PDB-3itk: Crystal structure of human UDP-glucose dehydrogenase Thr131Ala, a...

ID or keywords:

Entry

Database: PDB / ID: 3itk

Title

Crystal structure of human UDP-glucose dehydrogenase Thr131Ala, apo form.

Components

UDP-glucose 6-dehydrogenase

Keywords

OXIDOREDUCTASE /

Structural Genomics /

Structural Genomics Consortium / SGC / NAD /

Phosphoprotein

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: 2.4 Å

Authors

Chaikuad, A. / Egger, S. / Yue, W.W. / Sethi, R. / Filippakopoulos, P. / Muniz, J.R.C. / von Delft, F. / Bountra, C. / Arrowsmith, C.H. / Weigelt, J. ...

Citation

Journal: J.Biol.Chem. / Year: 2011
Title: Structure and mechanism of human UDP-glucose 6-dehydrogenase.
Authors: Egger, S. / Chaikuad, A. / Kavanagh, K.L. / Oppermann, U. / Nidetzky, B.

History

Deposition	Aug 28, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 15, 2009	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Aug 31, 2011	Group: Database references
Revision 1.3	Oct 13, 2021	Group: Database references / Derived calculations / Category: database_2 / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4	Sep 6, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/it/3itk ftp://data.pdbj.org/pub/pdb/validation_reports/it/3itk	HTTPS FTP

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Related structure data

Related structure data	2q3eSC 2qg4C S: Starting model for refinement C: citing same article (ref.)
Similar structure data	5tjh-d 5w4x-1 6c4k-2 3khu-d 2o3j-1 2qg4-4 6c4j-1 2qg4-5 2qg4-1 6c4j-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

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	89.060, 106.610, 349.120
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS ensembles :

ID
1
2
3
4

Details

THE HEXAMER IN THE ASYMMETRIC UNIT REPRESENTS THE HEXAMERIC BIOLOGICAL UNIT.

#1: Protein	UDP-glucose 6-dehydrogenase / / UDP-Glc dehydrogenase / UDP-GlcDH / UDPGDH Mass: 52053.395 Da / Num. of mol.: 6 / Fragment: UNP residues 1-466 / Mutation: T131A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UGDH / Plasmid: pBEN1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-R3-pRARE2 / References: UniProt: O60701, UDP-glucose 6-dehydrogenase
#2: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol Mass: 194.226 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#3: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C₂H₆O₂
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1188 / 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: 2.65 Å³/Da / Density % sol: 53.64 %
Crystal grow	Temperature: 293.15 K / pH: 6 Details: 15% PEG smears (PEG 400, 600, 1000, 2000, 3350, 4000, MME 5000, 6000, 8000, 10000), 0.1M MES pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 293.15K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
Detector	Type: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 15, 2009 / Details: MIRRORS
Radiation	Monochromator: SI(111) DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9763 Å / Relative weight: 1
Reflection	Resolution: 2.4→52.9 Å / Num. obs: 130411 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 4 % / B_iso Wilson estimate: 40.1 Å² / R_merge(I) obs: 0.131 / Net I/σ(I): 7.9
Reflection shell	Resolution: 2.4→2.53 Å / Redundancy: 3.3 % / R_merge(I) obs: 0.55 / Mean I/σ(I) obs: 2.1 / % possible all: 99.4

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Processing

Software

Name	Version	Classification
ADSC	Quantum	data collection
PHASER		phasing
REFMAC	5.5.0089	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2Q3E

2q3e

Resolution: 2.4→52.9 Å / Cor.coef. F_o:F_c: 0.935 / Cor.coef. F_o:F_c free: 0.906 / SU B: 16.607 / SU ML: 0.174 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.381 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES: RESIDUAL ONLY. THE NCS RESTRAINTS HAVE BEEN USED IN REFINEMENT.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.241	2134	1.6 %	RANDOM
R_work	0.198	-	-	-
obs	0.199	128277	99.7 %	-
all	-	130411	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 12.77 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.23 Å²	0 Å²	0 Å²
2-	-	0.37 Å²	0 Å²
3-	-	-	-0.14 Å²

Refine analyze

Luzzati coordinate error obs: 0.328 Å

Refinement step

Cycle: LAST / Resolution: 2.4→52.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	21621	0	133	1188	22942

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.016	0.022	22169
X-RAY DIFFRACTION	r_bond_other_d	0.003	0.02	15064
X-RAY DIFFRACTION	r_angle_refined_deg	1.463	1.96	29990
X-RAY DIFFRACTION	r_angle_other_deg	1.096	3	36789
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.449	5	2795
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	35.487	24.344	976
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.546	15	3816
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	17.501	15	142
X-RAY DIFFRACTION	r_chiral_restr	0.083	0.2	3425
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.021	24613
X-RAY DIFFRACTION	r_gen_planes_other	0.003	0.02	4367
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.793	3	13907
X-RAY DIFFRACTION	r_mcbond_other	0.618	3	5650
X-RAY DIFFRACTION	r_mcangle_it	3.257	5	22479
X-RAY DIFFRACTION	r_scbond_it	5.506	8	8262
X-RAY DIFFRACTION	r_scangle_it	7.877	11	7506
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION

Ens-ID	Dom-ID	Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
1	1	A	457	tight positional	0.04	0.05
1	1	B	457	tight positional	0.03	0.05
1	1	C	457	tight positional	0.04	0.05
1	1	D	457	tight positional	0.04	0.05
1	1	E	457	tight positional	0.05	0.05
2	2	A	847	tight positional	0.04	0.05
2	2	B	847	tight positional	0.05	0.05
2	2	C	847	tight positional	0.06	0.05
2	2	D	847	tight positional	0.05	0.05
2	2	E	847	tight positional	0.07	0.05
3	3	A	267	tight positional	0.04	0.05
3	3	B	267	tight positional	0.06	0.05
3	3	C	267	tight positional	0.04	0.05
3	3	D	267	tight positional	0.04	0.05
3	3	E	267	tight positional	0.04	0.05
3	3	F	267	tight positional	0.05	0.05
4	4	A	895	tight positional	0.13	0.05
4	4	B	895	tight positional	0.14	0.05
4	4	C	895	tight positional	0.15	0.05
4	4	D	895	tight positional	0.1	0.05
4	4	E	895	tight positional	0.12	0.05
1	1	A	523	medium positional	0.06	0.5
1	1	B	523	medium positional	0.05	0.5
1	1	C	523	medium positional	0.13	0.5
1	1	D	523	medium positional	0.05	0.5
1	1	E	523	medium positional	0.06	0.5
2	2	A	917	medium positional	0.05	0.5
2	2	B	917	medium positional	0.09	0.5
2	2	C	917	medium positional	0.06	0.5
2	2	D	917	medium positional	0.05	0.5
2	2	E	917	medium positional	0.1	0.5
3	3	A	271	medium positional	0.05	0.5
3	3	B	271	medium positional	0.07	0.5
3	3	C	271	medium positional	0.05	0.5
3	3	D	271	medium positional	0.14	0.5
3	3	E	271	medium positional	0.05	0.5
3	3	F	271	medium positional	0.06	0.5
4	4	A	1610	medium positional	0.22	0.5
4	4	B	1610	medium positional	0.3	0.5
4	4	C	1610	medium positional	0.32	0.5
4	4	D	1610	medium positional	0.18	0.5
4	4	E	1610	medium positional	0.25	0.5
1	1	A	457	tight thermal	0.11	0.5
1	1	B	457	tight thermal	0.11	0.5
1	1	C	457	tight thermal	0.14	0.5
1	1	D	457	tight thermal	0.13	0.5
1	1	E	457	tight thermal	0.14	0.5
2	2	A	847	tight thermal	0.14	0.5
2	2	B	847	tight thermal	0.16	0.5
2	2	C	847	tight thermal	0.16	0.5
2	2	D	847	tight thermal	0.14	0.5
2	2	E	847	tight thermal	0.16	0.5
3	3	A	267	tight thermal	0.17	0.5
3	3	B	267	tight thermal	0.18	0.5
3	3	C	267	tight thermal	0.16	0.5
3	3	D	267	tight thermal	0.19	0.5
3	3	E	267	tight thermal	0.16	0.5
3	3	F	267	tight thermal	0.19	0.5
4	4	A	895	tight thermal	0.99	0.5
4	4	B	895	tight thermal	0.93	0.5
4	4	C	895	tight thermal	1.03	0.5
4	4	D	895	tight thermal	0.94	0.5
4	4	E	895	tight thermal	0.88	0.5
1	1	A	523	medium thermal	0.12	2
1	1	B	523	medium thermal	0.09	2
1	1	C	523	medium thermal	0.12	2
1	1	D	523	medium thermal	0.11	2
1	1	E	523	medium thermal	0.11	2
2	2	A	917	medium thermal	0.12	2
2	2	B	917	medium thermal	0.13	2
2	2	C	917	medium thermal	0.14	2
2	2	D	917	medium thermal	0.12	2
2	2	E	917	medium thermal	0.13	2
3	3	A	271	medium thermal	0.15	2
3	3	B	271	medium thermal	0.15	2
3	3	C	271	medium thermal	0.14	2
3	3	D	271	medium thermal	0.14	2
3	3	E	271	medium thermal	0.14	2
3	3	F	271	medium thermal	0.17	2
4	4	A	1610	medium thermal	1.04	2
4	4	B	1610	medium thermal	0.96	2
4	4	C	1610	medium thermal	1.08	2
4	4	D	1610	medium thermal	1.02	2
4	4	E	1610	medium thermal	1.06	2

LS refinement shell

Resolution: 2.4→2.46 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.355	129	-
R_work	0.318	9292	-
obs	-	-	98.55 %

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	0.3789	-0.2314	-0.217	0.6521	-0.3495	3.435	-0.0063	-0.2842	-0.0799	-0.0259	0.0608	-0.0089	0.0539	0.5257	-0.0545	0.1837	-0.0342	-0.0558	0.3074	0.0451	0.0788	22.7497	-16.0982	7.8955
2	0.5348	-0.1017	-0.1578	2.9354	0.5379	2.9233	-0.0511	-0.1438	-0.1305	0.0171	0.1295	0.0493	0.0275	-0.1211	-0.0784	0.2019	-0.0568	-0.0738	0.1903	0.112	0.149	10.028	-16.1209	3.5163
3	1.0666	0.2283	0.1812	0.3481	-0.1045	0.3227	0.0909	-0.0337	-0.1153	0.0472	0.0022	0.012	0.0641	-0.0166	-0.0931	0.1626	0.0048	-0.0517	0.0497	-0.0274	0.0589	29.4205	9.4161	-13.1758
4	1.1303	0.1188	-0.2707	1.4157	-0.4188	1.9866	-0.0022	0.0255	0.1443	-0.0556	-0.1985	-0.1856	-0.0491	0.3207	0.2007	0.0932	-0.0109	-0.0198	0.0997	0.043	0.1704	61.0972	24.0955	-40.9747
5	1.4875	0.4315	-0.0146	0.5676	-0.2744	5.0355	-0.0144	0.0695	0.2828	-0.0028	-0.1123	-0.035	-0.194	-0.1002	0.1267	0.152	0.0195	-0.0628	0.0667	-0.0011	0.1995	50.0303	31.8466	-42.4552
6	0.593	-0.3733	0.0406	1.4892	0.0486	0.0238	-0.0149	-0.0024	0.0212	-0.0212	0.0087	-0.1877	-0.0397	-0.0226	0.0062	0.1102	0.021	-0.0079	0.1222	0.0055	0.059	46.4944	-0.0918	-57.8219
7	0.4835	0.1187	0.3412	0.9093	-0.088	0.4477	-0.0481	0.0906	0.1228	0.0818	0.0243	0.1882	0.0597	-0.1352	0.0238	0.1559	-0.0666	-0.0017	0.3031	0.0694	0.0727	15.0024	15.1065	-86.4272
8	1.3967	0.7468	1.4207	2.5285	-0.135	1.8858	0.0852	-0.0122	-0.0271	0.0624	-0.1285	-0.1614	0.1489	-0.0735	0.0433	0.1038	-0.0441	0.0347	0.2827	0.0153	0.0271	26.0913	7.3263	-85.8254
9	0.7945	-0.6142	-0.5995	0.8207	0.4411	0.4768	0.0472	0.0952	0.0463	-0.0572	-0.013	0.0952	-0.0414	-0.0315	-0.0342	0.1419	0.0172	-0.0304	0.1141	0.0363	0.1022	18.2525	25.9738	-55.6078
10	2.8098	0.5352	-0.4328	1.7933	-1.5753	3.5481	0.157	-0.2133	-0.5606	0.0785	-0.1774	-0.1974	0.3083	0.148	0.0204	0.1712	0.0148	-0.0297	0.066	-0.0252	0.3879	42.2797	-51.3417	-57.6441
11	1.2503	-0.2002	-0.1233	0.4213	0.0959	0.5805	0.087	0.0586	-0.2905	0.021	-0.0601	0.0395	0.1232	-0.0124	-0.0269	0.1056	0.0192	0.0175	0.0946	-0.0561	0.1511	36.7212	-36.9932	-63.6767
12	0.102	-0.1193	0.0467	0.3254	-0.2794	1.8145	-0.0248	0.0237	-0.0689	0.1269	-0.0061	-0.0792	0.191	0.0773	0.0308	0.2083	-0.0138	-0.0518	0.1304	0.0216	0.2627	21.9177	-34.81	-32.4917
13	0.6378	-0.3063	-0.3715	0.8986	0.3209	1.1749	0.0861	0.0171	0.1181	-0.1864	-0.124	0.1347	-0.0861	-0.2274	0.038	0.0584	0.0242	-0.014	0.1197	-0.0752	0.1173	-6.7259	35.8581	-21.1369
14	1.252	0.2566	-0.6179	1.4782	-1.5303	2.9431	-0.0068	-0.1196	0.1134	-0.1544	-0.0414	0.0025	0.0598	-0.0806	0.0481	0.0889	0.005	0.0141	0.0412	-0.0551	0.1298	6.2062	35.1769	-17.0765
15	1.2687	-0.6035	0.4569	0.8768	0.0483	0.8536	0.185	-0.1092	-0.4077	0.0545	0.0371	0.3259	0.2014	-0.3132	-0.2221	0.1691	-0.0704	-0.055	0.1737	0.0912	0.2321	-6.6093	1.5998	-21.3521
16	2.4104	-0.2699	0.5997	1.2052	-0.8238	2.3911	0.0273	-0.2035	-0.012	0.2406	-0.0712	0.0726	-0.0483	-0.4033	0.0439	0.0637	-0.0554	0.0164	0.1353	-0.0215	0.0112	-20.8269	-31.2527	-50.152
17	1.3423	0.1138	-0.7491	0.1574	-0.4644	2.7072	0.1087	-0.3495	-0.1209	0.1322	-0.0942	-0.034	-0.0481	0.0499	-0.0146	0.2535	-0.1472	-0.0275	0.2698	0.0717	0.0899	-14.2185	-36.7565	-39.8411
18	1.0396	0.4056	0.278	0.5311	-0.207	1.0321	-0.0992	0.0775	0.04	0.0334	0.0191	0.0201	-0.0265	-0.0345	0.0801	0.0542	-0.0246	0.007	0.0972	-0.0163	0.09	3.8638	-20.727	-62.914

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 120
2	X-RAY DIFFRACTION	2	A	121 - 204
3	X-RAY DIFFRACTION	3	A	205 - 466
4	X-RAY DIFFRACTION	4	C	1 - 120
5	X-RAY DIFFRACTION	5	C	121 - 204
6	X-RAY DIFFRACTION	6	C	205 - 466
7	X-RAY DIFFRACTION	7	D	0 - 117
8	X-RAY DIFFRACTION	8	D	118 - 209
9	X-RAY DIFFRACTION	9	D	210 - 466
10	X-RAY DIFFRACTION	10	E	1 - 79
11	X-RAY DIFFRACTION	11	E	80 - 204
12	X-RAY DIFFRACTION	12	E	205 - 466
13	X-RAY DIFFRACTION	13	B	1 - 120
14	X-RAY DIFFRACTION	14	B	121 - 204
15	X-RAY DIFFRACTION	15	B	205 - 466
16	X-RAY DIFFRACTION	16	F	0 - 120
17	X-RAY DIFFRACTION	17	F	121 - 204
18	X-RAY DIFFRACTION	18	F	205 - 466

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