PDB-3cko: Crystal Structure of a Mycobacterial Protein

ID or keywords:

Entry

Database: PDB / ID: 3cko

Title

Crystal Structure of a Mycobacterial Protein

Components

Putative uncharacterized protein

Keywords

UNKNOWN FUNCTION /

mycobacteria

Function / homology

Function and homology information

glucosyl-3-phosphoglycerate synthase /

glycosyltransferase activity /

metal ion binding
Similarity search - Function

Biological species

Mycobacterium paratuberculosis (bacteria)

Method

X-RAY DIFFRACTION / Rigid body refinement / Resolution: 2.5 Å

Authors

Marland, Z. / Rossjohn, J.

Citation

Journal: J.Biol.Chem. / Year: 2008
Title: Crystal structure of a UDP-glucose-specific glycosyltransferase from a Mycobacterium species.
Authors: Fulton, Z. / McAlister, A. / Wilce, M.C. / Brammananth, R. / Zaker-Tabrizi, L. / Perugini, M.A. / Bottomley, S.P. / Coppel, R.L. / Crellin, P.K. / Rossjohn, J. / Beddoe, T.

History

Deposition	Mar 16, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 29, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Feb 21, 2024	Group: Data collection / Database references / Derived calculations Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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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PDBx/mmCIF format	3cko.cif.gz	70.9 KB	Display	PDBx/mmCIF format
PDB format	pdb3cko.ent.gz	52.6 KB	Display	PDB format
PDBx/mmJSON format	3cko.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ck/3cko ftp://data.pdbj.org/pub/pdb/validation_reports/ck/3cko	HTTPS FTP

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Related structure data

Related structure data	3ckjC 3cknC 3ckqC 3ckvC C: citing same article (ref.)
Similar structure data	3ckv-1 3h2m-1 3qvm-d 4nir-1 3ckn-1 4nl1-1 4dec-1 3tyc-1 3a2m-d 4y7f-1 3tya-1 117e-d 3h22-1 3h2o-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#254 - Feb 2021 Cellulose Synthase similarity (4) #156 - Dec 2012 ABO Blood Type Glycosyltransferases similarity (2) #141 - Sep 2011 O-GlcNAc Transferase similarity (1)

Deposited unit

A: Putative uncharacterized protein

hetero molecules

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

1

A: Putative uncharacterized protein

hetero molecules

A: Putative uncharacterized protein

hetero molecules

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

Unit cell

Length a, b, c (Å)	86.823, 86.823, 103.829
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	92
Space group name H-M	P4₁2₁2

#1: Protein	Putative uncharacterized protein Mass: 34827.434 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Mycobacterium paratuberculosis (bacteria) / Strain: K-10 / References: UniProt: Q73WU1
#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE / Uridine diphosphate Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Comment: UDP*YM
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 24 / 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: 2.81 Å³/Da / Density % sol: 56.21 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1 M Ammonium sulphate, 0.1 M Sodium citrate pH 5.5, 20 mM Manganese chloride, 1 mM Sodium thiosulphate, 100 mM uridine-5 -diphosphate-glucose , VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
Detector	Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 17, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.5→33.3 Å / Num. all: 14197 / Num. obs: 13439 / Redundancy: 4.4 % / Net I/σ(I): 9.3
Reflection shell	Highest resolution: 2.5 Å / R_sym value: 0.515

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Processing

Software

Name	Version	Classification
REFMAC	5.2.0019	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure: Rigid body refinement / Resolution: 2.5→33.3 Å / Cor.coef. F_o:F_c: 0.945 / Cor.coef. F_o:F_c free: 0.945 / SU B: 17.483 / SU ML: 0.195 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.428 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23035	711	5 %	RANDOM
R_work	0.21992	-	-	-
obs	0.22044	13439	98.99 %	-

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: 23.946 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.24 Å²	0 Å²	0 Å²
2-	-	0.24 Å²	0 Å²
3-	-	-	-0.47 Å²

Refinement step

Cycle: LAST / Resolution: 2.5→33.3 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2250	0	38	24	2312

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.022	2382
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	0.887	2.005	3273
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	3.788	5	316
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	29.539	22.609	92
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.04	15	364
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.153	15	24
X-RAY DIFFRACTION	r_chiral_restr	0.051	0.2	385
X-RAY DIFFRACTION	r_gen_planes_refined	0.002	0.02	1807
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.15	0.2	1063
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.295	0.2	1605
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.079	0.2	105
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	0.129	0.2	60
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.131	0.2	8
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	0.109	1.5	1554
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.198	2	2463
X-RAY DIFFRACTION	r_scbond_it	0.197	3	926
X-RAY DIFFRACTION	r_scangle_it	0.349	4.5	801
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.5→2.565 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.308	52	-
R_work	0.345	943	-
obs	-	-	96.23 %

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	4.9824	-0.3364	0.309	3.6558	2.5075	1.7787	-0.644	-0.9668	-0.5029	1.4692	0.8691	-0.4467	1.9828	1.1575	-0.2251	1.6005	0.4498	0.0622	0.6435	0.276	0.4904	24.8057	11.1862	29.7548
2	5.9402	-2.1493	1.4075	5.1743	-0.0742	6.4304	-0.5901	-0.665	-0.4084	1.2882	0.1226	1.0455	1.0679	-0.6421	0.4675	0.7725	-0.1002	0.4118	0.3321	0.0774	0.4901	6.917	22.8112	28.4568
3	2.2221	-0.1568	-2.153	4.7474	-0.1193	4.5012	-0.1987	-0.3054	-0.0724	0.7723	-0.0158	1.1769	0.1455	-1.1	0.2146	0.4074	-0.0576	0.2251	0.39	-0.0494	0.5626	2.608	33.2881	22.8871
4	3.2926	-1.2159	-0.9488	5.1761	0.1503	4.1489	-0.3462	-0.5844	-0.4209	0.9919	0.1991	0.4455	1.0332	0.1074	0.1471	0.7203	0.041	0.136	0.2524	0.0607	0.3133	15.8128	22.2765	24.5502
5	2.0131	-0.9435	-1.6403	3.1068	1.5643	5.3499	-0.1839	-0.3268	-0.0713	0.6277	0.2077	0.107	0.5398	0.3592	-0.0239	0.368	0.0285	-0.0571	0.1949	0.01	0.3297	23.0109	24.7896	13.7607
6	8.8894	3.3876	-4.2372	8.4869	-1.6122	4.9149	-0.2914	-0.706	-0.0133	1.2075	0.27	-0.4877	0.9888	1.2994	0.0214	0.6252	0.2182	-0.1482	0.3925	0.0282	0.2095	28.1526	22.4251	21.5605
7	0.8083	0.216	-2.1261	0.0577	-0.5681	5.5926	-0.1929	0.212	-0.4606	0.5269	-0.231	0.5408	0.9608	-0.3373	0.4239	0.8502	-0.115	0.0692	0.6431	0.0397	0.888	8.1362	15.4587	11.1623
8	3.4	-3.1275	3.2248	9.4162	1.1748	5.6809	0.0617	-0.5289	-0.2603	0.2897	-0.2382	0.7226	0.1633	-0.7732	0.1764	0.2481	-0.0267	-0.0065	0.2367	-0.0115	0.4178	14.3845	26.108	3.0386
9	4.6886	0.0996	1.535	2.797	1.3378	6.494	0.1657	0.4575	-0.2398	-0.1608	-0.129	0.3061	-0.1832	-0.4443	-0.0367	0.2317	0.0409	-0.0651	0.2768	-0.0209	0.417	13.9322	29.2745	-3.8754
10	8.6372	-1.3415	3.5127	5.4573	0.5575	4.7708	-0.1635	-1.0575	0.4642	0.7205	0.1589	-0.0193	-0.4866	0.0456	0.0046	0.5151	-0.0313	0.0138	0.1676	-0.1145	0.4419	18.5467	41.8752	21.4916

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	X-RAY DIFFRACTION	1	A	A	15 - 45	15 - 45
2	X-RAY DIFFRACTION	2	A	A	46 - 78	46 - 78
3	X-RAY DIFFRACTION	3	A	A	79 - 117	79 - 117
4	X-RAY DIFFRACTION	4	A	A	118 - 173	118 - 173
5	X-RAY DIFFRACTION	5	A	A	189 - 245	189 - 245
6	X-RAY DIFFRACTION	6	A	A	246 - 258	246 - 258
7	X-RAY DIFFRACTION	7	A	A	259 - 269	259 - 269
8	X-RAY DIFFRACTION	8	A	A	270 - 278	270 - 278
9	X-RAY DIFFRACTION	9	A	A	279 - 317	279 - 317
10	X-RAY DIFFRACTION	10	A	A	318 - 329	318 - 329

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