PDB-8du1: Crystal Structure of NAD bound dTDP-glucose 4,6-dehydratase from ...

ID or keywords:

Entry

Database: PDB / ID: 8du1

Title

Crystal Structure of NAD bound dTDP-glucose 4,6-dehydratase from Elizabethkingia anophelis

Components

dTDP-glucose 4,6-dehydratase

Keywords

LYASE / SSGCID / nucleotide-sugar metabolic process / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Function and homology information

dTDP-glucose 4,6-dehydratase / dTDP-glucose 4,6-dehydratase activity / nucleotide-sugar metabolic process / nucleotide binding / metal ion binding
Similarity search - Function

Biological species

Elizabethkingia anophelis NUHP1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.85 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Funding support

1items

Citation

Journal: to be published
Title: Crystal Structure of DNA Polymerase III beta subunit from Elizabethkingia anophelis
Authors: DeBouver, N.D. / Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Jul 26, 2022	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Aug 10, 2022	Provider: repository / Type: Initial release
Revision 1.1	Dec 27, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.2	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	8du1.cif.gz	616.3 KB	Display	PDBx/mmCIF format
PDB format	pdb8du1.ent.gz	505.1 KB	Display	PDB format
PDBx/mmJSON format	8du1.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	8du1_validation.pdf.gz	1.5 MB	Display	wwPDB validaton report
Full document	8du1_full_validation.pdf.gz	1.5 MB	Display
Data in XML	8du1_validation.xml.gz	64.6 KB	Display
Data in CIF	8du1_validation.cif.gz	96.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/du/8du1 ftp://data.pdbj.org/pub/pdb/validation_reports/du/8du1	HTTPS FTP

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Related structure data

Related structure data	8dt6C C: citing same article (ref.)
Similar structure data	Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: ElanA.00085.a.B1

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: dTDP-glucose 4,6-dehydratase

B: dTDP-glucose 4,6-dehydratase

C: dTDP-glucose 4,6-dehydratase

D: dTDP-glucose 4,6-dehydratase

hetero molecules

172 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: dTDP-glucose 4,6-dehydratase

C: dTDP-glucose 4,6-dehydratase

hetero molecules

defined by author&software
Evidence: gel filtration
85.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: dTDP-glucose 4,6-dehydratase

D: dTDP-glucose 4,6-dehydratase

hetero molecules

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

Unit cell

Length a, b, c (Å)	66.740, 84.620, 130.870
Angle α, β, γ (deg.)	90.000, 101.180, 90.000
Int Tables number	4
Space group name H-M	P12₁1

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Protein , 1 types, 4 molecules ABCD

#1: Protein	dTDP-glucose 4,6-dehydratase Mass: 42004.910 Da / Num. of mol.: 4 / Fragment: ElanA.00085.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Elizabethkingia anophelis NUHP1 (bacteria) Gene: BD94_3274 / Plasmid: ElanA.00085.a.B1 / Production host: Escherichia coli BL21(DE3) (bacteria) References: UniProt: A0A077ELH2, dTDP-glucose 4,6-dehydratase

#1: Protein

dTDP-glucose 4,6-dehydratase

Mass: 42004.910 Da / Num. of mol.: 4 / Fragment: ElanA.00085.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Elizabethkingia anophelis NUHP1 (bacteria)
Gene: BD94_3274 / Plasmid: ElanA.00085.a.B1 / Production host:

Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A077ELH2, dTDP-glucose 4,6-dehydratase

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Non-polymers , 5 types, 1349 molecules

#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₂₁H₂₇N₇O₁₄P₂ / Feature type: SUBJECT OF INVESTIGATION / Comment: NAD*YM
#4: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-MG / MAGNESIUM ION Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#6: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1327 / Source method: isolated from a natural source / Formula: H₂O

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Details

Has ligand of interest	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: 2.16 Å³/Da / Density % sol: 42.99 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7 Details: [Target: ElanA.00085.a.B1.PS38380 - 21.5 mg/mL] [Barcode: 324703c1] [Pin: iyi1-8] [Crystallization: sparse screen - MCSG4 C1 - 0.1 M Bis-Tris Propane:HCl pH 7, 2 M Di-Ammonium Hydrogen ...Details: [Target: ElanA.00085.a.B1.PS38380 - 21.5 mg/mL] [Barcode: 324703c1] [Pin: iyi1-8] [Crystallization: sparse screen - MCSG4 C1 - 0.1 M Bis-Tris Propane:HCl pH 7, 2 M Di-Ammonium Hydrogen Citrate, 14C, 0.2:0.2 drop ratio] [Cryo: 20% EG]

Crystal

Density Matthews: 2.16 Å³/Da / Density % sol: 42.99 %

Crystal grow

Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7
Details: [Target: ElanA.00085.a.B1.PS38380 - 21.5 mg/mL] [Barcode: 324703c1] [Pin: iyi1-8] [Crystallization: sparse screen - MCSG4 C1 - 0.1 M Bis-Tris Propane:HCl pH 7, 2 M Di-Ammonium Hydrogen ...

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.9787 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Jul 14, 2022 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9787 Å / Relative weight: 1

Reflection

Resolution: 1.85→42.8 Å / Num. obs: 121703 / % possible obs: 99.8 % / Redundancy: 5.411 % / B_iso Wilson estimate: 23.7 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.064 / R_rim(I) all: 0.071 / Χ²: 0.929 / Net I/σ(I): 16.26 / Num. measured all: 658558 / Scaling rejects: 54

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. possible	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
1.85-1.9	4.661	0.513	2.59	41533	8982	8911	0.837	0.58	99.2
1.9-1.95	5.385	0.437	3.43	47160	8755	8758	0.9	0.484	100
1.95-2.01	5.491	0.32	4.8	46629	8500	8492	0.945	0.353	99.9
2.01-2.07	5.494	0.249	6.07	45473	8281	8277	0.967	0.276	100
2.07-2.14	5.509	0.207	7.37	44188	8023	8021	0.977	0.229	100
2.14-2.21	5.507	0.176	8.64	42561	7735	7729	0.982	0.195	99.9
2.21-2.29	5.523	0.145	10.46	41621	7546	7536	0.988	0.16	99.9
2.29-2.39	5.515	0.123	12.22	39556	7178	7173	0.991	0.136	99.9
2.39-2.49	5.511	0.105	14.23	38030	6899	6901	0.993	0.116	100
2.49-2.62	5.519	0.09	16.38	36355	6588	6587	0.995	0.099	100
2.62-2.76	5.518	0.076	19.44	34868	6321	6319	0.996	0.083	100
2.76-2.93	5.502	0.065	22.46	32803	5974	5962	0.997	0.072	99.8
2.93-3.13	5.485	0.054	26.31	30660	5593	5590	0.998	0.059	99.9
3.13-3.38	5.453	0.046	30.5	28487	5241	5224	0.998	0.051	99.7
3.38-3.7	5.43	0.04	34.66	26075	4810	4802	0.998	0.044	99.8
3.7-4.14	5.429	0.036	38.48	23540	4349	4336	0.999	0.039	99.7
4.14-4.78	5.39	0.034	40.04	20847	3874	3868	0.999	0.038	99.8
4.78-5.85	5.394	0.033	39.38	17605	3267	3264	0.999	0.037	99.9
5.85-8.27	5.328	0.034	39	13607	2553	2554	0.999	0.037	100
8.27-42.8	4.975	0.034	40.62	6960	1437	1399	0.999	0.038	97.4

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.20-4487	refinement
PDB_EXTRACT	3.27	data extraction
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: AlphaFold2

Resolution: 1.85→42.8 Å / SU ML: 0.18 / Cross valid method: THROUGHOUT / σ(F): 1.35 / Phase error: 19.29 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1948	2071	1.7 %
R_work	0.1555	119601	-
obs	0.1562	121672	99.84 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 105.04 Å² / B_iso mean: 31.5382 Å² / B_iso min: 10.39 Å²

Refinement step

Cycle: final / Resolution: 1.85→42.8 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11386	0	230	1355	12971
B_iso mean	-	-	22.67	36.07	-
Num. residues	-	-	-	-	1432

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / R_factor R_free error: 0 / Total num. of bins used: 15

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.85-1.89	0.283	126	0.2289	7870	7996	99
1.89-1.94	0.2281	148	0.197	7928	8076	100
1.94-1.99	0.2118	145	0.1714	7945	8090	100
1.99-2.05	0.2186	138	0.1608	7951	8089	100
2.05-2.12	0.2205	120	0.1619	7972	8092	100
2.12-2.19	0.2215	125	0.1607	7945	8070	100
2.19-2.28	0.2262	117	0.1628	7999	8116	100
2.28-2.39	0.1909	133	0.1608	7985	8118	100
2.39-2.51	0.2284	155	0.1613	7945	8100	100
2.51-2.67	0.2176	116	0.1605	7994	8110	100
2.67-2.87	0.2136	164	0.1655	7950	8114	100
2.87-3.16	0.2125	109	0.1622	8039	8148	100
3.16-3.62	0.1758	148	0.1432	7975	8123	100
3.62-4.56	0.1485	188	0.1274	7967	8155	100
4.56-42.8	0.1945	139	0.1553	8136	8275	99

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	5.1297	-0.1218	1.4429	2.6775	-1.4338	3.175	0.0763	-0.3338	-0.169	0.2758	0.0443	-0.0775	0.2211	0.2049	-0.0816	0.1873	0.0194	-0.057	0.1734	-0.0418	0.1158	8.2577	0.0413	20.2083
2	1.3571	-0.4012	-0.4462	1.46	0.1133	1.4832	0.0385	-0.2343	0.1311	0.0855	0.041	-0.2713	0.0185	0.1983	-0.0541	0.1323	-0.0171	-0.0614	0.1736	-0.0416	0.1852	15.0143	4.5319	12.3029
3	1.0179	-0.3614	-0.7791	0.9855	0.2601	1.2625	0.0081	0.0665	-0.0438	-0.0741	-0.0258	0.0051	0.1041	-0.1025	0.004	0.1085	-0.0086	-0.0301	0.1248	-0.0115	0.1174	5.6367	-4.2075	2.0702
4	1.1487	-0.2756	-1.1738	1.3913	0.5355	0.8374	0.0227	0.3537	-0.121	-0.0527	-0.1401	0.1983	0.0818	-0.1602	0.0251	0.1512	-0.0319	-0.0447	0.1931	-0.0218	0.1291	-6.6243	-4.3027	8.038
5	2.8107	-1.3695	-0.7082	1.355	0.3847	0.8122	0.0566	0.4645	-0.077	-0.12	-0.1797	0.1657	0.0423	-0.3353	0.0771	0.1724	-0.0383	-0.0431	0.2799	-0.0387	0.2084	-15.532	-5.4065	6.411
6	3.2362	0.9314	-1.1264	4.3708	-0.4116	1.7948	0.1845	-0.2778	0.4332	0.3438	-0.0223	0.0522	-0.2408	-0.013	-0.077	0.15	0.0138	-0.0023	0.2057	-0.0282	0.1418	-7.2424	10.8444	18.7279
7	1.2998	-0.0674	-0.0803	1.719	-0.3775	1.072	0.0492	-0.359	0.1476	0.4505	-0.0174	-0.0429	-0.1957	0.1355	-0.0731	0.2638	-0.0097	-0.025	0.2134	-0.004	0.1543	-36.5166	6.1064	83.6811
8	1.3246	-0.1896	-0.2508	1.9867	-0.4414	1.7511	0.0345	-0.211	0.0098	0.0808	-0.0709	-0.2444	-0.0685	0.2616	-0.0185	0.1176	-0.0138	-0.0291	0.1558	0.0278	0.1507	-27.313	3.2728	70.9819
9	0.9125	0.1395	-0.998	1.0588	-0.3608	1.3462	-0.0724	-0.0171	-0.0763	-0.0496	0.0286	0.0379	0.0736	-0.1103	-0.0464	0.1224	0.0001	-0.0202	0.1136	0.0134	0.1628	-40.0822	-4.5043	66.3175
10	2.6257	-0.2281	-0.8064	0.7206	-0.1648	1.1342	0.0365	0.1739	-0.1345	-0.0244	0.0231	0.1775	0.0273	-0.2825	0.0531	0.152	0.0031	-0.0126	0.1881	0.0594	0.1907	-56.0614	-5.5773	74.2738
11	2.7833	-0.3811	-0.4742	3.1541	-1.3424	1.6209	0.2674	-0.4881	0.8368	0.9036	0.059	0.0993	-0.5998	0.0782	0.2438	0.5357	0.0282	0.159	0.2151	-0.0295	0.4201	-49.0226	16.6269	83.5118
12	2.0708	-0.2607	-1.5328	1.7968	0.8258	3.7529	0.5117	0.2657	0.3956	-0.6005	-0.1494	-0.1524	-1.0095	-0.3365	0.0856	0.5214	0.1387	0.1254	0.1368	0.0619	0.1812	16.0747	6.2768	-19.4934
13	2.9754	-0.3238	-0.7532	1.2753	0.5273	2.8375	0.1639	-0.1217	0.0041	-0.0717	0.0648	-0.325	-0.149	0.4757	-0.012	0.2858	0.0164	0.0061	0.2892	-0.0477	0.2292	31.499	-7.9975	-22.8295
14	1.8826	0.3859	-0.8258	2.1723	-0.7285	3.1339	0.0288	0.1212	0.0762	-0.0857	-0.116	-0.0098	-0.0959	0.0406	0.0898	0.155	0.0221	-0.0211	0.1363	0.0129	0.1252	-28.4173	10.8808	37.4709
15	1.0025	0.4859	-0.923	0.9505	-0.7802	2.5422	-0.0476	0.155	-0.1457	-0.2328	-0.0352	0.002	0.2851	-0.1202	0.0212	0.1775	-0.0027	-0.0147	0.1117	-0.0171	0.1326	-35.0694	-0.6195	47.6166
16	1.9268	0.18	-0.4467	1.227	-0.475	1.8856	-0.1296	-0.0416	-0.389	-0.1222	-0.1966	-0.3192	0.5346	0.487	0.1885	0.4356	0.128	0.0811	0.34	0.0538	0.276	-15.3969	-7.8327	38.7174

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 -1 through 24 )	A	-1 - 24
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 25 through 135 )	A	25 - 135
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 136 through 206 )	A	136 - 206
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 207 through 265 )	A	207 - 265
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 266 through 323 )	A	266 - 323
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 324 through 359 )	A	324 - 359
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 0 through 63 )	B	0 - 63
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 64 through 135 )	B	64 - 135
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 136 through 206 )	B	136 - 206
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 207 through 336 )	B	207 - 336
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 337 through 358 )	B	337 - 358
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 0 through 185 )	C	0 - 185
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 186 through 357 )	C	186 - 357
14	X-RAY DIFFRACTION	14	chain 'D' and (resid -3 through 96 )	D	-3 - 96
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 97 through 206 )	D	97 - 206
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 207 through 359 )	D	207 - 359

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Protein , 1 types, 4 molecules ABCD

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Non-polymers , 5 types, 1349 molecules

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