PDB-6c5z: Human UDP-Glucose Dehydrogenase A225L substitutuion with UDP-gluc...

ID or keywords:

Entry

Database: PDB / ID: 6c5z

Title

Human UDP-Glucose Dehydrogenase A225L substitutuion with UDP-glucose and NADH bound

Components

UDP-glucose 6-dehydrogenase

Keywords

OXIDOREDUCTASE / dehydrogenase / udp-glucose / hUGDH / NADH

Function / homology

Function and homology information

Formation of the active cofactor, UDP-glucuronate / UDP-glucose 6-dehydrogenase activity / UDP-glucose 6-dehydrogenase / UDP-glucuronate biosynthetic process / glycosaminoglycan biosynthetic process / chondroitin sulfate proteoglycan biosynthetic process / heparan sulfate proteoglycan 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: 2.95 Å

Authors

Gross, P.G. / Sidlo, A.M. / Walsh, R.M. / Peeples, W.B. / 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 17, 2018	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jan 23, 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
Revision 1.3	Dec 25, 2024	Group: Advisory / Derived calculations / Structure summary Category: pdbx_entry_details / pdbx_validate_close_contact / struct_conn

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	6c5z.cif.gz	1 MB	Display	PDBx/mmCIF format
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Validation report

Summary document	6c5z_validation.pdf.gz	3.5 MB	Display	wwPDB validaton report
Full document	6c5z_full_validation.pdf.gz	3.5 MB	Display
Data in XML	6c5z_validation.xml.gz	108 KB	Display
Data in CIF	6c5z_validation.cif.gz	137.2 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/c5/6c5z ftp://data.pdbj.org/pub/pdb/validation_reports/c5/6c5z	HTTPS FTP

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Related structure data

Related structure data	6c58C 6c5aC 2q3eS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	2qg4-1 6c4j-1 2q3e-1 2qg4-4 2qg4-5 3khu-d 2o3j-1 6c4j-2 3itk-d 6c4k-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	#254 - Feb 2021 Cellulose Synthase similarity (1) #111 - Mar 2009 Hydrogenase similarity (1) #228 - Dec 2018 Directed Evolution of Enzymes similarity (1) #102 - Jun 2008 Lactate Dehydrogenase similarity (1) #93 - Sep 2007 Citrate Synthase 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

338 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 is supported by sedimentation velocity studies using analytical ultracentrifugation.

Unit cell

Length a, b, c (Å)	93.770, 199.800, 200.820
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	18
Space group name H-M	P22₁2₁

#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-NAI / 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE / NADH Mass: 665.441 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₂₁H₂₉N₇O₁₄P₂
#3: Chemical	ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER Mass: 566.302 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C₁₅H₂₄N₂O₁₇P₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 294 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.84 Å³/Da / Density % sol: 56.74 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.8 Details: 20% PEG3350, 50 mM dipotassium phosphate, 100 mM sodium glycine

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Data collection

Diffraction	Mean temperature: 77 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Apr 20, 2012
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: 2.9497→30.0627 Å / Num. obs: 79604 / % possible obs: 99.1 % / Redundancy: 4.63 % / CC_1/2: 0.992 / R_rim(I) all: 0.167 / R_sym value: 0.148 / Net I/σ(I): 7.91
Reflection shell	Resolution: 2.9497→3.02 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 1.44 / Num. unique obs: 5781 / CC_1/2: 0.608 / R_rim(I) all: 1.142 / R_sym value: 0.998 / % possible all: 98.5

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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 2Q3E

2q3e

Resolution: 2.95→30.061 Å / SU ML: 0.44 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.68

	R_factor	Num. reflection	% reflection
R_free	0.2589	3977	5 %
R_work	0.2032	-	-
obs	0.206	79534	99.26 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å

Refinement step

Cycle: LAST / Resolution: 2.95→30.061 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	20523	0	436	294	21253

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	21359
X-RAY DIFFRACTION	f_angle_d	1.007	28952
X-RAY DIFFRACTION	f_dihedral_angle_d	18.582	7954
X-RAY DIFFRACTION	f_chiral_restr	0.061	3316
X-RAY DIFFRACTION	f_plane_restr	0.005	3652

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 (%)
2.9497-2.9856	0.3839	139	0.3325	2594	X-RAY DIFFRACTION	97
2.9856-3.0234	0.3503	141	0.3191	2694	X-RAY DIFFRACTION	100
3.0234-3.0631	0.3833	141	0.2937	2630	X-RAY DIFFRACTION	99
3.0631-3.1051	0.3196	138	0.2818	2657	X-RAY DIFFRACTION	100
3.1051-3.1494	0.3368	143	0.2726	2691	X-RAY DIFFRACTION	99
3.1494-3.1963	0.3127	139	0.2793	2671	X-RAY DIFFRACTION	99
3.1963-3.2462	0.3097	139	0.2748	2694	X-RAY DIFFRACTION	100
3.2462-3.2994	0.3391	141	0.274	2666	X-RAY DIFFRACTION	99
3.2994-3.3562	0.3467	141	0.2718	2701	X-RAY DIFFRACTION	99
3.3562-3.4171	0.256	142	0.2626	2633	X-RAY DIFFRACTION	99
3.4171-3.4828	0.2697	140	0.244	2697	X-RAY DIFFRACTION	99
3.4828-3.5538	0.2982	138	0.2124	2649	X-RAY DIFFRACTION	99
3.5538-3.6309	0.2692	137	0.2126	2714	X-RAY DIFFRACTION	99
3.6309-3.7152	0.2664	145	0.2079	2644	X-RAY DIFFRACTION	99
3.7152-3.8079	0.2864	141	0.2041	2682	X-RAY DIFFRACTION	99
3.8079-3.9107	0.2882	140	0.2059	2712	X-RAY DIFFRACTION	99
3.9107-4.0255	0.2436	142	0.1917	2685	X-RAY DIFFRACTION	100
4.0255-4.1551	0.235	144	0.1879	2695	X-RAY DIFFRACTION	99
4.1551-4.3032	0.2127	141	0.1686	2691	X-RAY DIFFRACTION	99
4.3032-4.475	0.2182	143	0.1593	2690	X-RAY DIFFRACTION	99
4.475-4.6779	0.2172	142	0.1563	2704	X-RAY DIFFRACTION	99
4.6779-4.9236	0.2057	142	0.1548	2715	X-RAY DIFFRACTION	99
4.9236-5.2305	0.2353	145	0.1683	2723	X-RAY DIFFRACTION	100
5.2305-5.6319	0.2562	143	0.1753	2722	X-RAY DIFFRACTION	100
5.6319-6.1942	0.2712	144	0.1934	2747	X-RAY DIFFRACTION	100
6.1942-7.0803	0.2247	149	0.1879	2778	X-RAY DIFFRACTION	100
7.0803-8.8821	0.2261	149	0.1675	2798	X-RAY DIFFRACTION	100
8.8821-30.0627	0.2348	148	0.1898	2880	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	1.4367	0.3056	-0.6606	0.5777	-0.7773	1.6551	0.1439	0.0104	0.0281	-0.3296	-0.3082	-1.1614	-0.0475	0.7715	-0.2093	1.1736	-0.1041	0.8044	0.8828	-0.0224	0.7432	144.5998	69.5215	403.975
2	1.5885	-0.353	0.6234	1.7465	0.2372	2.353	0.1421	-0.0602	0.4712	-0.4878	-0.2488	-0.4059	-0.5823	0.2939	0.1088	1.0572	-0.1805	0.4271	0.77	-0.0346	0.7607	138.3054	80.5714	409.1973
3	1.9876	-0.974	-1.0807	2.1691	-0.5999	2.3429	0.1387	0.2746	0.0692	-0.779	-0.0616	-0.0636	-0.056	-0.013	-0.0465	0.6185	0.0078	0.0284	0.4231	0.0139	0.277	117.2935	64.3949	411.4872
4	1.205	0.733	-0.8552	3.1599	0.1728	3.1808	-0.3829	0.2688	-0.4811	-1.3203	0.1214	-0.4943	0.3634	-0.1496	0.2314	0.9783	-0.0821	0.2656	0.4928	-0.0929	0.4999	124.5103	41.7694	404.4482
5	0.2028	0.1023	0.8839	0.3586	1.1632	6.4269	0.7317	1.3991	0.4958	0.0207	0.167	0.5064	-0.0509	-1.1396	-0.8191	0.8988	0.2298	0.1946	1.762	0.3568	0.7073	83.2626	57.112	407.3628
6	2.8055	-0.1499	0.0717	0.6571	0.6944	0.6778	0.0267	0.9144	0.6519	0.3017	-0.072	-0.2588	-0.2844	-0.3118	0.0235	0.7939	0.0405	-0.0402	1.7119	0.1705	0.3531	93.612	65.625	396.0883
7	0.6525	-0.3832	1.0432	0.4196	-0.8249	1.8905	-0.0648	0.9451	0.379	-0.6041	0.1399	0.2066	0.0969	-0.3492	0.0511	0.7826	0.2253	-0.1602	2.487	0.1154	0.6435	94.0506	63.4074	388.2583
8	1.3003	-1.0849	-0.4473	2.5359	0.7535	1.307	0.168	0.2041	0.0871	-0.3097	-0.0604	0.077	0.0379	-0.277	-0.1124	0.5817	0.001	0.0656	0.5742	-0.0029	0.2654	107.5731	72.0182	415.0407
9	3.1941	2.0462	0.6277	4.5408	0.8812	3.0475	-0.2658	0.2523	0.6339	-0.7697	0.1862	0.2989	-0.6679	-0.409	0.0783	0.5965	0.1768	0.0249	0.5366	0.1482	0.4765	99.9602	93.3416	421.8922
10	1.496	-1.0233	-0.4137	3.7612	0.0102	4.5441	-0.3229	0.5765	-0.6221	-0.3584	0.4851	-0.3183	0.6226	0.0628	-0.1808	0.7507	-0.135	0.271	0.5075	-0.1909	0.7161	111.2411	6.3862	423.8125
11	1.4054	0.6614	-0.0365	1.6979	0.0334	3.5356	-0.4917	0.2863	-0.6658	-0.3941	0.2939	-0.709	0.5839	0.3536	0.1734	0.6528	-0.0788	0.2541	0.6025	-0.1198	0.682	116.6209	14.9483	423.6512
12	2.2583	-0.6278	-0.5622	1.2314	1.1217	6.0155	-0.288	0.5264	-0.0944	-0.5751	0.095	-0.2781	-0.0207	-0.3947	0.1564	0.7983	-0.2593	0.229	0.4672	-0.1149	0.5136	105.0343	17.6682	420.3946
13	2.1572	0.6241	-0.1775	2.3517	0.4931	2.3416	-0.0992	0.0811	-0.2261	-0.2557	0.0892	0.0571	0.3141	-0.058	0.0331	0.417	-0.0839	0.078	0.3249	0.0457	0.3401	99.448	23.6243	437.7758
14	3.1344	-1.1833	2.9127	2.1936	-1.819	3.5017	-0.1866	0.2629	0.1723	-0.2555	-0.023	-0.3052	-0.1696	0.2107	0.2173	0.3417	-0.1204	0.0951	0.4112	-0.0515	0.3531	109.3611	38.2322	439.2065
15	4.6221	1.1746	2.2629	5.0588	1.9232	4.8499	0.093	0.0395	-0.2688	0.0722	0.056	-0.8854	0.1027	0.2164	-0.1383	0.3386	-0.0134	0.0663	0.3473	0.0222	0.4614	124.1272	28.2296	450.517
16	4.9509	0.5331	-2.1595	0.8034	1.4673	6.8732	-0.064	-0.0966	-0.2163	-0.6805	0.1501	-0.8629	0.7777	0.9785	-0.015	0.5159	0.0708	0.0339	0.3901	-0.108	0.8427	131.4785	24.3876	449.1371
17	4.2551	0.24	1.5152	5.9115	1.431	4.1918	0.1472	-0.6032	-0.2297	0.2872	-0.1423	-0.3694	0.7193	0.1236	-0.0363	0.585	0.023	-0.0959	0.4167	0.1158	0.4477	121.3946	23.5565	462.8862
18	4.2494	-1.99	3.9474	2.2094	-1.0927	4.3327	0.1741	-0.9075	-0.1568	0.3811	0.3297	0.0968	0.44	-0.9616	-0.4834	0.5871	-0.0462	0.0821	0.593	0.0837	0.3724	111.9706	28.0538	465.1272
19	2.5399	0.6173	-0.703	4.1764	1.8123	2.1256	-0.2698	0.077	0.1446	0.2561	-0.2984	1.5425	0.2083	-0.1334	0.4252	0.4039	-0.016	0.1008	0.3905	-0.0474	0.8244	78.0376	38.6903	465.2175
20	1.8627	-0.26	-0.3172	1.6184	-0.357	2.6536	-0.0117	0.4758	0.0156	-0.151	-0.0321	0.4998	0.0452	-0.6965	-0.0253	0.359	-0.0835	0.0507	0.6015	-0.0352	0.5001	82.7624	41.5484	433.4164
21	4.9249	1.0039	-0.8716	4.1052	-0.2554	3.1767	-0.2384	-0.5681	-0.2778	0.6896	0.1274	-1.2228	-0.2886	0.1881	0.1258	0.5516	0.2233	-0.3316	0.6639	-0.2388	1.0345	142.4179	54.6818	481.0339
22	1.9041	-0.5378	0.0018	1.8205	-0.5069	0.1642	-0.1746	-0.3458	-0.2311	0.4963	0.2568	-2.5449	-0.2434	0.3786	0.1202	0.2909	0.1103	-0.2044	0.6562	-0.1392	1.6548	149.2384	53.8534	476.4636
23	2.7295	1.0043	0.1613	4.477	-1.2146	8.3134	-0.1866	-0.067	-0.003	-0.4454	0.2319	-0.9236	0.1765	0.2607	-0.0629	0.3732	0.1126	0.0617	0.4886	-0.0955	0.4886	133.1765	45.2486	463.162
24	2.7918	0.9237	0.1453	7.9548	0.9598	2.3898	-0.0802	-0.5828	0.1836	0.7028	0.1199	-0.1933	0.1678	-0.1264	-0.0806	0.4099	0.1799	-0.128	0.6703	0.0197	0.442	130.2928	54.1458	478.6005
25	1.2751	-0.3121	0.1386	2.2596	-0.5254	2.1022	0.1109	0.0828	0.0817	-0.031	0.1146	-0.3263	-0.0044	0.2372	-0.2153	0.2272	0.0158	0.0004	0.3498	-0.0895	0.4022	126.6708	69.9208	456.3722
26	2.0928	0.668	-0.5563	2.0535	-1.1153	2.7798	0.101	-0.0187	0.3011	-0.1229	0.0701	-0.9458	-0.283	1.3067	-0.0845	0.4715	-0.1534	0.1858	1.0178	-0.2467	0.9446	147.0904	73.6366	442.262
27	1.1926	-0.1462	-0.3536	2.3833	0.7099	2.3376	0.0568	-0.0152	0.2063	-0.0661	0.2281	0.0448	-0.3839	-0.0322	-0.2637	0.3922	0.0776	0.1165	0.3433	0.0747	0.5189	105.813	101.4016	456.4586
28	0.8815	-0.1374	-0.4763	2.8236	-0.611	0.8277	0.1038	-0.0176	0.2024	0.0864	-0.0046	-0.2875	-0.2346	0.199	-0.0659	0.3076	-0.0195	0.0191	0.3182	-0.0496	0.4491	118.8136	89.0681	458.3742
29	2.4067	0.3	-1.5718	1.4943	0.0948	2.3756	-0.0227	0.0012	0.0649	0.1711	-0.0449	0.2634	0.007	-0.2485	0.0604	0.2343	0.0647	0.0028	0.3102	-0.028	0.3563	98.7436	70.8641	465.8771

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 2 through 106 )
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 107 through 204 )
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 205 through 321 )
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 322 through 465 )
5	X-RAY DIFFRACTION	5	chain 'B' and (resid 103 through 145 )
6	X-RAY DIFFRACTION	6	chain 'B' and (resid 146 through 189 )
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 190 through 212 )
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 213 through 321 )
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 322 through 465 )
10	X-RAY DIFFRACTION	10	chain 'C' and (resid 1 through 38 )
11	X-RAY DIFFRACTION	11	chain 'C' and (resid 39 through 135 )
12	X-RAY DIFFRACTION	12	chain 'C' and (resid 136 through 185 )
13	X-RAY DIFFRACTION	13	chain 'C' and (resid 186 through 276 )
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 277 through 321 )
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 322 through 372 )
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 373 through 405 )
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 406 through 440 )
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 441 through 466 )
19	X-RAY DIFFRACTION	19	chain 'D' and (resid 1 through 204 )
20	X-RAY DIFFRACTION	20	chain 'D' and (resid 205 through 465 )
21	X-RAY DIFFRACTION	21	chain 'E' and (resid 1 through 38 )
22	X-RAY DIFFRACTION	22	chain 'E' and (resid 39 through 87 )
23	X-RAY DIFFRACTION	23	chain 'E' and (resid 88 through 119 )
24	X-RAY DIFFRACTION	24	chain 'E' and (resid 120 through 204 )
25	X-RAY DIFFRACTION	25	chain 'E' and (resid 205 through 321 )
26	X-RAY DIFFRACTION	26	chain 'E' and (resid 322 through 465 )
27	X-RAY DIFFRACTION	27	chain 'F' and (resid 2 through 135 )
28	X-RAY DIFFRACTION	28	chain 'F' and (resid 136 through 276 )
29	X-RAY DIFFRACTION	29	chain 'F' and (resid 277 through 466 )

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