PDB-2hy7: Crystal Structure of GumK, a beta-glucuronosyltransferase from Xa...

ID or keywords:

Entry

Database: PDB / ID: 2hy7

Title

Crystal Structure of GumK, a beta-glucuronosyltransferase from Xanthomonas campestris

Components

Glucuronosyltransferase GumK

Keywords

TRANSFERASE / glucuronosyltransferase / glycosyltransferases / xanthan / membrane-associated proteins / Xanthomonas campestris

Function / homology

Function and homology information

D-Man-alpha-(1->3)-D-Glc-beta-(1->4)-D-Glc-alpha-1-diphosphoundecaprenol 2-beta-glucuronosyltransferase / glucuronosyltransferase activity / polysaccharide biosynthetic process / plasma membrane
Similarity search - Function

Biological species

Xanthomonas campestris (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MAD / Resolution: 1.9 Å

Authors

Barreras, M.

Citation

Journal: J.Biol.Chem. / Year: 2008
Title: Structure and mechanism of GumK, a membrane-associated glucuronosyltransferase.
Authors: Barreras, M. / Salinas, S.R. / Abdian, P.L. / Kampel, M.A. / Ielpi, L.

History

Deposition	Aug 4, 2006	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 22, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Feb 14, 2024	Group: Data collection / Database references Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	2hy7.cif.gz	99.1 KB	Display	PDBx/mmCIF format
PDB format	pdb2hy7.ent.gz	73.4 KB	Display	PDB format
PDBx/mmJSON format	2hy7.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	2hy7_validation.pdf.gz	423.8 KB	Display	wwPDB validaton report
Full document	2hy7_full_validation.pdf.gz	427.3 KB	Display
Data in XML	2hy7_validation.xml.gz	19.9 KB	Display
Data in CIF	2hy7_validation.cif.gz	31.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/hy/2hy7 ftp://data.pdbj.org/pub/pdb/validation_reports/hy/2hy7	HTTPS FTP

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Related structure data

Related structure data	2q6vC 3cuyC 3cv3C C: citing same article (ref.)
Similar structure data	3uqw-d 4wam-d 3r5f-d 1nw9-d 4pca-3 3iw4-2 4me6-d 2a7w-2 3ogo-3 5qd3-1 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

Deposited unit

A: Glucuronosyltransferase GumK

45.3 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

Unit cell

Length a, b, c (Å)	123.629, 123.629, 174.307
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	179
Space group name H-M	P6₅22

Components on special symmetry positions

ID	Model	Components
1	1	A-418- HOH

Details

The biological unit is the monomer present in the asymmetric unit.

#1: Protein	Glucuronosyltransferase GumK Mass: 45335.438 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Xanthomonas campestris (bacteria) / Gene: gumK / Plasmid: pET22(b) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8GCH2, glucuronosyltransferase
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Glucuronosyltransferase GumK

Mass: 45335.438 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Xanthomonas campestris (bacteria) / Gene: gumK / Plasmid: pET22(b) / Species (production host): Escherichia coli / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8GCH2, glucuronosyltransferase

#2: Water

ChemComp-HOH / water

Mass: 18.015 Da / Num. of mol.: 462 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 2

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Sample preparation

Crystal	Density Matthews: 4.24 Å³/Da / Density % sol: 58.8 %
Crystal grow	Temperature: 293 K / pH: 8.2 Details: 0.1 M Tris-HCl, 35% (w/v) PEG 3350, 0.2 M Li2SO4, 0.1 M CsCl, pH 8.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.20

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Data collection

Diffraction

ID	Mean temperature (K)	Crystal-ID
1	100	1
2		1

Diffraction source

Source:

SYNCHROTRON / Site:

NSLS

/ Beamline: X12C / Wavelength: 1.1

Detector

Type: ADSC QUANTUM 210 / Detector: CCD / Date: Apr 27, 2006 / Details: BEAM FOCUSED BY A TOROIDAL MIRROR

Radiation

Monochromator: DOUBLE-CRYSTAL MONOCHROMATOR SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 1.1 Å / Relative weight: 1

Reflection

R_merge(I) obs: 0.073 / R_sym value: 0.073 / D res high: 2 Å / % possible obs: 95.5

Redundancy (%)	ID	Av σ(I) over netI	Number	D res low (Å)	Num. obs
6.3	1	9.6	325071	30.92	51441
6.4	2	10	330711	33.278	51635

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	R_sym value	Redundancy
6.32	33.22	99.1	1	0.025	0.025	6.2
4.47	6.32	100	1	0.031	0.031	6.8
3.65	4.47	100	1	0.032	0.032	7
3.16	3.65	100	1	0.047	0.047	7.1
2.83	3.16	100	1	0.075	0.075	7.1
2.58	2.83	100	1	0.115	0.115	7.1
2.39	2.58	100	1	0.172	0.172	7.2
2.24	2.39	100	1	0.222	0.222	6.7
2.11	2.24	94.2	1	0.276	0.276	4.8
2	2.11	75.1	1	0.383	0.383	3.9
6.32	33.28	99.2	2	0.024	0.024	6.3
4.47	6.32	100	2	0.029	0.029	6.9
3.65	4.47	100	2	0.031	0.031	7.1
3.16	3.65	100	2	0.045	0.045	7.2
2.83	3.16	100	2	0.078	0.078	7.2
2.58	2.83	100	2	0.12	0.12	7.3
2.39	2.58	100	2	0.181	0.181	7.3
2.24	2.39	100	2	0.228	0.228	6.7
2.11	2.24	94.1	2	0.287	0.287	4.8
2	2.11	74.8	2	0.389	0.389	3.9

Reflection

Resolution: 1.9→107.211 Å / Num. obs: 62401 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.1 % / R_merge(I) obs: 0.069 / R_sym value: 0.069 / Net I/σ(I): 9.9

Reflection shell

Resolution: 1.9→2 Å / Redundancy: 12.4 % / R_merge(I) obs: 0.344 / Mean I/σ(I) obs: 2.2 / R_sym value: 0.344 / % possible all: 100

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Phasing

Phasing

Method:

MAD

Phasing MAD set

ID	Highest resolution (Å)	Lowest resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	2	19.76	0	0	44807	6022
ISO_2	2	19.76	0.335	0.303	43407	3024
ANO_1	2	19.76	1.094	0	42574	0
ANO_2	2	19.76	0.667	0	43342	0

Phasing MAD set shell

ID	Resolution (Å)	Power acentric	Power centric	Reflection acentric	Reflection centric
ISO_1	8.18-19.76	0	0	525	308
ISO_1	6.05-8.18	0	0	930	298
ISO_1	5.02-6.05	0	0	1199	287
ISO_1	4.38-5.02	0	0	1443	289
ISO_1	3.94-4.38	0	0	1644	285
ISO_1	3.61-3.94	0	0	1828	287
ISO_1	3.35-3.61	0	0	1985	282
ISO_1	3.14-3.35	0	0	2171	310
ISO_1	2.96-3.14	0	0	2299	320
ISO_1	2.81-2.96	0	0	2421	321
ISO_1	2.69-2.81	0	0	2575	323
ISO_1	2.57-2.69	0	0	2700	326
ISO_1	2.47-2.57	0	0	2805	325
ISO_1	2.39-2.47	0	0	2909	320
ISO_1	2.31-2.39	0	0	3042	328
ISO_1	2.23-2.31	0	0	3138	326
ISO_1	2.17-2.23	0	0	3185	311
ISO_1	2.11-2.17	0	0	2986	273
ISO_1	2.05-2.11	0	0	2681	271
ISO_1	2-2.05	0	0	2341	232
ANO_1	8.18-19.76	8.229	0	523	0
ANO_1	6.05-8.18	6.242	0	930	0
ANO_1	5.02-6.05	5.202	0	1199	0
ANO_1	4.38-5.02	4.437	0	1443	0
ANO_1	3.94-4.38	3.309	0	1641	0
ANO_1	3.61-3.94	2.858	0	1826	0
ANO_1	3.35-3.61	2.282	0	1983	0
ANO_1	3.14-3.35	1.759	0	2170	0
ANO_1	2.96-3.14	1.453	0	2297	0
ANO_1	2.81-2.96	1.239	0	2420	0
ANO_1	2.69-2.81	1.023	0	2575	0
ANO_1	2.57-2.69	0.91	0	2700	0
ANO_1	2.47-2.57	0.74	0	2805	0
ANO_1	2.39-2.47	0.602	0	2908	0
ANO_1	2.31-2.39	0.517	0	3040	0
ANO_1	2.23-2.31	0.419	0	3117	0
ANO_1	2.17-2.23	0.339	0	2818	0
ANO_1	2.11-2.17	0.299	0	2380	0
ANO_1	2.05-2.11	0.268	0	2115	0
ANO_1	2-2.05	0.274	0	1684	0
ISO_2	8.18-19.76	1.418	0.956	525	153
ISO_2	6.05-8.18	1.554	1.055	930	148
ISO_2	5.02-6.05	1.219	0.837	1199	146
ISO_2	4.38-5.02	0.995	0.624	1443	143
ISO_2	3.94-4.38	0.808	0.548	1644	149
ISO_2	3.61-3.94	0.697	0.474	1828	148
ISO_2	3.35-3.61	0.601	0.419	1985	138
ISO_2	3.14-3.35	0.518	0.324	2171	152
ISO_2	2.96-3.14	0.465	0.275	2299	159
ISO_2	2.81-2.96	0.412	0.225	2421	162
ISO_2	2.69-2.81	0.355	0.229	2575	164
ISO_2	2.57-2.69	0.315	0.182	2700	153
ISO_2	2.47-2.57	0.261	0.156	2805	166
ISO_2	2.39-2.47	0.216	0.144	2909	150
ISO_2	2.31-2.39	0.187	0.123	3041	166
ISO_2	2.23-2.31	0.153	0.109	3136	167
ISO_2	2.17-2.23	0.115	0.085	2888	172
ISO_2	2.11-2.17	0.094	0.078	2477	138
ISO_2	2.05-2.11	0.079	0.055	2310	133
ISO_2	2-2.05	0.071	0.059	2121	117
ANO_2	8.18-19.76	5.758	0	525	0
ANO_2	6.05-8.18	4.3	0	930	0
ANO_2	5.02-6.05	3.269	0	1199	0
ANO_2	4.38-5.02	2.904	0	1443	0
ANO_2	3.94-4.38	2.171	0	1644	0
ANO_2	3.61-3.94	1.838	0	1828	0
ANO_2	3.35-3.61	1.474	0	1985	0
ANO_2	3.14-3.35	1.136	0	2171	0
ANO_2	2.96-3.14	0.897	0	2299	0
ANO_2	2.81-2.96	0.758	0	2421	0
ANO_2	2.69-2.81	0.634	0	2575	0
ANO_2	2.57-2.69	0.575	0	2700	0
ANO_2	2.47-2.57	0.454	0	2805	0
ANO_2	2.39-2.47	0.38	0	2909	0
ANO_2	2.31-2.39	0.321	0	3040	0
ANO_2	2.23-2.31	0.264	0	3133	0
ANO_2	2.17-2.23	0.218	0	2851	0
ANO_2	2.11-2.17	0.194	0	2468	0
ANO_2	2.05-2.11	0.164	0	2299	0
ANO_2	2-2.05	0.158	0	2117	0

Phasing dm

Method: Solvent flattening and Histogram matching / Reflection: 51311

Phasing dm shell

Resolution (Å)	Delta phi final	FOM	Reflection
9.64-100	46.8	0.877	508
7.2-9.64	39.1	0.91	746
6-7.2	39.7	0.922	903
5.25-6	42.3	0.928	1037
4.72-5.25	41.2	0.944	1159
4.33-4.72	43.6	0.941	1260
4.02-4.33	46.5	0.948	1348
3.77-4.02	50.7	0.952	1445
3.56-3.77	50.1	0.95	1529
3.38-3.56	52.2	0.953	1606
3.23-3.38	55.2	0.945	1683
3.1-3.23	57.5	0.943	1734
2.98-3.1	57.7	0.941	1817
2.87-2.98	60.7	0.933	1901
2.77-2.87	62.1	0.932	1939
2.69-2.77	62.9	0.934	1995
2.61-2.69	67.6	0.936	2085
2.54-2.61	69.4	0.926	2118
2.47-2.54	70	0.931	2184
2.41-2.47	73.7	0.929	2231
2.35-2.41	73	0.931	2292
2.3-2.35	75.7	0.941	2332
2.25-2.3	78.4	0.935	2389
2.2-2.25	78.8	0.929	2445
2.16-2.2	79.8	0.929	2383
2.12-2.16	83.6	0.917	2248
2.08-2.12	84	0.913	2090
2.04-2.08	84.7	0.905	1973
2-2.04	82.9	0.819	1931

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Processing

Software

Name	Version	Classification
SCALA		data scaling
SHARP		phasing
DM	5	phasing
REFMAC		refinement
PDB_EXTRACT	2	data extraction
MOSFLM		data reduction

Refinement

Method to determine structure:

MAD / Resolution: 1.9→107.21 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.93 / SU B: 1.775 / SU ML: 0.055 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.096 / ESU R Free: 0.095 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.204	3159	5.1 %	RANDOM
R_work	0.181	-	-	-
obs	0.182	62363	100 %	-
all	-	62367	-	-

Solvent computation

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

Displacement parameters

B_iso mean: 18.6 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.27 Å²	0.13 Å²	0 Å²
2-	-	0.27 Å²	0 Å²
3-	-	-	-0.4 Å²

Refinement step

Cycle: LAST / Resolution: 1.9→107.21 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2963	0	0	462	3425

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.013	0.022	3049
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.277	1.943	4155
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.444	5	372
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.711	21.862	145
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.046	15	462
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.438	15	31
X-RAY DIFFRACTION	r_chiral_restr	0.089	0.2	449
X-RAY DIFFRACTION	r_gen_planes_refined	0.006	0.02	2390
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.213	0.2	1580
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.31	0.2	2090
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.179	0.2	392
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	0.224	0.2	46
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.228	0.2	40
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	0.919	1.5	1919
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	1.472	2	3027
X-RAY DIFFRACTION	r_scbond_it	2.218	3	1296
X-RAY DIFFRACTION	r_scangle_it	3.491	4.5	1128
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.9→1.95 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.225	245	-
R_work	0.194	4286	-
obs	-	-	100 %

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