PDB-7yan: UDP-glucuronosyltransferase2B17 C-terminal domain

ID or keywords:

Entry

Database: PDB / ID: 7yan

Title

UDP-glucuronosyltransferase2B17 C-terminal domain

Components

UDP-glucuronosyltransferase 2B17

Keywords

TRANSFERASE / Complex / truncation

Function / homology

Function and homology information

glucuronosyltransferase / cellular glucuronidation / Glucuronidation / glucuronosyltransferase activity / estrogen metabolic process / Prednisone ADME / Aspirin ADME / steroid metabolic process / xenobiotic metabolic process / endoplasmic reticulum membrane / membrane
Similarity search - Function

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.5 Å

Authors

Wang, C.Y. / Zhang, L.

Funding support

China, 1items

Citation

Journal: To Be Published
Title: UDP-glucuronosyltransferase2B17 C-terminal domain
Authors: Wang, C.Y. / Zhang, L.

History

Deposition	Jun 28, 2022	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Jul 12, 2023	Provider: repository / Type: Initial release
Revision 1.1	Nov 29, 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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Download

PDBx/mmCIF format	7yan.cif.gz	142 KB	Display	PDBx/mmCIF format
PDB format	pdb7yan.ent.gz	106.4 KB	Display	PDB format
PDBx/mmJSON format	7yan.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7yan_validation.pdf.gz	1.7 MB	Display	wwPDB validaton report
Full document	7yan_full_validation.pdf.gz	1.7 MB	Display
Data in XML	7yan_validation.xml.gz	26.5 KB	Display
Data in CIF	7yan_validation.cif.gz	35.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ya/7yan ftp://data.pdbj.org/pub/pdb/validation_reports/ya/7yan	HTTPS FTP

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Related structure data

Related structure data	6ipbS S: Starting model for refinement
Similar structure data	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	#228 - Dec 2018 Directed Evolution of Enzymes similarity (1)

Deposited unit

A: UDP-glucuronosyltransferase 2B17

B: UDP-glucuronosyltransferase 2B17

C: UDP-glucuronosyltransferase 2B17

D: UDP-glucuronosyltransferase 2B17

hetero molecules

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

1

A: UDP-glucuronosyltransferase 2B17

B: UDP-glucuronosyltransferase 2B17

hetero molecules

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

2

C: UDP-glucuronosyltransferase 2B17

hetero molecules

D: UDP-glucuronosyltransferase 2B17

hetero molecules

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

Unit cell

Length a, b, c (Å)	38.150, 57.308, 74.074
Angle α, β, γ (deg.)	99.245, 94.715, 90.118
Int Tables number	1
Space group name H-M	P1

#1: Protein	UDP-glucuronosyltransferase 2B17 / UDPGT 2B17 / UGT2B17 / C19-steroid-specific UDP-glucuronosyltransferase / C19-steroid-specific UDPGT Mass: 21046.270 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: UGT2B17 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: O75795, glucuronosyltransferase
#2: Chemical	ChemComp-TLA / L(+)-TARTARIC ACID Mass: 150.087 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₄H₆O₆ / Feature type: SUBJECT OF INVESTIGATION
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 46 / Source method: isolated from a natural source / Formula: H₂O
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: 1.89 Å³/Da / Density % sol: 34.99 %
Crystal grow	Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 20% PEG 6000, 0.2M Na-Tartrate, 0.2M KCl, 2% glycerol

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.54184 Å
Detector	Type: DECTRIS PILATUS 200K / Detector: PIXEL / Date: Jun 17, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.54184 Å / Relative weight: 1
Reflection	Resolution: 2.5→19.11 Å / Num. obs: 20837 / % possible obs: 97.45 % / Redundancy: 2.7 % / CC_1/2: 0.985 / R_merge(I) obs: 0.0978 / Net I/σ(I): 8.05
Reflection shell	Resolution: 2.5→2.589 Å / Num. unique obs: 2019 / CC_1/2: 0.893

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0258	refinement
CrysalisPro		data reduction
SCALA		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 6IPB

6ipb

Resolution: 2.5→19.11 Å / Cor.coef. F_o:F_c: 0.838 / Cor.coef. F_o:F_c free: 0.763 / SU B: 17.612 / SU ML: 0.388 / Cross valid method: THROUGHOUT / ESU R Free: 0.432
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.3308	1012	4.857 %
R_work	0.2677	19825	-
all	0.271	-	-
obs	-	20837	97.469 %

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT

Displacement parameters

B_iso mean: 18.094 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.008 Å²	0.001 Å²	0.025 Å²
2-	-	0.002 Å²	-0.027 Å²
3-	-	-	-0.006 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→19.11 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5052	0	40	46	5138

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.006	0.013	5196
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.017	4907
X-RAY DIFFRACTION	r_angle_refined_deg	1.459	1.644	7014
X-RAY DIFFRACTION	r_angle_other_deg	1.138	1.576	11473
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	7.858	5	651
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	41.607	24.182	220
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	17.184	15	941
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.802	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.051	0.2	692
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	5688
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	944
X-RAY DIFFRACTION	r_nbd_refined	0.211	0.2	1182
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.198	0.2	4689
X-RAY DIFFRACTION	r_nbtor_refined	0.156	0.2	2432
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.085	0.2	2196
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.182	0.2	132
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.143	0.2	2
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.304	0.2	41
X-RAY DIFFRACTION	r_nbd_other	0.336	0.2	163
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.414	0.2	1
X-RAY DIFFRACTION	r_mcbond_it	1.225	1.89	2613
X-RAY DIFFRACTION	r_mcbond_other	1.224	1.889	2612
X-RAY DIFFRACTION	r_mcangle_it	2.153	2.831	3260
X-RAY DIFFRACTION	r_mcangle_other	2.153	2.832	3261
X-RAY DIFFRACTION	r_scbond_it	1.108	2.003	2583
X-RAY DIFFRACTION	r_scbond_other	1.108	2.004	2580
X-RAY DIFFRACTION	r_scangle_it	1.917	2.941	3754
X-RAY DIFFRACTION	r_scangle_other	1.917	2.941	3753
X-RAY DIFFRACTION	r_lrange_it	4.688	22.432	5671
X-RAY DIFFRACTION	r_lrange_other	4.689	22.433	5668

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 (%)
2.5-2.565	0.448	70	0.303	1434	X-RAY DIFFRACTION	92.8395
2.565-2.635	0.423	74	0.299	1399	X-RAY DIFFRACTION	97.2277
2.635-2.711	0.424	69	0.299	1431	X-RAY DIFFRACTION	98.7492
2.711-2.795	0.388	77	0.29	1336	X-RAY DIFFRACTION	99.3671
2.795-2.886	0.327	86	0.325	1346	X-RAY DIFFRACTION	99.5828
2.886-2.987	0.445	67	0.308	1302	X-RAY DIFFRACTION	99.7087
2.987-3.1	0.325	64	0.281	1210	X-RAY DIFFRACTION	99.376
3.1-3.226	0.352	49	0.27	1212	X-RAY DIFFRACTION	99.6051
3.226-3.369	0.324	49	0.244	1165	X-RAY DIFFRACTION	99.0212
3.369-3.533	0.314	40	0.257	1107	X-RAY DIFFRACTION	99.3934
3.533-3.724	0.347	50	0.258	1030	X-RAY DIFFRACTION	98.7203
3.724-3.949	0.264	44	0.245	979	X-RAY DIFFRACTION	97.6145
3.949-4.221	0.245	50	0.227	916	X-RAY DIFFRACTION	98.0711
4.221-4.558	0.271	41	0.235	842	X-RAY DIFFRACTION	97.033
4.558-4.991	0.326	44	0.256	766	X-RAY DIFFRACTION	96.5435
4.991-5.577	0.293	47	0.271	696	X-RAY DIFFRACTION	96.8709
5.577-6.434	0.352	30	0.273	616	X-RAY DIFFRACTION	96.4179
6.434-7.864	0.277	33	0.256	497	X-RAY DIFFRACTION	93.8053
7.864-11.057	0.216	20	0.223	379	X-RAY DIFFRACTION	91.3044
11.057-19.11	0.233	8	0.286	162	X-RAY DIFFRACTION	68.5484

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