PDB-7vz6: The crystal structure of Non-hydrolyzing UDPGlcNAc 2-epimerase in...

ID or keywords:

Entry

Database: PDB / ID: 7vz6

Title

The crystal structure of Non-hydrolyzing UDPGlcNAc 2-epimerase in complex with UDP-glucose

Components

Putative UDP-N-acetylglucosamine 2-epimerase

Keywords

ISOMERASE / Epimerase / UDP-sugars

Function / homology

UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing) / UDP-N-acetylglucosamine 2-epimerase WecB-like / UDP-N-acetylglucosamine 2-epimerase domain / UDP-N-acetylglucosamine 2-epimerase / isomerase activity / nucleotide binding / URIDINE-5'-DIPHOSPHATE-GLUCOSE / UDP-N-acetylglucosamine 2-epimerase (non-hydrolyzing)

Function and homology information

Biological species

Streptomyces kasugaensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.092 Å

Authors

Li, T.L. / Rattinam, R.

Funding support

Taiwan, 1items

Citation

Journal: Biomedicines / Year: 2022
Title: KasQ an Epimerase Primes the Biosynthesis of Aminoglycoside Antibiotic Kasugamycin and KasF/H Acetyltransferases Inactivate Its Activity.
Authors: Rattinam, R. / Basha, R.S. / Wang, Y.L. / Wang, Z.C. / Hsu, N.S. / Lin, K.H. / Zadeh, S.M. / Adhikari, K. / Lin, J.P. / Li, T.L.

History

Deposition	Nov 15, 2021	Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0	Nov 16, 2022	Provider: repository / Type: Initial release
Revision 1.1	Jun 7, 2023	Group: Database references / Refinement description / Structure summary Category: audit_author / citation ...audit_author / citation / citation_author / struct_ncs_dom_lim Item: _audit_author.name / _citation.country ..._audit_author.name / _citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.2	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	7vz6.cif.gz	615.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7vz6.ent.gz	484.3 KB	Display	PDB format
PDBx/mmJSON format	7vz6.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7vz6_validation.pdf.gz	5.9 MB	Display	wwPDB validaton report
Full document	7vz6_full_validation.pdf.gz	5.9 MB	Display
Data in XML	7vz6_validation.xml.gz	113.5 KB	Display
Data in CIF	7vz6_validation.cif.gz	162.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/vz/7vz6 ftp://data.pdbj.org/pub/pdb/validation_reports/vz/7vz6	HTTPS FTP

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Related structure data

Related structure data	7vyyC 7vzaC 1vgvS S: Starting model for refinement C: citing same article (ref.)
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	#254 - Feb 2021 Cellulose Synthase similarity (1)

Deposited unit

A: Putative UDP-N-acetylglucosamine 2-epimerase

B: Putative UDP-N-acetylglucosamine 2-epimerase

C: Putative UDP-N-acetylglucosamine 2-epimerase

D: Putative UDP-N-acetylglucosamine 2-epimerase

E: Putative UDP-N-acetylglucosamine 2-epimerase

F: Putative UDP-N-acetylglucosamine 2-epimerase

G: Putative UDP-N-acetylglucosamine 2-epimerase

H: Putative UDP-N-acetylglucosamine 2-epimerase

hetero molecules

344 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Putative UDP-N-acetylglucosamine 2-epimerase

B: Putative UDP-N-acetylglucosamine 2-epimerase

E: Putative UDP-N-acetylglucosamine 2-epimerase

F: Putative UDP-N-acetylglucosamine 2-epimerase

G: Putative UDP-N-acetylglucosamine 2-epimerase

H: Putative UDP-N-acetylglucosamine 2-epimerase

hetero molecules

C: Putative UDP-N-acetylglucosamine 2-epimerase

D: Putative UDP-N-acetylglucosamine 2-epimerase

hetero molecules

defined by author&software
344 kDa, 8 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	82.833, 104.941, 106.840
Angle α, β, γ (deg.)	74.867, 72.918, 68.076
Int Tables number	1
Space group name H-M	P1

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: PRO / End label comp-ID: PRO / Auth seq-ID: -1 - 374 / Label seq-ID: 1 - 376

NCS ensembles :

ID	Details
1	Local NCS retraints between domains: 1 2
2	Local NCS retraints between domains: 3 4
3	Local NCS retraints between domains: 5 6
4	Local NCS retraints between domains: 7 8
5	Local NCS retraints between domains: 9 10
6	Local NCS retraints between domains: 11 12
7	Local NCS retraints between domains: 13 14
8	Local NCS retraints between domains: 15 16
9	Local NCS retraints between domains: 17 18
10	Local NCS retraints between domains: 19 20
11	Local NCS retraints between domains: 21 22
12	Local NCS retraints between domains: 23 24
13	Local NCS retraints between domains: 25 26
14	Local NCS retraints between domains: 27 28
15	Local NCS retraints between domains: 29 30
16	Local NCS retraints between domains: 31 32
17	Local NCS retraints between domains: 33 34
18	Local NCS retraints between domains: 35 36
19	Local NCS retraints between domains: 37 38
20	Local NCS retraints between domains: 39 40
21	Local NCS retraints between domains: 41 42
22	Local NCS retraints between domains: 43 44
23	Local NCS retraints between domains: 45 46
24	Local NCS retraints between domains: 47 48
25	Local NCS retraints between domains: 49 50
26	Local NCS retraints between domains: 51 52
27	Local NCS retraints between domains: 53 54
28	Local NCS retraints between domains: 55 56

#1: Protein	Putative UDP-N-acetylglucosamine 2-epimerase Mass: 42388.500 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Streptomyces kasugaensis (bacteria) / Gene: kasQ / Production host: Escherichia coli (E. coli) / References: UniProt: A0A0K1H2R6
#2: Chemical	ChemComp-UPG / URIDINE-5'-DIPHOSPHATE-GLUCOSE / URIDINE-5'-MONOPHOSPHATE GLUCOPYRANOSYL-MONOPHOSPHATE ESTER Mass: 566.302 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C₁₅H₂₄N₂O₁₇P₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: Na / Feature type: SUBJECT OF INVESTIGATION
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1499 / 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: 2.39 Å³/Da / Density % sol: 48.6 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2M lithium sulfate, 0.1M Bis tris pH 5.5, 25% PEG 3350

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: NSRRC / Beamline: TPS 05A / Wavelength: 1 Å
Detector	Type: RAYONIX MX300HE / Detector: CCD / Date: Dec 22, 2019
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 2.09→21.56 Å / Num. obs: 176474 / % possible obs: 95.2 % / Redundancy: 2.2 % / R_rim(I) all: 0.057 / Net I/σ(I): 19.7
Reflection shell	Resolution: 2.1→2.18 Å / Num. unique obs: 176474 / R_rim(I) all: 0.057

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Processing

Software

Name	Version	Classification
PHENIX	5.8.0267	refinement
HKL-2000		data reduction
HKL-2000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1vgv

1vgv

Resolution: 2.092→21.558 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.923 / SU B: 5.184 / SU ML: 0.137 / Cross valid method: NONE / ESU R: 0.254 / ESU R Free: 0.187
Details: Hydrogens have been added in their riding positions

	R_factor	Num. reflection	% reflection
R_free	0.2278	8824	5 %
R_work	0.2008	167650	-
all	0.202	-	-
obs	-	176474	95.09 %

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: 28.96 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.119 Å²	0.018 Å²	0.108 Å²
2-	-	0.052 Å²	0.02 Å²
3-	-	-	-0.096 Å²

Refinement step

Cycle: LAST / Resolution: 2.092→21.558 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	22403	0	295	1499	24197

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.013	23095
X-RAY DIFFRACTION	r_bond_other_d	0.018	0.017	22416
X-RAY DIFFRACTION	r_angle_refined_deg	1.495	1.65	31420
X-RAY DIFFRACTION	r_angle_other_deg	1.558	1.573	51402
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.585	5	2882
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	30.758	19.398	1313
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.3	15	3769
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.456	15	294
X-RAY DIFFRACTION	r_chiral_restr	0.074	0.2	3074
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	25674
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	5222
X-RAY DIFFRACTION	r_nbd_refined	0.203	0.2	4504
X-RAY DIFFRACTION	r_symmetry_nbd_other	0.2	0.2	20565
X-RAY DIFFRACTION	r_nbtor_refined	0.148	0.2	11185
X-RAY DIFFRACTION	r_symmetry_nbtor_other	0.067	0.2	11062
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.181	0.2	1251
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_other	0.07	0.2	7
X-RAY DIFFRACTION	r_metal_ion_refined	0.168	0.2	18
X-RAY DIFFRACTION	r_symmetry_nbd_refined	0.211	0.2	82
X-RAY DIFFRACTION	r_nbd_other	0.209	0.2	194
X-RAY DIFFRACTION	r_symmetry_xyhbond_nbd_refined	0.167	0.2	23
X-RAY DIFFRACTION	r_mcbond_it	2.532	2.792	11618
X-RAY DIFFRACTION	r_mcbond_other	2.53	2.791	11617
X-RAY DIFFRACTION	r_mcangle_it	3.749	4.166	14470
X-RAY DIFFRACTION	r_mcangle_other	3.75	4.166	14471
X-RAY DIFFRACTION	r_scbond_it	3.305	3.287	11477
X-RAY DIFFRACTION	r_scbond_other	3.305	3.287	11478
X-RAY DIFFRACTION	r_scangle_it	5.225	4.751	16950
X-RAY DIFFRACTION	r_scangle_other	5.225	4.751	16951
X-RAY DIFFRACTION	r_lrange_it	7.12	33.44	24837
X-RAY DIFFRACTION	r_lrange_other	7.077	33.262	24528
X-RAY DIFFRACTION	r_ncsr_local_group_1	0.083	0.05	11108
X-RAY DIFFRACTION	r_ncsr_local_group_2	0.072	0.05	11148
X-RAY DIFFRACTION	r_ncsr_local_group_3	0.076	0.05	11214
X-RAY DIFFRACTION	r_ncsr_local_group_4	0.068	0.05	11401
X-RAY DIFFRACTION	r_ncsr_local_group_5	0.079	0.05	11213
X-RAY DIFFRACTION	r_ncsr_local_group_6	0.068	0.05	11280
X-RAY DIFFRACTION	r_ncsr_local_group_7	0.084	0.05	11331
X-RAY DIFFRACTION	r_ncsr_local_group_8	0.088	0.05	11051
X-RAY DIFFRACTION	r_ncsr_local_group_9	0.086	0.05	11083
X-RAY DIFFRACTION	r_ncsr_local_group_10	0.083	0.05	11024
X-RAY DIFFRACTION	r_ncsr_local_group_11	0.088	0.05	11040
X-RAY DIFFRACTION	r_ncsr_local_group_12	0.081	0.05	11035
X-RAY DIFFRACTION	r_ncsr_local_group_13	0.09	0.05	10915
X-RAY DIFFRACTION	r_ncsr_local_group_14	0.08	0.05	11129
X-RAY DIFFRACTION	r_ncsr_local_group_15	0.073	0.05	11067
X-RAY DIFFRACTION	r_ncsr_local_group_16	0.072	0.05	11158
X-RAY DIFFRACTION	r_ncsr_local_group_17	0.071	0.05	11066
X-RAY DIFFRACTION	r_ncsr_local_group_18	0.085	0.05	10997
X-RAY DIFFRACTION	r_ncsr_local_group_19	0.078	0.05	11041
X-RAY DIFFRACTION	r_ncsr_local_group_20	0.086	0.05	11146
X-RAY DIFFRACTION	r_ncsr_local_group_21	0.074	0.05	11078
X-RAY DIFFRACTION	r_ncsr_local_group_22	0.087	0.05	10989
X-RAY DIFFRACTION	r_ncsr_local_group_23	0.073	0.05	11108
X-RAY DIFFRACTION	r_ncsr_local_group_24	0.072	0.05	11264
X-RAY DIFFRACTION	r_ncsr_local_group_25	0.078	0.05	11222
X-RAY DIFFRACTION	r_ncsr_local_group_26	0.069	0.05	11139
X-RAY DIFFRACTION	r_ncsr_local_group_27	0.077	0.05	11144
X-RAY DIFFRACTION	r_ncsr_local_group_28	0.081	0.05	11102

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)	Weight position
1	1	A	X-RAY DIFFRACTION	Local ncs	0.08273	0.05009
1	2	B	X-RAY DIFFRACTION	Local ncs	0.08273	0.05009
2	3	A	X-RAY DIFFRACTION	Local ncs	0.07199	0.05009
2	4	C	X-RAY DIFFRACTION	Local ncs	0.07199	0.05009
3	5	A	X-RAY DIFFRACTION	Local ncs	0.07618	0.05009
3	6	D	X-RAY DIFFRACTION	Local ncs	0.07618	0.05009
4	7	A	X-RAY DIFFRACTION	Local ncs	0.0675	0.05009
4	8	E	X-RAY DIFFRACTION	Local ncs	0.0675	0.05009
5	9	A	X-RAY DIFFRACTION	Local ncs	0.07908	0.05009
5	10	F	X-RAY DIFFRACTION	Local ncs	0.07908	0.05009
6	11	A	X-RAY DIFFRACTION	Local ncs	0.06788	0.05009
6	12	G	X-RAY DIFFRACTION	Local ncs	0.06788	0.05009
7	13	A	X-RAY DIFFRACTION	Local ncs	0.08374	0.05008
7	14	H	X-RAY DIFFRACTION	Local ncs	0.08374	0.05008
8	15	B	X-RAY DIFFRACTION	Local ncs	0.08762	0.05009
8	16	C	X-RAY DIFFRACTION	Local ncs	0.08762	0.05009
9	17	B	X-RAY DIFFRACTION	Local ncs	0.0864	0.05009
9	18	D	X-RAY DIFFRACTION	Local ncs	0.0864	0.05009
10	19	B	X-RAY DIFFRACTION	Local ncs	0.08272	0.05009
10	20	E	X-RAY DIFFRACTION	Local ncs	0.08272	0.05009
11	21	B	X-RAY DIFFRACTION	Local ncs	0.08838	0.05009
11	22	F	X-RAY DIFFRACTION	Local ncs	0.08838	0.05009
12	23	B	X-RAY DIFFRACTION	Local ncs	0.08071	0.05009
12	24	G	X-RAY DIFFRACTION	Local ncs	0.08071	0.05009
13	25	B	X-RAY DIFFRACTION	Local ncs	0.09043	0.05008
13	26	H	X-RAY DIFFRACTION	Local ncs	0.09043	0.05008
14	27	C	X-RAY DIFFRACTION	Local ncs	0.08011	0.05009
14	28	D	X-RAY DIFFRACTION	Local ncs	0.08011	0.05009
15	29	C	X-RAY DIFFRACTION	Local ncs	0.07321	0.05009
15	30	E	X-RAY DIFFRACTION	Local ncs	0.07321	0.05009
16	31	C	X-RAY DIFFRACTION	Local ncs	0.07229	0.05009
16	32	F	X-RAY DIFFRACTION	Local ncs	0.07229	0.05009
17	33	C	X-RAY DIFFRACTION	Local ncs	0.07123	0.05009
17	34	G	X-RAY DIFFRACTION	Local ncs	0.07123	0.05009
18	35	C	X-RAY DIFFRACTION	Local ncs	0.08504	0.05008
18	36	H	X-RAY DIFFRACTION	Local ncs	0.08504	0.05008
19	37	D	X-RAY DIFFRACTION	Local ncs	0.07752	0.05009
19	38	E	X-RAY DIFFRACTION	Local ncs	0.07752	0.05009
20	39	D	X-RAY DIFFRACTION	Local ncs	0.08579	0.05009
20	40	F	X-RAY DIFFRACTION	Local ncs	0.08579	0.05009
21	41	D	X-RAY DIFFRACTION	Local ncs	0.07384	0.05009
21	42	G	X-RAY DIFFRACTION	Local ncs	0.07384	0.05009
22	43	D	X-RAY DIFFRACTION	Local ncs	0.0869	0.05008
22	44	H	X-RAY DIFFRACTION	Local ncs	0.0869	0.05008
23	45	E	X-RAY DIFFRACTION	Local ncs	0.07339	0.05009
23	46	F	X-RAY DIFFRACTION	Local ncs	0.07339	0.05009
24	47	E	X-RAY DIFFRACTION	Local ncs	0.07221	0.05009
24	48	G	X-RAY DIFFRACTION	Local ncs	0.07221	0.05009
25	49	E	X-RAY DIFFRACTION	Local ncs	0.07775	0.05008
25	50	H	X-RAY DIFFRACTION	Local ncs	0.07775	0.05008
26	51	F	X-RAY DIFFRACTION	Local ncs	0.06856	0.05009
26	52	G	X-RAY DIFFRACTION	Local ncs	0.06856	0.05009
27	53	F	X-RAY DIFFRACTION	Local ncs	0.07706	0.05009
27	54	H	X-RAY DIFFRACTION	Local ncs	0.07706	0.05009
28	55	G	X-RAY DIFFRACTION	Local ncs	0.08142	0.05008
28	56	H	X-RAY DIFFRACTION	Local ncs	0.08142	0.05008

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 (%)
2.092-2.146	0.271	537	0.259	10358	X-RAY DIFFRACTION	79.9047
2.146-2.205	0.281	617	0.251	11900	X-RAY DIFFRACTION	94.1765
2.205-2.269	0.253	610	0.242	11782	X-RAY DIFFRACTION	95.2864
2.269-2.338	0.271	559	0.235	11578	X-RAY DIFFRACTION	96.5399
2.338-2.414	0.255	582	0.22	11212	X-RAY DIFFRACTION	96.7514
2.414-2.498	0.254	586	0.207	10872	X-RAY DIFFRACTION	96.8964
2.498-2.592	0.239	565	0.209	10515	X-RAY DIFFRACTION	97.0313
2.592-2.697	0.231	561	0.201	9989	X-RAY DIFFRACTION	96.6206
2.697-2.816	0.246	534	0.2	9696	X-RAY DIFFRACTION	97.068
2.816-2.952	0.255	499	0.206	9277	X-RAY DIFFRACTION	96.9649
2.952-3.11	0.252	405	0.204	8820	X-RAY DIFFRACTION	97.0746
3.11-3.296	0.225	441	0.203	8353	X-RAY DIFFRACTION	97.0105
3.296-3.521	0.22	444	0.196	7799	X-RAY DIFFRACTION	96.8056
3.521-3.799	0.207	379	0.192	7334	X-RAY DIFFRACTION	96.6178
3.799-4.155	0.22	337	0.182	6701	X-RAY DIFFRACTION	96.4374
4.155-4.634	0.171	314	0.166	6040	X-RAY DIFFRACTION	95.866
4.634-5.329	0.209	297	0.174	5231	X-RAY DIFFRACTION	94.8524
5.329-6.476	0.201	251	0.201	4495	X-RAY DIFFRACTION	95.5506
6.476-8.953	0.185	187	0.168	3687	X-RAY DIFFRACTION	99.3079

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-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi