PDB-4zas: Crystal structure of sugar aminotransferase CalS13 from Micromono...

ID or keywords:

Entry

Database: PDB / ID: 4zas

Title

Crystal structure of sugar aminotransferase CalS13 from Micromonospora echinospora

Components

CalS13

Keywords

TRANSFERASE / sugar aminotransferase / Structural Genomics / PSI-Biology / Protein Structure Initiative / Enzyme Discovery for Natural Product Biosynthesis / NatPro

Function / homology

Function and homology information

catalytic activity
Similarity search - Function

Biological species

Micromonospora echinospora (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON / Resolution: 2.47 Å

Authors

Wang, F. / Singh, S. / Miller, M.D. / Thorson, J.S. / Phillips Jr., G.N. / Enzyme Discovery for Natural Product Biosynthesis (NatPro)

Funding support

United States, 2items

Organization	Grant number	Country
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	U01GM098248	United States
National Institutes of Health/National Cancer Institute (NIH/NCI)	CA84374	United States

Citation

Journal: To Be Published
Title: Structure characterization of sugar aminotransferases CalS13 and WecE provides the basis for a unifying structural model for stereochemical outcome.
Authors: Wang, F. / Singh, S. / Miller, M.D. / Thorson, J.S. / Phillips Jr., G.N.

History

Deposition	Apr 13, 2015	Deposition site: RCSB / Processing site: RCSB
Supersession	Apr 29, 2015	ID: 4YTJ
Revision 1.0	Apr 29, 2015	Provider: repository / Type: Initial release
Revision 2.0	Sep 6, 2017	Group: Author supporting evidence / Derived calculations ...Author supporting evidence / Derived calculations / Non-polymer description / Source and taxonomy / Structure summary Category: entity / entity_src_gen ...entity / entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list Item: _chem_comp.formula / _chem_comp.name ..._chem_comp.formula / _chem_comp.name / _entity.formula_weight / _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 2.1	Dec 4, 2019	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4zas.cif.gz	877.4 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4zas_validation.pdf.gz	523 KB	Display	wwPDB validaton report
Full document	4zas_full_validation.pdf.gz	543.5 KB	Display
Data in XML	4zas_validation.xml.gz	78.5 KB	Display
Data in CIF	4zas_validation.cif.gz	108.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/za/4zas ftp://data.pdbj.org/pub/pdb/validation_reports/za/4zas	HTTPS FTP

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Related structure data

Similar structure data	4zah-2 4oca-1 5u20-1 3p1t-1 4zwv-d 7mfp-1 5u1z-2 3frk-d 5uid-1 7mfo-1 Search similar-shape structures by Omokage search (details) 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
Other databases	TargetTrack: NatPro-GO.119384

Similar structure data

Other databases

TargetTrack: NatPro-GO.119384

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: CalS13

B: CalS13

C: CalS13

D: CalS13

E: CalS13

F: CalS13

hetero molecules

269 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: CalS13

B: CalS13

hetero molecules

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

2

C: CalS13

D: CalS13

hetero molecules

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

3

E: CalS13

F: CalS13

hetero molecules

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

Unit cell

Length a, b, c (Å)	71.570, 88.740, 189.810
Angle α, β, γ (deg.)	90.00, 96.22, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	CalS13 Mass: 44464.992 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Micromonospora echinospora (bacteria) / Gene: calS13 / Plasmid: pET28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q8KND8
#2: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-T46 / dTDP-4-keto-6-deoxyglucose Mass: 546.314 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₁₆H₂₄N₂O₁₅P₂
#4: Chemical	ChemComp-TYD / THYMIDINE-5'-DIPHOSPHATE Mass: 402.188 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₁₀H₁₆N₂O₁₁P₂
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 502 / 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: 2.25 Å³/Da / Density % sol: 45.23 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 200 mM ammonium sulfate, 100 mM Bis-Tris, pH 6.5, 25% w/v PEG 3350

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.98 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 23, 2014

Radiation

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

Radiation wavelength

Wavelength: 0.98 Å / Relative weight: 1

Reflection

Resolution: 2.47→50 Å / Num. obs: 84933 / % possible obs: 100 % / Observed criterion σ(I): -3 / Redundancy: 8.8 % / B_iso Wilson estimate: 46.77 Å² / R_merge F obs: 0.991 / R_merge(I) obs: 0.117 / R_rim(I) all: 0.269 / R_sym value: 0.111 / Χ²: 1.057 / Net I/σ(I): 11.61 / Num. measured all: 1022296

Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)	Highest resolution (Å)	R_merge F obs	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	R_rim(I) all	% possible all
2.47-2.5		0.065	1.57	0.15	12918	23647	9660	4.834	40.9
2.04-2.1		0.072	2.336	0.24	18789	23002	13209	3.168	57.4
2.1-2.16		0.037	6.892	0.32	26519	22448	15226	8.632	67.8
2.16-2.22		0.034	7.146	0.39	38188	21637	16839	8.615	77.8
2.22-2.3		0.071	3.949	0.51	47603	21076	18735	4.708	88.9
2.3-2.38		0.149	2.629	0.77	61737	20463	20032	3.097	97.9
2.38-2.47		0.253	2.292	1	70088	19661	19623	2.668	99.8
2.47-2.57		0.372	1.883	1.36	76940	18786	18771	2.159	99.9
2.57-2.68		0.54	1.384	1.84	78007	18196	18186	1.579	99.9
2.68-2.81		0.719	0.981	2.5	75666	17303	17303	1.116	100
2.81-2.97		0.822	0.711	3.44	73641	16514	16515	0.807	100
2.97-3.14		0.908	0.482	4.85	70814	15604	15594	0.546	99.9
3.14-3.36		0.954	0.322	7.02	67265	14624	14623	0.364	100
3.36-3.63		0.974	0.223	9.42	62822	13621	13614	0.252	99.9
3.63-3.98		0.987	0.15	12.64	58133	12607	12606	0.17	100
3.98-4.45		0.994	0.104	16.27	52235	11326	11322	0.117	100
4.45-5.14		0.994	0.088	18.1	46187	9996	9987	0.1	99.9
5.14-6.29		0.993	0.096	17.03	39074	8453	8448	0.108	99.9
6.29-8.9		0.997	0.063	21.75	30054	6530	6517	0.072	99.8
	8.9	0.998	0.041	29.31	15616	3564	3469	0.046	97.3

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Processing

Software

Name	Version	Classification
PHENIX	(phenix.refine: dev_1951)	refinement
XSCALE		data scaling
PDB_EXTRACT	3.15	data extraction
XDS		data reduction
PHENIX		phasing

Refinement

Resolution: 2.47→43.192 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 25.83 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.229	3944	2.37 %	Random selection
R_work	0.1729	-	-	-
obs	0.1742	84933	99.85 %	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Refinement step

Cycle: LAST / Resolution: 2.47→43.192 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	17208	0	120	502	17830

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	17703
X-RAY DIFFRACTION	f_angle_d	1.23	24165
X-RAY DIFFRACTION	f_dihedral_angle_d	13.707	6387
X-RAY DIFFRACTION	f_chiral_restr	0.056	2716
X-RAY DIFFRACTION	f_plane_restr	0.007	3113

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.47-2.5001	0.3376	147	0.311	5653	X-RAY DIFFRACTION	100
2.5001-2.5318	0.3632	145	0.2999	5864	X-RAY DIFFRACTION	100
2.5318-2.5651	0.3384	150	0.2954	5714	X-RAY DIFFRACTION	100
2.5651-2.6002	0.3241	117	0.2805	5819	X-RAY DIFFRACTION	100
2.6002-2.6374	0.3038	118	0.2648	5849	X-RAY DIFFRACTION	100
2.6374-2.6767	0.2919	139	0.2465	5861	X-RAY DIFFRACTION	100
2.6767-2.7186	0.2777	178	0.2397	5717	X-RAY DIFFRACTION	100
2.7186-2.7631	0.2979	133	0.2336	5839	X-RAY DIFFRACTION	100
2.7631-2.8108	0.3027	142	0.2443	5782	X-RAY DIFFRACTION	100
2.8108-2.8619	0.2809	147	0.2367	5875	X-RAY DIFFRACTION	100
2.8619-2.9169	0.351	132	0.2403	5731	X-RAY DIFFRACTION	100
2.9169-2.9764	0.2704	130	0.2253	5811	X-RAY DIFFRACTION	100
2.9764-3.0411	0.2458	138	0.2251	5764	X-RAY DIFFRACTION	100
3.0411-3.1118	0.2905	144	0.2175	5859	X-RAY DIFFRACTION	100
3.1118-3.1896	0.283	164	0.219	5738	X-RAY DIFFRACTION	100
3.1896-3.2758	0.2962	134	0.2154	5878	X-RAY DIFFRACTION	100
3.2758-3.3722	0.2787	127	0.1909	5806	X-RAY DIFFRACTION	100
3.3722-3.481	0.2402	155	0.1885	5751	X-RAY DIFFRACTION	100
3.481-3.6054	0.2371	128	0.1801	5834	X-RAY DIFFRACTION	100
3.6054-3.7496	0.2546	147	0.1667	5815	X-RAY DIFFRACTION	100
3.7496-3.9202	0.2201	136	0.1535	5783	X-RAY DIFFRACTION	100
3.9202-4.1267	0.185	144	0.1395	5794	X-RAY DIFFRACTION	100
4.1267-4.385	0.205	140	0.1191	5841	X-RAY DIFFRACTION	100
4.385-4.7232	0.1282	137	0.1112	5794	X-RAY DIFFRACTION	100
4.7232-5.1978	0.1916	151	0.1193	5821	X-RAY DIFFRACTION	100
5.1978-5.9483	0.2581	143	0.141	5788	X-RAY DIFFRACTION	100
5.9483-7.4879	0.1743	136	0.1352	5780	X-RAY DIFFRACTION	100
7.4879-43.1985	0.1314	142	0.1217	5686	X-RAY DIFFRACTION	98

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	1.1698	0.1747	-0.3362	2.0425	0.1347	1.5379	-0.0723	-0.1065	-0.0584	0.1222	0.2353	0.1512	-0.0632	-0.081	-0.1599	0.269	0.038	-0.0217	0.374	0.0716	0.2739	13.7985	7.861	93.3593
2	1.2348	-0.1414	-0.6155	0.9952	0.2753	1.6406	0.0197	0.159	0.0172	-0.0913	0.1298	-0.1661	-0.0102	0.0936	-0.1573	0.3168	-0.0481	0.0074	0.311	-0.0118	0.3114	28.0379	16.2138	63.9305
3	1.5787	-0.3124	-0.2729	1.5066	-0.0579	1.7847	0.06	0.1946	0.017	-0.4545	0.0125	-0.16	0.1829	0.2598	-0.0514	0.6909	-0.0291	0.0923	0.3631	-0.0702	0.3672	8.0813	8.7049	-1.7177
4	1.3092	-0.0182	-0.0646	1.3661	-0.379	1.9791	-0.0071	-0.0856	0.0829	0.0365	0.1057	0.1733	-0.2329	-0.0952	-0.1221	0.4833	0.0254	0.0765	0.2703	-0.0016	0.3299	-9.1721	18.1077	25.5817
5	1.461	0.0521	-0.5878	1.6793	-0.1902	2.72	0.2713	-0.1824	0.4914	0.0658	-0.1989	0.1316	-0.5015	0.1298	-0.0516	0.4298	-0.0332	0.0854	0.3698	-0.1054	0.5302	-1.0765	55.4561	56.4088
6	2.3023	0.2371	-0.4446	2.3242	0.1791	2.4517	0.0968	0.3181	0.274	-0.3768	-0.1012	-0.4259	-0.2217	0.6211	0.0023	0.533	0.0137	0.1336	0.6815	0.1505	0.5516	26.9759	49.6237	39.0877

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 9:384 ) OR ( CHAIN B AND RESID 402:402 )	A	9 - 384
2	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 9:384 ) OR ( CHAIN B AND RESID 402:402 )	B	402
3	X-RAY DIFFRACTION	2	( CHAIN B AND RESID 9:384 )	B	9 - 384
4	X-RAY DIFFRACTION	3	( CHAIN C AND RESID 9:384 ) OR ( CHAIN D AND RESID 500:500 )	C	9 - 384
5	X-RAY DIFFRACTION	3	( CHAIN C AND RESID 9:384 ) OR ( CHAIN D AND RESID 500:500 )	D	500
6	X-RAY DIFFRACTION	4	( CHAIN D AND RESID 9:384 )	D	9 - 384
7	X-RAY DIFFRACTION	5	( CHAIN E AND RESID 9:384 ) OR ( CHAIN F AND RESID 500:500 )	E	9 - 384
8	X-RAY DIFFRACTION	5	( CHAIN E AND RESID 9:384 ) OR ( CHAIN F AND RESID 500:500 )	F	500
9	X-RAY DIFFRACTION	6	( CHAIN E AND RESID 500:500 ) OR ( CHAIN F AND RESID 9:384 )	E	500
10	X-RAY DIFFRACTION	6	( CHAIN E AND RESID 500:500 ) OR ( CHAIN F AND RESID 9:384 )	F	9 - 384

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