PDB-5u9c: 1.9 Angstrom Resolution Crystal Structure of dTDP-4-dehydrorhamno...

ID or keywords:

Entry

Database: PDB / ID: 5u9c

Title

1.9 Angstrom Resolution Crystal Structure of dTDP-4-dehydrorhamnose Reductase from Yersinia enterocolitica

Components

dTDP-4-dehydrorhamnose Reductase

Keywords

HYDROLASE /

OXIDOREDUCTASE /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID /

dTDP-4-dehydrorhamnose Reductase

Function / homology

Function and homology information

dTDP-4-dehydrorhamnose reductase /

dTDP-4-dehydrorhamnose reductase activity / O antigen biosynthetic process / dTDP-rhamnose biosynthetic process
Similarity search - Function

Biological species

Yersinia enterocolitica (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.9 Å

Authors

Minasov, G. / Shuvalova, L. / Flores, K. / Dubrovska, I. / Olphie, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To Be Published
Title: 1.9 Angstrom Resolution Crystal Structure of dTDP-4-dehydrorhamnose Reductase from Yersinia enterocolitica.
Authors: Minasov, G. / Shuvalova, L. / Flores, K. / Dubrovska, I. / Olphie, A. / Grimshaw, S. / Kwon, K. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Dec 15, 2016	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 28, 2016	Provider: repository / Type: Initial release
Revision 1.1	Jul 29, 2020	Group: Data collection / Derived calculations / Structure summary Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_site / struct_site_gen Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name Description: Carbohydrate remediation / Provider: repository / Type: Remediation

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5u9c.cif.gz	726 KB	Display	PDBx/mmCIF format
PDB format	pdb5u9c.ent.gz	613.5 KB	Display	PDB format
PDBx/mmJSON format	5u9c.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/u9/5u9c ftp://data.pdbj.org/pub/pdb/validation_reports/u9/5u9c	HTTPS FTP

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Related structure data

Similar structure data	5u4j-d 4y7j-d 2yid-2 6eo1-d 6ku9-d 6tx0-1 6i8a-2 6g0a-d 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	TargetTrack: CSGID-IDP93871

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#21 - Sep 2001 Antibodies similarity (1) #154 - Oct 2012 Citric Acid Cycle similarity (1) #134 - Feb 2011 Integrin similarity (1) #172 - Apr 2014 RecA and Rad51 similarity (1) #194 - Feb 2016 Designer Insulins similarity (1) #234 - Jun 2019 MDM2 and Cancer similarity (1) #259 - Jul 2021 Designed Proteins and Citizen Science similarity (1)

Deposited unit

A: dTDP-4-dehydrorhamnose Reductase

B: dTDP-4-dehydrorhamnose Reductase

C: dTDP-4-dehydrorhamnose Reductase

D: dTDP-4-dehydrorhamnose Reductase

E: dTDP-4-dehydrorhamnose Reductase

F: dTDP-4-dehydrorhamnose Reductase

hetero molecules

194 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)	132.445, 184.871, 187.017
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	23
Space group name H-M	I222

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Protein / Sugars , 2 types, 9 molecules ABCDEF

#1: Protein

dTDP-4-dehydrorhamnose Reductase /

Mass: 32101.846 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Yersinia enterocolitica (bacteria) / Gene: wbbW / Plasmid: pMCSG53 / Production host:

Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q56905

#2: Sugar

ChemComp-BDF / beta-D-fructopyranose /

Fructose

Type: D-saccharide, beta linking / Mass: 180.156 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Formula: C₆H₁₂O₆

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Non-polymers , 6 types, 1455 molecules

#3: Chemical	ChemComp-IMD / IMIDAZOLE / Imidazole Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₅N₂
#4: Chemical	ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₅
#5: Chemical	ChemComp-CIT / CITRIC ACID / Citric acid Mass: 192.124 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₈O₇
#6: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#7: Chemical	ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER / Tris Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₂NO₃ / Comment: pH buffer*YM
#8: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1446 / 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: 2.9 Å³/Da / Density % sol: 57.7 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Protein: 7.2 mg/ml, 0.25M Sodium chloride, 0.01M Tris HCl (pH 8.3); Screen: Classics II (C5), 0.96M Sodium citrate (pH 7.0); Cryo: Screen : 50% Sucrose (1:1)

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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: Aug 14, 2014 / Details: C(111)
Radiation	Monochromator: beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 1.9→30 Å / Num. obs: 179762 / % possible obs: 99.6 % / Observed criterion σ(I): -3 / Redundancy: 7.5 % / B_iso Wilson estimate: 28.2 Å² / R_merge(I) obs: 0.07 / R_sym value: 0.07 / Net I/σ(I): 28.8
Reflection shell	Resolution: 1.9→1.93 Å / Redundancy: 6.8 % / R_merge(I) obs: 0.649 / Mean I/σ(I) obs: 2.7 / CC_1/2: 0.887 / % possible all: 96.3

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0158	refinement
HKL-3000		data reduction
HKL-3000		data scaling
PHENIX		phasing

Refinement

Method to determine structure:

SAD / Resolution: 1.9→29.94 Å / Cor.coef. F_o:F_c: 0.974 / Cor.coef. F_o:F_c free: 0.964 / SU B: 7.005 / SU ML: 0.098 / Cross valid method: THROUGHOUT / ESU R: 0.119 / ESU R Free: 0.112 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.19066	8981	5 %	RANDOM
R_work	0.15993	-	-	-
obs	0.16146	169660	99.57 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å

Displacement parameters

B_iso mean: 40.524 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-2.11 Å²	0 Å²	0 Å²
2-	-	4.39 Å²	0 Å²
3-	-	-	-2.27 Å²

Refinement step

Cycle: 1 / Resolution: 1.9→29.94 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	13282	0	116	1446	14844

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.019	14595
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	13628
X-RAY DIFFRACTION	r_angle_refined_deg	1.474	1.98	19911
X-RAY DIFFRACTION	r_angle_other_deg	0.875	3	31719
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	2.94	5	1919
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	32.252	23.739	559
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	8.865	15	2330
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.654	15	76
X-RAY DIFFRACTION	r_chiral_restr	0.102	0.2	2238
X-RAY DIFFRACTION	r_gen_planes_refined	0.023	0.021	16583
X-RAY DIFFRACTION	r_gen_planes_other	0.019	0.02	2973
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	1.403	2.461	7437
X-RAY DIFFRACTION	r_mcbond_other	1.399	2.459	7435
X-RAY DIFFRACTION	r_mcangle_it	2.233	3.675	9435
X-RAY DIFFRACTION	r_mcangle_other	2.234	3.676	9436
X-RAY DIFFRACTION	r_scbond_it	2.112	2.799	7158
X-RAY DIFFRACTION	r_scbond_other	2.103	2.796	7155
X-RAY DIFFRACTION	r_scangle_it
X-RAY DIFFRACTION	r_scangle_other	3.3	4.082	10475
X-RAY DIFFRACTION	r_long_range_B_refined	6.606	31.757	16918
X-RAY DIFFRACTION	r_long_range_B_other	6.337	30.707	16457
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→1.949 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.294	644	-
R_work	0.286	12079	-
obs	-	-	96.69 %

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	2.8055	-2.0318	-1.2977	3.8999	1.3075	5.8101	-0.109	-0.2496	-0.5484	0.2641	-0.07	0.307	0.5006	-0.2777	0.179	0.103	-0.0876	0.0016	0.1219	0.0815	0.2167	50.7338	25.0059	74.9722
2	1.7467	0.0551	-0.1298	0.4931	-0.1134	0.7126	0.0426	-0.2005	-0.0871	0.0414	0.005	0.0052	0.042	-0.057	-0.0476	0.0293	-0.0186	-0.0107	0.0794	-0.0125	0.0558	53.1918	40.1886	68.4732
3	1.6849	0.0269	-0.3547	0.6833	-0.0469	3.6085	-0.0177	0.1062	-0.3736	-0.063	0.0642	0.0824	0.5427	-0.1912	-0.0465	0.0871	-0.0319	-0.0233	0.0445	-0.0226	0.1962	59.3133	27.3804	56.6255
4	2.8747	-0.1559	1.6772	0.4059	-0.5398	2.5447	0.0341	0.399	-0.3068	-0.0951	-0.0127	-0.0212	0.2477	0.04	-0.0215	0.045	-0.0138	0.0209	0.1364	-0.0834	0.1091	60.6859	34.6879	46.5796
5	2.0744	-0.0845	0.5342	3.2201	-0.0045	5.3024	0.0267	0.1405	-0.7176	-0.1462	0.0442	-0.1358	0.717	0.2803	-0.0709	0.1314	0.0302	0.0049	0.0351	-0.0192	0.3125	65.5685	20.611	58.5631
6	3.2816	-2.5789	0.2767	3.6012	0.9246	6.9306	0.2252	0.528	-0.2543	-0.7804	-0.0946	0.6455	-0.1495	-0.1976	-0.1305	0.2763	-0.0555	-0.2011	0.6786	0.0907	0.1784	48.1785	61.8511	9.1578
7	1.4098	0.1963	0.8087	2.3623	-0.4765	2.7028	-0.0538	0.8581	-0.19	-0.5219	0.141	0.0135	0.0562	0.2142	-0.0873	0.133	-0.0363	0.0092	0.7139	-0.0835	0.0443	58.0577	50.8925	15.5741
8	2.1991	0.5868	0.3781	2.0028	0.6045	1.2471	-0.1295	0.7944	0.0812	-0.2494	0.1331	-0.1737	-0.1387	0.3044	-0.0036	0.056	-0.0505	0.0326	0.4442	0.043	0.0488	62.7977	60.709	25.9686
9	4.0559	0.9164	-1.456	1.1147	-0.49	1.2948	-0.0471	0.6841	0.1474	-0.1044	-0.0041	0.1288	-0.0246	-0.0871	0.0511	0.0342	-0.0215	-0.032	0.1861	0.0398	0.0454	43.9548	64.0836	31.1926
10	2.3932	0.4354	-0.1954	1.1729	-0.3946	0.5103	-0.0058	0.3712	0.329	-0.0628	-0.024	0.1442	-0.0938	0.0229	0.0298	0.093	-0.0169	-0.019	0.211	0.0326	0.0746	46.9106	65.5886	35.204
11	2.9901	3.4419	0.6358	5.5159	-0.7976	3.5167	-0.0372	0.4354	-0.4371	-0.3291	-0.0661	-0.379	0.3632	0.16	0.1033	0.0969	0.0772	0.0477	0.3986	-0.1933	0.2015	89.1948	35.2438	13.7089
12	1.6936	-0.0351	-0.2478	0.5772	0.1999	1.3843	0.0353	0.4525	-0.053	-0.0654	-0.0427	-0.0296	-0.0391	-0.1729	0.0074	0.0268	0.0367	0.0007	0.2031	-0.0591	0.0507	85.5583	47.6569	23.5271
13	1.435	-0.0908	0.3682	0.8894	-0.5617	4.9077	0.0051	0.1652	-0.2712	-0.0255	0.028	-0.1076	0.6443	0.18	-0.0331	0.1004	0.0278	-0.0137	0.1588	-0.1569	0.1785	81.1987	29.3311	32.8246
14	2.4076	-0.2267	1.1648	0.0422	-0.0207	2.6288	0.0463	0.0507	-0.2681	0.0107	-0.0575	0.0198	0.3458	-0.1664	0.0112	0.1336	-0.0127	0.0169	0.1702	-0.0743	0.1895	79.2283	34.6494	43.1256
15	3.8638	-1.6725	1.4969	2.8661	-1.6109	4.8991	0.0376	0.25	-0.5456	0.0323	0.0417	0.0777	0.5979	-0.1	-0.0793	0.1874	-0.0363	-0.008	0.236	-0.2244	0.2491	74.6555	25.7024	27.0669
16	1.2044	0.5581	0.105	1.9428	0.088	3.4201	0.1306	-0.2435	-0.1948	0.2792	-0.0637	-0.2521	0.1835	0.4062	-0.0669	0.0837	0.0445	-0.0524	0.188	-0.0164	0.0952	87.7511	46.5282	87.2619
17	0.8242	0.0327	0.461	0.6894	-0.1694	1.4961	-0.0078	-0.0793	-0.0278	0.0808	0.0779	0.0116	-0.0262	-0.1225	-0.0701	0.0238	0.0244	0.0088	0.0936	-0.0124	0.062	78.4489	49.5056	72.2655
18	3.1156	-0.2016	-1.7842	0.5939	0.6307	2.3129	-0.0279	-0.2261	-0.1676	0.0638	0.0149	-0.0955	0.0847	0.3079	0.013	0.0625	0.0376	-0.004	0.0945	-0.0273	0.1275	98.2412	55.8895	63.4921
19	0.8659	0.0258	-0.3159	0.5864	0.1918	1.0008	0.0447	-0.0895	0.0864	0.05	0.0517	-0.0707	-0.1243	0.1392	-0.0963	0.0609	0.0158	0.005	0.0711	-0.0427	0.0833	90.3067	61.6417	66.3168
20	9.9301	-3.5613	-0.8024	10.251	-0.1547	4.8767	-0.1003	-0.363	0.4486	0.0925	0.0432	-0.5055	-0.123	0.3435	0.0571	0.0627	-0.0206	0.0029	0.1116	-0.0589	0.068	102.366	64.152	68.6556
21	2.7597	-0.6441	1.1962	2.8323	-1.9889	2.995	0.0373	-0.3375	0.1979	0.3526	0.1606	0.2773	-0.4653	-0.5084	-0.1979	0.2512	0.094	0.0938	0.2352	-0.0864	0.1444	47.6443	73.5166	83.6965
22	1.2911	0.1421	-0.01	0.8563	0.3411	0.9988	0.0099	-0.2148	0.0532	0.2075	0.016	-0.034	0.0476	-0.1278	-0.0259	0.1348	0.0421	0.0156	0.0877	-0.0264	0.0838	60.9132	66.9001	73.9949
23	0.1801	-0.3197	-0.2337	1.1622	0.2691	1.5005	0.0446	-0.0578	0.0719	0.1647	-0.0242	-0.068	0.1549	-0.0055	-0.0204	0.2344	-0.011	0.0253	0.1754	-0.0256	0.165	57.1314	66.178	68.8529
24	0.3833	-0.0838	0.0813	2.3598	-1.6457	1.8016	-0.0703	0.0436	0.1033	0.169	-0.0036	0.0284	-0.2962	-0.3167	0.0739	0.209	0.044	-0.006	0.1842	-0.007	0.229	48.9924	77.2398	59.9483
25	0.7515	-0.0616	0.0917	0.9204	-0.0949	0.7211	0.0337	0.0106	0.1641	0.0291	-0.0155	0.1803	-0.0925	-0.1373	-0.0182	0.0691	0.0306	0.0238	0.0545	0.0038	0.1305	47.4223	71.3598	57.5101
26	7.7156	0.3541	-0.6219	3.5909	0.1127	6.5135	-0.0433	0.4044	0.8893	-0.2995	0.1314	-0.1271	-0.3913	0.3053	-0.0881	0.1652	-0.016	0.101	0.0718	0.0838	0.2162	91.0498	84.6328	21.1851
27	1.7912	-0.2457	-0.3706	1.2803	-0.342	0.9466	0.0783	0.4076	0.2689	-0.2911	0.0491	0.0838	-0.0709	-0.1711	-0.1274	0.1208	0.0025	0.0212	0.1221	0.0723	0.1048	78.3177	74.6485	26.7118
28	1.3564	-0.3026	-1.744	1.3968	0.0562	2.8439	0.0078	0.197	0.1492	-0.3472	0.0416	0.1477	0.1869	-0.2399	-0.0494	0.188	0.0013	-0.0028	0.1492	0.0357	0.1101	78.877	68.3453	28.2251
29	1.0889	-0.0085	-0.0442	2.5495	1.2211	2.4845	0.0151	-0.0717	0.1536	0.002	0.0133	-0.1846	-0.2787	0.0404	-0.0284	0.0924	0.0034	0.0251	0.0249	0	0.1697	89.1309	81.8416	46.886
30	0.9393	-0.2223	-0.48	1.2363	0.3821	0.9026	0.0111	0.0245	0.0761	-0.0636	0.0607	-0.2234	-0.0854	0.1387	-0.0718	0.0518	-0.0108	0.0299	0.0543	-0.0015	0.1291	92.3957	73.9019	42.3325

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 24
2	X-RAY DIFFRACTION	2	A	25 - 138
3	X-RAY DIFFRACTION	3	A	139 - 235
4	X-RAY DIFFRACTION	4	A	236 - 264
5	X-RAY DIFFRACTION	5	A	265 - 288
6	X-RAY DIFFRACTION	6	B	2 - 34
7	X-RAY DIFFRACTION	7	B	35 - 92
8	X-RAY DIFFRACTION	8	B	93 - 150
9	X-RAY DIFFRACTION	9	B	151 - 235
10	X-RAY DIFFRACTION	10	B	236 - 288
11	X-RAY DIFFRACTION	11	C	2 - 24
12	X-RAY DIFFRACTION	12	C	25 - 152
13	X-RAY DIFFRACTION	13	C	153 - 234
14	X-RAY DIFFRACTION	14	C	235 - 264
15	X-RAY DIFFRACTION	15	C	265 - 288
16	X-RAY DIFFRACTION	16	D	-2 - 52
17	X-RAY DIFFRACTION	17	D	53 - 148
18	X-RAY DIFFRACTION	18	D	149 - 195
19	X-RAY DIFFRACTION	19	D	196 - 276
20	X-RAY DIFFRACTION	20	D	277 - 288
21	X-RAY DIFFRACTION	21	E	-2 - 35
22	X-RAY DIFFRACTION	22	E	36 - 123
23	X-RAY DIFFRACTION	23	E	124 - 162
24	X-RAY DIFFRACTION	24	E	163 - 204
25	X-RAY DIFFRACTION	25	E	205 - 288
26	X-RAY DIFFRACTION	26	F	2 - 34
27	X-RAY DIFFRACTION	27	F	35 - 123
28	X-RAY DIFFRACTION	28	F	124 - 149
29	X-RAY DIFFRACTION	29	F	150 - 195
30	X-RAY DIFFRACTION	30	F	196 - 288

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