PDB-3ia7: Crystal Structure of CalG4, the Calicheamicin Glycosyltransferase

ID or keywords:

Entry

Database: PDB / ID: 3ia7

Title

Crystal Structure of CalG4, the Calicheamicin Glycosyltransferase

Components

CalG4

Keywords

TRANSFERASE / Glycosysltransferase / Calicheamicin / CalG4 / enediyne

Function / homology

Function and homology information

UDP-glycosyltransferase activity / hexosyltransferase activity / antibiotic biosynthetic process / metal ion binding
Similarity search - Function

Biological species

Micromonospora echinospora (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.91 Å

Authors

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

Citation

Journal: Proc.Natl.Acad.Sci.USA / Year: 2011
Title: Complete set of glycosyltransferase structures in the calicheamicin biosynthetic pathway reveals the origin of regiospecificity.
Authors: Chang, A. / Singh, S. / Helmich, K.E. / Goff, R.D. / Bingman, C.A. / Thorson, J.S. / Phillips, G.N.

History

Deposition	Jul 13, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 2, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 2, 2011	Group: Database references
Revision 1.3	Nov 1, 2017	Group: Refinement description / Category: software Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4	Nov 27, 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 / pdbx_struct_conn_angle / 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 / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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	3ia7.cif.gz	173.7 KB	Display	PDBx/mmCIF format
PDB format	pdb3ia7.ent.gz	136 KB	Display	PDB format
PDBx/mmJSON format	3ia7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3ia7_validation.pdf.gz	441.3 KB	Display	wwPDB validaton report
Full document	3ia7_full_validation.pdf.gz	454 KB	Display
Data in XML	3ia7_validation.xml.gz	39 KB	Display
Data in CIF	3ia7_validation.cif.gz	53.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ia/3ia7 ftp://data.pdbj.org/pub/pdb/validation_reports/ia/3ia7	HTTPS FTP

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Related structure data

Related structure data	3iaaC 3otgC 3othC 3otiC 3rscC C: citing same article (ref.)
Similar structure data	1z7d-2 6b6g-1 6tbl-2 2dgk-2 3lg0-1 6m3m-d 3e30-d 6g1f-3 6khp-d 6eei-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: CalG4

B: CalG4

hetero molecules

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

1

Idetical with deposited unit
defined by software

2

A: CalG4

hetero molecules

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

3

B: CalG4

hetero molecules

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

Unit cell

Length a, b, c (Å)	84.749, 66.966, 86.616
Angle α, β, γ (deg.)	90.000, 93.530, 90.000
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	CalG4 Mass: 44424.797 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora echinospora (bacteria) / Strain: Micromonospora echinospora / Gene: calG4, Q8KNC3 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / Strain (production host): B834 P(RARE2) / References: UniProt: Q8KNC3
#2: Chemical	ChemComp-CA / CALCIUM ION Mass: 40.078 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ca
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 437 / 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: 2.76 Å³/Da / Density % sol: 55.45 %
Crystal grow	Temperature: 277 K / Method: vapor diffusion, hanging drop Details: Protein Solution (10 mg/ml CalG4 Protein, 0.05 M NaCl, 0.005 M Tris pH 8) mixed in a 1:1 ratio with the Well Solution (19% PEG4K, 0.08 M CaCl2, 0.1 M CHES pH 9.5) Cryoprotected with 25% ...Details: Protein Solution (10 mg/ml CalG4 Protein, 0.05 M NaCl, 0.005 M Tris pH 8) mixed in a 1:1 ratio with the Well Solution (19% PEG4K, 0.08 M CaCl2, 0.1 M CHES pH 9.5) Cryoprotected with 25% ethylene glycol, 19% PEG4K, 0.08 M CaCl2, 0.1 M CHES pH 9.5, vapor diffusion, hanging drop, temperature 277K

Crystal

Density Matthews: 2.76 Å³/Da / Density % sol: 55.45 %

Crystal grow

Temperature: 277 K / Method: vapor diffusion, hanging drop
Details: Protein Solution (10 mg/ml CalG4 Protein, 0.05 M NaCl, 0.005 M Tris pH 8) mixed in a 1:1 ratio with the Well Solution (19% PEG4K, 0.08 M CaCl2, 0.1 M CHES pH 9.5) Cryoprotected with 25% ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 23-ID-D / Wavelength: 0.97945, 0.96421

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 31, 2008 / 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	0.97945	1
2	0.96421	1

Reflection

Redundancy: 7.2 % / Av σ(I) over netI: 21.83 / Number: 537130 / R_merge(I) obs: 0.074 / Χ²: 1.04 / D res high: 1.91 Å / D res low: 50 Å / Num. obs: 74332 / % possible obs: 98.4

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
4.11	50	99.9	1	0.049	0.912	7.6
3.27	4.11	100	1	0.06	1.028	7.7
2.85	3.27	100	1	0.068	1.059	7.7
2.59	2.85	100	1	0.097	1.036	7.7
2.41	2.59	100	1	0.123	1.073	7.7
2.26	2.41	100	1	0.151	1.047	7.7
2.15	2.26	100	1	0.206	1.025	7.7
2.06	2.15	100	1	0.294	1.068	7.4
1.98	2.06	99.4	1	0.37	1.064	6.3
1.91	1.98	84.6	1	0.451	1.08	4.4

Reflection

Resolution: 1.91→50 Å / Num. obs: 74332 / % possible obs: 98.4 % / Redundancy: 7.2 % / R_merge(I) obs: 0.074 / Χ²: 1.036 / Net I/σ(I): 11.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.91-1.98	4.4	0.451	6358	1.08	1	84.6
1.98-2.06	6.3	0.37	7470	1.064	1	99.4
2.06-2.15	7.4	0.294	7502	1.068	1	100
2.15-2.26	7.7	0.206	7493	1.025	1	100
2.26-2.41	7.7	0.151	7552	1.047	1	100
2.41-2.59	7.7	0.123	7504	1.073	1	100
2.59-2.85	7.7	0.097	7551	1.036	1	100
2.85-3.27	7.7	0.068	7578	1.059	1	100
3.27-4.11	7.7	0.06	7581	1.028	1	100
4.11-50	7.6	0.049	7743	0.912	1	99.9

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Phasing

Phasing

Method:

MAD

Phasing MAD set

ID	Highest resolution (Å)	Lowest resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	1.91	45.66	0	0	71126	3134
ISO_2	1.91	45.66	0.751	0.664	62618	2869
ANO_1	1.91	45.66	1.023	0	69696	0
ANO_2	1.91	45.66	0.62	0	62232	0

Phasing MAD set shell

ID	Resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	8.41-45.66	0	0	768	154
ISO_1	6-8.41	0	0	1450	159
ISO_1	4.91-6	0	0	1884	157
ISO_1	4.26-4.91	0	0	2230	157
ISO_1	3.81-4.26	0	0	2535	157
ISO_1	3.48-3.81	0	0	2810	153
ISO_1	3.23-3.48	0	0	3062	164
ISO_1	3.02-3.23	0	0	3287	154
ISO_1	2.85-3.02	0	0	3537	159
ISO_1	2.7-2.85	0	0	3692	157
ISO_1	2.58-2.7	0	0	3902	152
ISO_1	2.47-2.58	0	0	4107	162
ISO_1	2.37-2.47	0	0	4265	157
ISO_1	2.28-2.37	0	0	4456	155
ISO_1	2.21-2.28	0	0	4625	162
ISO_1	2.14-2.21	0	0	4739	149
ISO_1	2.07-2.14	0	0	4894	159
ISO_1	2.02-2.07	0	0	5065	151
ISO_1	1.96-2.02	0	0	5119	164
ISO_1	1.91-1.96	0	0	4699	152
ANO_1	8.41-45.66	1.769	0	767	0
ANO_1	6-8.41	2.35	0	1450	0
ANO_1	4.91-6	2.206	0	1884	0
ANO_1	4.26-4.91	1.744	0	2230	0
ANO_1	3.81-4.26	1.618	0	2535	0
ANO_1	3.48-3.81	1.631	0	2810	0
ANO_1	3.23-3.48	1.623	0	3061	0
ANO_1	3.02-3.23	1.587	0	3287	0
ANO_1	2.85-3.02	1.463	0	3537	0
ANO_1	2.7-2.85	1.217	0	3692	0
ANO_1	2.58-2.7	1.078	0	3902	0
ANO_1	2.47-2.58	0.921	0	4107	0
ANO_1	2.37-2.47	0.805	0	4265	0
ANO_1	2.28-2.37	0.674	0	4456	0
ANO_1	2.21-2.28	0.556	0	4625	0
ANO_1	2.14-2.21	0.459	0	4739	0
ANO_1	2.07-2.14	0.389	0	4886	0
ANO_1	2.02-2.07	0.33	0	4953	0
ANO_1	1.96-2.02	0.287	0	4711	0
ANO_1	1.91-1.96	0.258	0	3799	0
ISO_2	8.41-45.66	1.934	1.419	768	152
ISO_2	6-8.41	1.875	1.317	1450	159
ISO_2	4.91-6	1.492	1.071	1884	157
ISO_2	4.26-4.91	1.115	0.725	2230	156
ISO_2	3.81-4.26	0.949	0.674	2535	157
ISO_2	3.48-3.81	0.875	0.573	2810	153
ISO_2	3.23-3.48	0.878	0.552	3062	164
ISO_2	3.02-3.23	0.889	0.58	3286	154
ISO_2	2.85-3.02	0.86	0.557	3534	159
ISO_2	2.7-2.85	0.822	0.611	3691	156
ISO_2	2.58-2.7	0.743	0.476	3901	152
ISO_2	2.47-2.58	0.653	0.418	4105	162
ISO_2	2.37-2.47	0.563	0.388	4260	157
ISO_2	2.28-2.37	0.478	0.321	4450	155
ISO_2	2.21-2.28	0.404	0.322	4620	162
ISO_2	2.14-2.21	0.337	0.252	4734	149
ISO_2	2.07-2.14	0.275	0.204	4888	159
ISO_2	2.02-2.07	0.227	0.175	4969	151
ISO_2	1.96-2.02	0.197	0.18	1441	55
ISO_2	1.91-1.96	0	0	0	0
ANO_2	8.41-45.66	1.566	0	767	0
ANO_2	6-8.41	2.188	0	1450	0
ANO_2	4.91-6	2.051	0	1884	0
ANO_2	4.26-4.91	1.664	0	2230	0
ANO_2	3.81-4.26	1.409	0	2535	0
ANO_2	3.48-3.81	1.294	0	2810	0
ANO_2	3.23-3.48	1.193	0	3062	0
ANO_2	3.02-3.23	1.022	0	3286	0
ANO_2	2.85-3.02	0.887	0	3534	0
ANO_2	2.7-2.85	0.71	0	3691	0
ANO_2	2.58-2.7	0.582	0	3900	0
ANO_2	2.47-2.58	0.472	0	4105	0
ANO_2	2.37-2.47	0.389	0	4260	0
ANO_2	2.28-2.37	0.322	0	4450	0
ANO_2	2.21-2.28	0.261	0	4620	0
ANO_2	2.14-2.21	0.224	0	4733	0
ANO_2	2.07-2.14	0.183	0	4858	0
ANO_2	2.02-2.07	0.172	0	4737	0
ANO_2	1.96-2.02	0.16	0	1320	0
ANO_2	1.91-1.96	0	0	0	0

Phasing MAD set site

ID	Cartn x (Å)	Cartn y (Å)	Cartn z (Å)	Atom type symbol	B iso	Occupancy
1	37.289	10.982	47.389	SE	28.47	1.18
2	57.815	25.274	79.526	SE	32.29	1.34
3	37.564	-0.314	25.073	SE	30.89	1.39
4	63.18	0.027	72.856	SE	32.25	1.36
5	35.311	18.495	24.259	SE	60.64	1.05
6	31.688	23.481	44.008	SE	36.01	0.62
7	-42.529	-22.262	-77.553	SE	20.3	0.14
8	-57.826	-10.882	-52.105	SE	56.14	0.13
9	-40.958	-10.788	-55.442	SE	36.01	0.09
10	-37.551	-0.609	-59.159	SE	50.61	0.09
11	-21.167	-11.049	-42.145	SE	54.34	0.27

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 74260

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
10.36-100	57.7	0.847	508
7.33-10.36	48.1	0.942	890
5.98-7.33	50.6	0.941	1150
5.18-5.98	46.2	0.941	1341
4.63-5.18	51.2	0.95	1535
4.23-4.63	53.7	0.95	1669
3.92-4.23	50.3	0.952	1818
3.66-3.92	53.4	0.94	1954
3.45-3.66	54.6	0.94	2061
3.28-3.45	54.3	0.926	2202
3.12-3.28	55	0.92	2288
2.99-3.12	54.2	0.912	2395
2.87-2.99	55.7	0.913	2506
2.77-2.87	57.1	0.913	2594
2.68-2.77	58.5	0.909	2696
2.59-2.68	61.4	0.905	2791
2.51-2.59	61.5	0.9	2849
2.44-2.51	63	0.897	2945
2.38-2.44	65.5	0.9	3036
2.32-2.38	67.6	0.901	3105
2.26-2.32	70.2	0.903	3191
2.21-2.26	72.2	0.908	3257
2.16-2.21	73.9	0.897	3327
2.12-2.16	76.9	0.902	3383
2.07-2.12	77.6	0.893	3488
2.03-2.07	80.7	0.891	3545
1.99-2.03	82.6	0.89	3592
1.96-1.99	82.5	0.848	3565
1.91-1.96	83.9	0.794	4579

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
SHARP		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	3.005	data extraction
HKL-2000		data collection
HKL-2000		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.91→45.64 Å / Cor.coef. F_o:F_c: 0.919 / Cor.coef. F_o:F_c free: 0.882 / WR_factor R_free: 0.318 / WR_factor R_work: 0.266 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.797 / SU R Cruickshank DPI: 0.191 / SU R_free: 0.18 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.191 / ESU R Free: 0.18 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.301	3745	5 %	RANDOM
R_work	0.253	-	-	-
obs	0.256	74257	98.96 %	-

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 max: 63.6 Å² / B_iso mean: 21.459 Å² / B_iso min: 5.01 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.05 Å²	0 Å²	0.04 Å²
2-	-	0.07 Å²	0 Å²
3-	-	-	-0.01 Å²

Refinement step

Cycle: LAST / Resolution: 1.91→45.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6090	0	3	437	6530

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.018	0.022	6340
X-RAY DIFFRACTION	r_angle_refined_deg	1.567	1.951	8665
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.901	5	791
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.114	22.706	303
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.357	15	932
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	19.046	15	58
X-RAY DIFFRACTION	r_chiral_restr	0.111	0.2	949
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	5011
X-RAY DIFFRACTION	r_mcbond_it	0.947	1.5	3953
X-RAY DIFFRACTION	r_mcangle_it	1.565	2	6370
X-RAY DIFFRACTION	r_scbond_it	2.423	3	2387
X-RAY DIFFRACTION	r_scangle_it	3.643	4.5	2295

LS refinement shell

Resolution: 1.912→1.962 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.365	268	-
R_work	0.315	4615	-
all	-	4883	-
obs	-	-	88.52 %

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Movie

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Links

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Experimental details

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Experiment

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About Yorodumi

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Yorodumi