PDB-6c58: Human UDP-Glucose Dehydrogenase A225L substitutuion with UDP-xylo...

ID or keywords:

Entry

Database: PDB / ID: 6c58

Title

Human UDP-Glucose Dehydrogenase A225L substitutuion with UDP-xylose bound

Components

UDP-glucose 6-dehydrogenase

Keywords

OXIDOREDUCTASE / dehydrogenase / udp-xylose / hUGDH

Function / homology

Function and homology information

Formation of the active cofactor, UDP-glucuronate / chondroitin sulfate biosynthetic process / UDP-glucose 6-dehydrogenase / UDP-glucose 6-dehydrogenase activity / UDP-glucuronate biosynthetic process / heparan sulfate proteoglycan biosynthetic process / glycosaminoglycan biosynthetic process / gastrulation with mouth forming second / protein hexamerization / neuron development ...
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.198 Å

Authors

Gross, P.G. / Fallah, J. / Wood, Z.A.

Funding support

United States, 1items

Citation

Journal: To Be Published
Title: The A225L Substitution of hUGDH alters structure and function
Authors: Gross, P.G. / Wood, Z.A.

History

Deposition	Jan 15, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 16, 2019	Provider: repository / Type: Initial release
Revision 1.1	Jan 1, 2020	Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.2	Oct 4, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	6c58.cif.gz	1.1 MB	Display	PDBx/mmCIF format
PDB format	pdb6c58.ent.gz	915.1 KB	Display	PDB format
PDBx/mmJSON format	6c58.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	6c58_validation.pdf.gz	3.4 MB	Display	wwPDB validaton report
Full document	6c58_full_validation.pdf.gz	3.4 MB	Display
Data in XML	6c58_validation.xml.gz	103 KB	Display
Data in CIF	6c58_validation.cif.gz	142.8 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c5/6c58 ftp://data.pdbj.org/pub/pdb/validation_reports/c5/6c58	HTTPS FTP

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Related structure data

Related structure data	6c5aC 6c5zC 3ptzS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	6om8-2 6om8-1 3tdk-2 5vr8-d 3ptz-d 3tdk-1 3prj-d 6dvr-2 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
Related items in Molecule of the Month	#111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1) #127 - Jul 2010 Crystallins similarity (1)

Deposited unit

A: UDP-glucose 6-dehydrogenase

B: UDP-glucose 6-dehydrogenase

C: UDP-glucose 6-dehydrogenase

D: UDP-glucose 6-dehydrogenase

E: UDP-glucose 6-dehydrogenase

F: UDP-glucose 6-dehydrogenase

hetero molecules

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

1

Idetical with deposited unit
defined by author&software
Evidence: Assembly supported by sedimentation velocity experiments using analytical ultracentrifugation.

Unit cell

Length a, b, c (Å)	93.520, 194.990, 109.540
Angle α, β, γ (deg.)	90.00, 110.71, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	UDP-glucose 6-dehydrogenase / UDPGDH Mass: 55136.020 Da / Num. of mol.: 6 / Mutation: A225L Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UGDH / Production host: Escherichia coli (E. coli) / References: UniProt: O60701, UDP-glucose 6-dehydrogenase
#2: Chemical	ChemComp-UDX / URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE / UDP-ALPHA-D-XYLOPYRANOSE Mass: 536.276 Da / Num. of mol.: 10 / Source method: obtained synthetically / Formula: C₁₄H₂₂N₂O₁₆P₂
#3: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1141 / 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: 2.82 Å³/Da / Density % sol: 56.44 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 / Details: 10% PEG3350, 16% 1,5-pentanediol, 100 mM HEPES

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Data collection

Diffraction	Mean temperature: 77 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: RAYONIX MX300-HS / Detector: CCD / Date: Nov 14, 2015
Radiation	Monochromator: double crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.198→51.288 Å / Num. obs: 178670 / % possible obs: 96.3 % / Redundancy: 2.82 % / CC_1/2: 0.992 / R_rim(I) all: 0.154 / R_sym value: 0.128 / Net I/σ(I): 5.95
Reflection shell	Resolution: 2.198→2.25 Å / Redundancy: 2.76 % / Num. unique obs: 13090 / CC_1/2: 0.436 / R_rim(I) all: 1.1195 / R_sym value: 0.986 / % possible all: 95.8

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Processing

Software

Name	Version	Classification
PHENIX	(1.12_2829: ???)	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing
Coot	0.8.2	model building

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 3PTZ

3ptz

Resolution: 2.198→51.288 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 26.94 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.2444	16100	10.03 %
R_work	0.2088	-	-
obs	0.2124	160457	86.4 %

Solvent computation

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

Refinement step

Cycle: LAST / Resolution: 2.198→51.288 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21484	0	343	1141	22968

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.005	22252
X-RAY DIFFRACTION	f_angle_d	0.557	30176
X-RAY DIFFRACTION	f_dihedral_angle_d	14.981	8360
X-RAY DIFFRACTION	f_chiral_restr	0.052	3455
X-RAY DIFFRACTION	f_plane_restr	0.003	3834

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 (%)
2.1984-2.2234	0.3828	394	0.3499	3657	X-RAY DIFFRACTION	65
2.2234-2.2495	0.3697	490	0.3522	4239	X-RAY DIFFRACTION	77
2.2495-2.277	0.3753	476	0.3304	4244	X-RAY DIFFRACTION	76
2.277-2.3058	0.3704	488	0.3099	4442	X-RAY DIFFRACTION	80
2.3058-2.3361	0.3293	492	0.3038	4503	X-RAY DIFFRACTION	80
2.3361-2.3681	0.3578	519	0.3106	4452	X-RAY DIFFRACTION	81
2.3681-2.402	0.353	513	0.297	4540	X-RAY DIFFRACTION	81
2.402-2.4378	0.335	510	0.2826	4576	X-RAY DIFFRACTION	83
2.4378-2.4759	0.3143	518	0.2746	4622	X-RAY DIFFRACTION	83
2.4759-2.5165	0.3054	535	0.2596	4655	X-RAY DIFFRACTION	84
2.5165-2.5599	0.3011	491	0.2698	4742	X-RAY DIFFRACTION	85
2.5599-2.6064	0.2979	553	0.2543	4807	X-RAY DIFFRACTION	86
2.6064-2.6566	0.3057	517	0.2552	4751	X-RAY DIFFRACTION	86
2.6566-2.7108	0.3161	520	0.2555	4850	X-RAY DIFFRACTION	87
2.7108-2.7697	0.2943	548	0.2497	4887	X-RAY DIFFRACTION	87
2.7697-2.8342	0.3026	542	0.2417	4902	X-RAY DIFFRACTION	88
2.8342-2.905	0.2815	572	0.2289	4899	X-RAY DIFFRACTION	89
2.905-2.9836	0.2642	568	0.2262	4968	X-RAY DIFFRACTION	89
2.9836-3.0713	0.2644	536	0.2239	4961	X-RAY DIFFRACTION	89
3.0713-3.1705	0.2531	554	0.2172	4998	X-RAY DIFFRACTION	90
3.1705-3.2838	0.2633	578	0.2102	5029	X-RAY DIFFRACTION	90
3.2838-3.4152	0.2602	578	0.213	5071	X-RAY DIFFRACTION	91
3.4152-3.5706	0.2502	563	0.2008	5087	X-RAY DIFFRACTION	92
3.5706-3.7588	0.2194	565	0.1847	5173	X-RAY DIFFRACTION	92
3.7588-3.9942	0.2198	564	0.182	5162	X-RAY DIFFRACTION	93
3.9942-4.3025	0.204	579	0.1713	5178	X-RAY DIFFRACTION	93
4.3025-4.7352	0.1683	591	0.1504	5198	X-RAY DIFFRACTION	93
4.7352-5.4197	0.1855	595	0.158	5254	X-RAY DIFFRACTION	94
5.4197-6.8257	0.1881	573	0.1778	5284	X-RAY DIFFRACTION	94
6.8257-51.3016	0.1689	578	0.1498	5226	X-RAY DIFFRACTION	92

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	0.9304	0.9202	0.2205	1.6446	1.1273	3.7582	-0.1279	0.1543	0.1608	-0.1068	0.1202	0.0412	-0.1041	0.4507	-0.0046	0.1778	-0.0218	0.0144	0.3017	0.0169	0.3797	-14.4445	26.9543	117.0921
2	1.7596	1.1537	-0.0198	7.4733	0.8576	2.3555	0.0422	-0.1687	-0.0915	0.0456	-0.1104	-0.1218	0.111	0.0978	0.0079	0.1742	0.0427	0.0029	0.2316	-0.0177	0.2232	-16.5237	15.1768	132.6665
3	0.8492	0.4153	-0.0171	0.216	0.0412	0.6928	-0.041	0.0161	0.1763	-0.0272	-0.0154	0.0747	-0.0946	-0.0922	0.0517	0.2197	0.0588	-0.0029	0.1852	-0.0236	0.2974	-37.977	16.0101	122.6826
4	3.0374	0.6434	1.2594	2.2076	1.0797	4.0956	-0.1613	0.3569	0.0991	-0.1633	0.1766	0.0007	-0.1224	0.1651	0.0392	0.2418	-0.0152	0.0576	0.252	-0.0043	0.2133	-35.6476	5.606	97.512
5	1.826	0.0051	0.2379	2.8729	0.3374	2.9365	-0.1326	-0.2651	0.2651	0.0394	0.1	0.2598	-0.4653	-0.6204	0.0412	0.3173	0.2079	-0.036	0.5568	-0.0705	0.4105	-81.1979	25.5481	125.1492
6	0.1798	-0.1891	0.5503	3.7957	-2.3023	2.7458	0.0831	-0.0285	-0.0468	-0.0927	-0.0032	0.0061	0.1199	-0.3692	-0.0331	0.2168	0.0602	0.0145	0.5626	-0.0629	0.3049	-76.3524	7.4571	120.1186
7	2.552	2.1058	1.3235	2.2624	1.3896	3.33	-0.2103	0.0931	0.2183	-0.2297	0.0276	0.1035	-0.1682	-0.2195	0.2463	0.2393	0.1616	-0.0219	0.4226	-0.0209	0.3601	-72.6844	16.721	113.8906
8	1.0539	-0.0879	0.386	0.7653	-0.0545	1.2537	-0.0588	-0.0204	0.0289	-0.0233	0.0574	0.0484	-0.1494	-0.2017	-0.015	0.1903	0.0402	0.0215	0.2338	-0.0307	0.2339	-55.0929	14.0191	125.4162
9	1.5919	-0.6425	0.3179	2.3502	-0.3353	3.2149	-0.2149	-0.5245	0.0701	0.3658	0.1506	0.1988	-0.1439	-0.4799	0.0103	0.2682	0.1253	0.037	0.5709	-0.0772	0.306	-61.3622	14.8213	151.8445
10	2.2	1.2642	0.4401	7.9765	5.1989	6.4341	-0.06	-0.6486	0.2283	0.1984	0.1835	-0.6819	-0.1492	0.4413	-0.2841	0.2796	0.0724	-0.0324	0.5251	-0.1329	0.3763	-46.1756	22.2875	150.9387
11	2.9271	-0.6711	0.2214	3.9995	-0.5191	3.079	0.0904	0.187	-0.0766	-0.3767	-0.0555	-0.1208	0.1089	0.2571	-0.0424	0.2724	0.0137	0.0308	0.2941	-0.0289	0.1745	-46.6155	-29.5739	74.6929
12	1.0079	0.3922	0.007	1.5113	0.226	1.1583	0.0067	0.0539	-0.0235	0.1683	0.0404	-0.0228	0.0447	0.0599	-0.0646	0.3189	0.0399	0.0183	0.3312	-0.0188	0.2073	-51.0088	-18.301	86.4617
13	0.8499	0.0932	-0.0925	1.2134	0.1039	1.5929	0.0264	-0.0439	-0.024	0.2133	0.0167	0.0267	0.2135	-0.0271	-0.0442	0.2858	0.0017	-0.0046	0.2781	-0.0013	0.2034	-56.0328	-32.5462	101.5731
14	3.4526	-1.5926	-0.0497	4.3023	-0.9782	3.2365	0.0366	-0.1471	-0.1506	0.2797	-0.0831	-0.3523	0.5179	0.4446	0.0789	0.4762	0.1119	-0.0654	0.3309	-0.0484	0.3234	-35.5049	-49.4727	102.497
15	2.5972	-0.2639	-0.4085	1.6237	0.389	0.8768	-0.1334	-0.3797	-0.495	0.1365	0.0616	0.0707	0.5143	-0.2049	0.1008	0.684	-0.1953	0.0475	0.4959	0.1679	0.479	-80.3529	-54.0312	122.2303
16	1.1791	-0.7087	-0.2606	1.3829	0.29	0.7939	-0.0219	-0.2019	0.0545	0.0218	0.0497	0.0767	0.1015	-0.2864	0.0071	0.2561	-0.0656	-0.0024	0.4828	0.0117	0.2301	-75.8069	-22.6961	114.8238
17	2.4055	0.2044	-0.4824	2.024	0.0598	1.6685	-0.1105	0.1207	-0.2559	-0.217	0.0485	-0.004	0.2794	0.0563	0.0712	0.3045	0.0493	0.0221	0.1995	0.007	0.2634	-7.5384	-43.5675	153.359
18	0.9594	0.3456	-0.1472	1.448	-0.4821	0.8062	-0.0651	-0.0083	0.0449	-0.0292	0.0098	-0.0757	-0.0989	0.0143	0.0605	0.2294	0.0339	-0.022	0.2532	0.0005	0.2277	-15.7988	-12.669	147.6535
19	0.9929	-0.2143	0.1198	2.0058	0.2696	1.5635	-0.4533	-0.6516	0.0434	0.4779	0.3485	0.0911	-0.4078	-0.3578	0.0451	0.5477	0.2969	-0.0195	0.8125	-0.1014	0.3176	-45.2837	-1.0626	179.025
20	1.2585	-0.6051	-0.2187	1.2648	-0.2302	1.2653	-0.2351	-0.3214	-0.1282	0.2517	0.1825	0.0731	-0.0696	-0.2318	0.039	0.2715	0.0665	0.017	0.4622	0.0429	0.2594	-37.0496	-19.046	166.1311
21	2.7935	1.0769	-0.6091	1.8788	0.8564	1.5488	-0.1875	-0.2508	-0.611	0.3848	0.0612	0.7086	0.2488	-0.4809	0.1541	0.3927	-0.0214	0.2045	0.8183	0.2495	0.7284	-52.8944	-37.3434	170.7945

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1 through 81 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 82 through 158 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 159 through 321 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 322 through 465 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 2 through 87 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 88 through 135 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 136 through 185 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 186 through 321 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 322 through 440 )
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 441 through 465 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 2 through 87 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 88 through 185 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 186 through 321 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 322 through 465 )
15	X-RAY DIFFRACTION	15	chain 'D' and (resid 2 through 212 )
16	X-RAY DIFFRACTION	16	chain 'D' and (resid 213 through 465 )
17	X-RAY DIFFRACTION	17	chain 'E' and (resid 1 through 212 )
18	X-RAY DIFFRACTION	18	chain 'E' and (resid 213 through 465 )
19	X-RAY DIFFRACTION	19	chain 'F' and (resid 2 through 158 )
20	X-RAY DIFFRACTION	20	chain 'F' and (resid 159 through 348 )
21	X-RAY DIFFRACTION	21	chain 'F' and (resid 349 through 465 )

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