg/mL protein, 0.050 M Sodium chloride, 0.010 M Tris-HCl pH 7.5) mixed in a 1:1 ratio with the Well solution (25% PEG 1500). Cryoprotected in FOMBLIN MW2500, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal

Density Matthews: 2.06 Å³/Da / Density % sol: 40.17 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein solution (10 mg/mL protein, 0.050 M Sodium chloride, 0.010 M Tris-HCl pH 7.5) mixed in a 1:1 ratio with the Well solution (25% PEG 1500). Cryoprotected in FOMBLIN MW2500, VAPOR ...

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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: 1.68→50 Å / Num. obs: 68513 / % possible obs: 86.3 % / Redundancy: 7 % / R_merge(I) obs: 0.051 / Χ²: 1.265 / Net I/σ(I): 25.11

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique all	Χ²	% possible all
1.68-1.74	3.9	0.496	2.426	3443	0.898	43.6
1.74-1.81	5.1	0.396		4770	0.936	60.3
1.81-1.89	6.1	0.323		5884	0.942	74.6
1.89-1.99	6.7	0.255		7008	1.005	88.1
1.99-2.12	7.3	0.185		7734	1.076	97.8
2.12-2.28	7.7	0.14		7916	1.24	99.9
2.28-2.51	7.8	0.096		7938	1.251	100
2.51-2.87	7.8	0.059		7952	1.297	100
2.87-3.62	7.6	0.042		7880	1.861	99.1
3.62-50	7.6	0.029		7988	1.431	99.1

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

R_factor: 0.496 / Cor.coef. F_o:F_c: 0.378

	Highest resolution	Lowest resolution
Rotation	3 Å	38.76 Å
Translation	3 Å	38.76 Å

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3D0Q

3d0q

Resolution: 1.9→38.75 Å / Cor.coef. F_o:F_c: 0.968 / Cor.coef. F_o:F_c free: 0.946 / WR_factor R_free: 0.214 / WR_factor R_work: 0.162 / SU B: 6.284 / SU ML: 0.099 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.156 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.212	2745	5.112 %	RANDOM
R_work	0.16	-	-	-
obs	0.162	53699	98.032 %	-

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: 15.847 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	1.171 Å²	0 Å²	-1.934 Å²
2-	-	-1.774 Å²	0 Å²
3-	-	-	0.561 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→38.75 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5754	0	13	579	6346

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	5934
X-RAY DIFFRACTION	r_angle_refined_deg	1.416	1.969	8111
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.61	5	769
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.32	22.49	253
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.578	15	916
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.414	15	64
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	944
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	4554
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	2966
X-RAY DIFFRACTION	r_nbtor_refined	0.307	0.2	4125
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.163	0.2	583
X-RAY DIFFRACTION	r_symmetry_vdw_refined	0.178	0.2	77
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.241	0.2	29
X-RAY DIFFRACTION	r_mcbond_it	1.988	3	3902
X-RAY DIFFRACTION	r_mcangle_it	3.006	6	6145
X-RAY DIFFRACTION	r_scbond_it	5.629	10	2270
X-RAY DIFFRACTION	r_scangle_it	7.825	14	1960

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 (%)
1.9-1.949	0.275	176	0.185	3299	4004	86.788
1.949-2.003	0.256	186	0.179	3486	3944	93.103
2.003-2.061	0.201	182	0.165	3538	3832	97.077
2.061-2.124	0.241	171	0.162	3543	3737	99.385
2.124-2.194	0.237	198	0.158	3393	3593	99.944
2.194-2.27	0.207	183	0.165	3293	3476	100
2.27-2.356	0.224	185	0.165	3181	3366	100
2.356-2.452	0.219	153	0.159	3078	3231	100
2.452-2.561	0.228	162	0.164	2936	3098	100
2.561-2.686	0.221	150	0.166	2821	2971	100
2.686-2.831	0.212	155	0.164	2692	2848	99.965
2.831-3.002	0.238	119	0.161	2552	2680	99.664
3.002-3.209	0.21	136	0.163	2355	2507	99.362
3.209-3.465	0.215	105	0.158	2218	2350	98.851
3.465-3.795	0.216	115	0.153	2028	2173	98.619
3.795-4.241	0.155	103	0.134	1823	1947	98.921
4.241-4.893	0.167	85	0.138	1651	1738	99.885
4.893-5.984	0.201	93	0.169	1375	1469	99.932
5.984-8.425	0.236	65	0.181	1086	1154	99.74
8.425-62.994	0.25	23	0.169	606	659	95.448

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	1.3152	-2.2563	-0.1608	4.1571	-0.2943	1.1555	-0.1963	-0.2609	-0.1524	0.2981	0.1569	0.2264	-0.0816	-0.2085	0.0393	-0.1215	0.0193	-0.0229	-0.096	-0.0013	-0.1506	36.1318	23.9502	18.7785
2	1.033	-0.8099	-0.1654	2.1604	0.2302	1.1315	-0.0606	-0.0539	0.2164	0.0433	0.0106	-0.1113	-0.2665	-0.0623	0.05	-0.1163	-0.0036	-0.0472	-0.1419	0.0107	-0.1404	36.5697	31.5412	12.1106
3	6.6041	0.5898	4.6184	5.3163	0.5006	4.2988	0.1224	-0.9354	-0.1227	0.2584	-0.3532	1.0039	0.0986	-0.9722	0.2308	-0.0789	-0.0152	-0.0017	0.0481	-0.0547	0.0645	22.784	9.2903	-2.4312
4	2.7196	0.8993	0.9782	5.5399	1.1383	3.3252	-0.0683	0.0496	0.3285	-0.3688	-0.2678	0.78	-0.3191	-0.2818	0.336	-0.0737	0.0485	-0.0761	-0.1281	-0.0345	-0.0744	27.7675	21.755	-6.5088
5	5.8906	0.4881	4.8675	2.0668	0.7439	6.9024	-0.0221	0.4972	0.1241	-0.3714	-0.0265	-0.1301	-0.1203	0.6079	0.0486	-0.0676	0.0033	0.0626	-0.1529	0.0868	-0.0936	45.6381	22.9169	-4.5674
6	2.5396	-1.2203	0.4785	3.3409	-0.186	1.4399	0.0175	-0.0279	-0.2248	0.0437	0.0456	0.0192	0.3185	0.0048	-0.0632	-0.1605	0.01	0.0226	-0.1543	0.0029	-0.1816	51.8596	-6.8147	11.6391
7	2.0965	-0.2185	0.7121	1.3491	-0.4702	2.1913	-0.07	-0.1623	0.2209	0.1976	0.1002	-0.3941	-0.1076	0.1381	-0.0302	-0.179	-0.0172	-0.0201	-0.1557	0.0064	-0.0918	57.8631	8.3038	22.1535
8	3.6852	0.6243	-2.2225	1.8877	-3.1975	5.8061	0.0176	0.0792	-0.279	0.0249	0.0217	0.1326	0.4353	-0.3799	-0.0393	-0.0593	-0.0212	0.003	-0.0645	-0.0254	-0.1206	46.762	5.3924	41.2168
9	5.2231	-0.5079	-1.7583	2.2848	0.2468	5.6413	-0.2176	-0.0587	-0.6138	0.2717	-0.0928	-0.0385	0.674	0.1555	0.3104	-0.1	-0.0021	-0.0122	-0.1451	-0.0179	-0.0783	59.5231	2.0597	36.2587
10	2.1318	0.3444	2.2551	1.1554	-0.2401	7.7528	-0.2092	0.0527	0.2534	0.0715	-0.0972	-0.2358	-0.5724	0.5454	0.3064	-0.248	0.0011	0.0228	-0.1196	0.0084	0.0448	64.6292	12.547	23.0511

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 - 375	361 - 397
6	X-RAY DIFFRACTION	6	B	B	-6 - 164	16 - 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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