PDB-3ot5: 2.2 Angstrom Resolution Crystal Structure of putative UDP-N-acety...

ID or keywords:

Entry

Database: PDB / ID: 3ot5

Title

2.2 Angstrom Resolution Crystal Structure of putative UDP-N-acetylglucosamine 2-epimerase from Listeria monocytogenes

Components

UDP-N-acetylglucosamine 2-epimerase

Keywords

ISOMERASE / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Alpha Beta / 3-Layer(aba) Sandwich / Rossmann fold / UDP-N-acetylglucosamine 2-epimerase

Function / homology

Function and homology information

UDP-N-acetylglucosamine 2-epimerase activity
Similarity search - Function

Biological species

Listeria monocytogenes (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: TO BE PUBLISHED
Title: 2.2 Angstrom Resolution Crystal Structure of putative UDP-N-acetylglucosamine 2-epimerase from Listeria monocytogenes.
Authors: Minasov, G. / Halavaty, A. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Sep 10, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Sep 22, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3ot5.cif.gz	594.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3ot5.ent.gz	493.9 KB	Display	PDB format
PDBx/mmJSON format	3ot5.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3ot5_validation.pdf.gz	484.8 KB	Display	wwPDB validaton report
Full document	3ot5_full_validation.pdf.gz	507.3 KB	Display
Data in XML	3ot5_validation.xml.gz	54.7 KB	Display
Data in CIF	3ot5_validation.cif.gz	76 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ot/3ot5 ftp://data.pdbj.org/pub/pdb/validation_reports/ot/3ot5	HTTPS FTP

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Related structure data

Related structure data	3beoS S: Starting model for refinement
Similar structure data	4fqd-3 5ci1-d 4j34-1 4a99-2 3p9u-2 3p9u-1 2o0d-d 1cj4-d 4a5z-2 1iux-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetDB: idp01656

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: UDP-N-acetylglucosamine 2-epimerase

B: UDP-N-acetylglucosamine 2-epimerase

C: UDP-N-acetylglucosamine 2-epimerase

D: UDP-N-acetylglucosamine 2-epimerase

hetero molecules

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

1

A: UDP-N-acetylglucosamine 2-epimerase

hetero molecules

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

2

B: UDP-N-acetylglucosamine 2-epimerase

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

3

C: UDP-N-acetylglucosamine 2-epimerase

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

4

D: UDP-N-acetylglucosamine 2-epimerase

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

5

A: UDP-N-acetylglucosamine 2-epimerase

hetero molecules

C: UDP-N-acetylglucosamine 2-epimerase

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

6

D: UDP-N-acetylglucosamine 2-epimerase

B: UDP-N-acetylglucosamine 2-epimerase

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

Unit cell

Length a, b, c (Å)	81.190, 84.405, 100.461
Angle α, β, γ (deg.)	90.00, 90.07, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	UDP-N-acetylglucosamine 2-epimerase Mass: 45057.164 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Listeria monocytogenes (bacteria) / Strain: EGD-e / Gene: lmo2537 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 "magic" References: UniProt: Q8Y4B4, UDP-N-acetylglucosamine 2-epimerase (non-hydrolysing)
#2: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#3: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 237 / 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: 1.91 Å³/Da / Density % sol: 35.6 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 8.3 Details: Protein: 7.4mGr/mL, 0.5 Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: PEGs II (H1), 0.01M tri-Sodium citrate, 33% (w/v) PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 19, 2010 / Details: Beryllium lenses
Radiation	Monochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.2→30 Å / Num. all: 67586 / Num. obs: 67586 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 3 % / B_iso Wilson estimate: 52.9 Å² / R_merge(I) obs: 0.046 / Net I/σ(I): 22.4
Reflection shell	Resolution: 2.2→2.24 Å / Redundancy: 2.9 % / R_merge(I) obs: 0.523 / Mean I/σ(I) obs: 2.06 / Num. unique all: 3349 / % possible all: 99.8

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
BALBES		phasing
REFMAC	5.5.0102	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3BEO

3beo

Resolution: 2.2→29.59 Å / Cor.coef. F_o:F_c: 0.964 / Cor.coef. F_o:F_c free: 0.944 / SU B: 10.269 / SU ML: 0.119 / Isotropic thermal model: Refined individually / Cross valid method: THROUGHOUT / ESU R Free: 0.229 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23474	3414	5.1 %	RANDOM
R_work	0.18724	-	-	-
all	0.18967	64131	-	-
obs	0.18967	64131	98.06 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 47.288 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.52 Å²	0 Å²	-1.88 Å²
2-	-	-1.41 Å²	0 Å²
3-	-	-	-1.11 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→29.59 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11700	0	17	237	11954

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	11971
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	8052
X-RAY DIFFRACTION	r_angle_refined_deg	1.378	1.972	16208
X-RAY DIFFRACTION	r_angle_other_deg	0.825	3	19787
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	1.901	5	1497
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	25.737	25.126	556
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	8.403	15	2138
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	8.49	15	66
X-RAY DIFFRACTION	r_chiral_restr	0.071	0.2	1860
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	13263
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	2203
X-RAY DIFFRACTION	r_mcbond_it	0.84	1.5	7490
X-RAY DIFFRACTION	r_mcbond_other	0.227	1.5	3019
X-RAY DIFFRACTION	r_mcangle_it	1.481	2	12125
X-RAY DIFFRACTION	r_scbond_it	2.525	3	4481
X-RAY DIFFRACTION	r_scangle_it	3.891	4.5	4083

LS refinement shell

Resolution: 2.201→2.258 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.342	196	-
R_work	0.263	3860	-
obs	-	3860	80.27 %

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	3.1319	0.6863	0.0782	6.0885	-1.0204	3.1832	0.0363	-0.2182	0.073	0.4438	0.0385	-0.1189	0.2418	0.0446	-0.0749	0.1532	0.0025	0.0162	0.0307	0.0005	0.0977	39.7492	-24.5361	3.879
2	15.245	-1.0965	-10.4878	0.788	-0.6568	10.1115	-0.1143	-1.3174	0.496	0.3931	0.0235	-0.285	-0.5161	1.1384	0.0907	0.5865	0.0769	-0.1527	0.4879	-0.0222	0.3985	46.8486	-18.9015	9.769
3	2.043	-0.3093	-0.8168	2.8308	-0.0402	2.781	0.0381	0.0584	0.0322	-0.041	-0.0911	-0.0973	0.0355	-0.1941	0.053	0.0169	-0.0096	0.0335	0.0213	-0.0176	0.0681	36.4607	-13.1609	-7.4229
4	1.8221	-0.22	-0.9663	3.5133	2.4629	4.0075	0.0012	-0.1927	0.1134	0.3618	-0.0017	-0.0439	-0.0646	-0.2188	0.0005	0.1454	0.0341	0.0241	0.1921	-0.0277	0.1259	26.5166	-3.747	22.1769
5	1.8653	0.6859	0.4564	4.0965	1.7305	4.7336	0.0991	-0.0231	0.0386	0.2022	-0.2175	0.0676	-0.2084	-0.4731	0.1183	0.0726	0.0381	0.0545	0.1887	-0.0367	0.1259	23.4262	-1.9856	19.4218
6	5.8243	-5.5361	-4.6845	7.21	6.6537	9.895	-0.2074	0.2403	-0.5883	0.2235	-0.5253	0.896	0.626	-0.6751	0.7326	0.2191	-0.1752	0.0998	0.2235	-0.0868	0.2929	22.6596	-23.9219	2.6414
7	3.1053	0.6656	0.04	4.488	1.3619	4.3143	0.0837	-0.1517	-0.0915	0.2628	-0.0829	-0.3191	0.4314	0.1086	-0.0008	0.1253	0.0301	-0.0781	0.0287	0.0005	0.1016	4.9598	-6.2492	-19.7265
8	6.8875	-3.987	-3.8109	2.7683	-0.0988	14.5778	-0.2302	-0.9671	1.4483	0.3582	0.4514	-1.0494	-0.5703	1.6949	-0.2212	0.3845	0.1188	-0.2542	0.4848	-0.3097	0.7326	15.2916	0.701	-18.0715
9	0.7726	-0.4825	0.1039	2.3434	-0.3915	4.1473	-0.0538	-0.0336	-0.0139	0.1443	0.1202	-0.024	0.045	-0.1808	-0.0664	0.0306	-0.0018	-0.0433	0.0292	0.0022	0.1023	-1.275	5.7578	-26.7291
10	5.4298	-1.6735	0.8057	6.0589	-0.0225	5.091	-0.0992	0.3756	0.7063	-0.1558	0.2204	-0.7384	0.0022	0.6572	-0.1212	0.1126	0.0143	-0.0709	0.3422	0.0283	0.3359	10.4547	21.2432	-2.1582
11	5.3212	0.0576	2.2411	2.6171	1.1274	4.1704	-0.1163	-0.0287	0.2293	0.1801	0.1071	0.0951	0.0528	-0.0973	0.0092	0.0902	0.0757	0.0296	0.1663	0.0623	0.0782	-3.9319	18.4326	-3.944
12	4.1483	-0.2119	-0.9335	11.6037	7.0006	10.3361	-0.2127	-0.2377	-0.3073	0.4935	-0.1183	0.9348	0.9882	-0.7854	0.3311	0.203	-0.0736	0.0331	0.2102	0.0861	0.2579	-10.0318	-6.2168	-17.3262
13	2.4836	0.0921	0.8549	3.5297	-1.1348	4.159	-0.0324	-0.1568	0.0482	0.3195	0.1782	0.3362	-0.5352	-0.1429	-0.1458	0.1557	0.0263	0.1014	0.0417	-0.0079	0.1295	35.7553	49.4224	30.5595
14	7.1616	-3.0209	1.0295	4.2855	5.886	14.3088	-0.13	-0.9228	-1.2686	0.6541	-0.1327	1.0562	0.8521	-1.7923	0.2627	0.4439	0.1114	0.3276	0.5862	0.3945	0.8914	25.1419	41.6571	31.6249
15	0.8369	-0.0813	-0.3171	1.3601	-0.345	3.4871	-0.0936	-0.1091	0.0554	0.1794	0.1316	0.0373	-0.1212	0.1651	-0.038	0.0616	0.0207	0.056	0.0484	-0.017	0.1346	40.7793	37.287	27.751
16	5.4674	-0.3597	-1.07	6.5677	0.3388	3.5867	-0.1308	0.6775	-0.9403	-0.6363	0.1868	0.9673	0.2164	-0.8356	-0.0559	0.2397	0.0041	-0.0114	0.4648	-0.0407	0.4977	30.2745	19.768	46.0407
17	7.0713	0.0218	-1.9844	1.7957	-0.8039	4.1396	-0.0377	0.2664	-0.2601	0.0959	0.0585	-0.1049	-0.1524	-0.1718	-0.0209	0.0785	0.063	0.0022	0.1564	-0.048	0.0582	43.3074	25.3263	43.4246
18	1.3103	0.3146	-0.3262	8.1099	-5.9623	5.7142	-0.1747	-0.208	0.1036	0.4679	-0.0911	-0.6487	-0.5283	0.4696	0.2658	0.1846	0.0089	-0.0165	0.2663	-0.1179	0.1757	49.4553	37.4049	41.6508
19	2.9087	-0.2415	1.3526	6.0469	-0.6838	3.988	0.0514	0.255	-0.0774	-0.6636	-0.0188	-0.097	-0.3434	0.1944	-0.0326	0.1462	0.015	-0.0096	0.0673	0.0077	0.1098	-1.7318	24.0099	45.7567
20	4.284	0.6041	1.0303	3.4894	-2.6236	2.6869	-0.1638	0.6532	-0.2811	-0.3451	0.0658	-0.256	0.1964	0.456	0.0979	0.2287	-0.0767	0.0343	0.4721	-0.0663	0.2407	4.4518	23.3395	42.8162
21	2.1949	0.0918	1.0335	2.8119	-0.0022	2.4449	0.0342	-0.0642	-0.0111	0.0509	-0.0688	-0.0317	-0.0488	-0.2059	0.0346	0.0036	0.0042	-0.0042	0.022	-0.0125	0.0394	-4.3953	14.2336	57.8572
22	2.1951	0.3066	0.6388	3.4998	2.6859	3.0639	-0.0747	0.2583	0.0194	-0.5829	0.0747	0.0017	-0.4637	-0.0292	-0	0.1552	0.01	-0.0145	0.145	-0.0043	0.0902	-12.0189	11.1503	28.8801
23	2.8093	-0.6719	-0.2253	4.3073	1.6459	4.5961	0.0758	0.0339	-0.1063	-0.1172	-0.1604	0.0642	0.4445	-0.4786	0.0846	0.101	-0.063	-0.0289	0.1849	-0.024	0.1085	-17.2152	1.2868	30.2068
24	5.9147	5.5275	4.5273	6.8239	6.5493	8.484	-0.2753	-0.153	0.6246	-0.2466	-0.4398	0.8474	-0.6436	-0.6729	0.7151	0.235	0.173	-0.0778	0.2495	-0.0803	0.3375	-18.3292	24.5437	47.2857

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 41
2	X-RAY DIFFRACTION	2	A	42 - 66
3	X-RAY DIFFRACTION	3	A	67 - 174
4	X-RAY DIFFRACTION	4	A	175 - 231
5	X-RAY DIFFRACTION	5	A	232 - 340
6	X-RAY DIFFRACTION	6	A	341 - 379
7	X-RAY DIFFRACTION	7	B	1 - 41
8	X-RAY DIFFRACTION	8	B	42 - 66
9	X-RAY DIFFRACTION	9	B	67 - 185
10	X-RAY DIFFRACTION	10	B	186 - 271
11	X-RAY DIFFRACTION	11	B	272 - 350
12	X-RAY DIFFRACTION	12	B	351 - 379
13	X-RAY DIFFRACTION	13	C	1 - 40
14	X-RAY DIFFRACTION	14	C	41 - 69
15	X-RAY DIFFRACTION	15	C	70 - 200
16	X-RAY DIFFRACTION	16	C	201 - 273
17	X-RAY DIFFRACTION	17	C	274 - 326
18	X-RAY DIFFRACTION	18	C	327 - 379
19	X-RAY DIFFRACTION	19	D	2 - 29
20	X-RAY DIFFRACTION	20	D	30 - 64
21	X-RAY DIFFRACTION	21	D	65 - 173
22	X-RAY DIFFRACTION	22	D	174 - 211
23	X-RAY DIFFRACTION	23	D	212 - 339
24	X-RAY DIFFRACTION	24	D	340 - 379

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