PDB-3ckn: Crystal Structure of a Mycobacterial Protein

ID or keywords:

Entry

Database: PDB / ID: 3ckn

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 /

SYNCHROTRON / Rigid body refinement / Resolution: 2.2 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 / pdbx_struct_conn_angle / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _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	3ckn.cif.gz	72.1 KB	Display	PDBx/mmCIF format
PDB format	pdb3ckn.ent.gz	53.2 KB	Display	PDB format
PDBx/mmJSON format	3ckn.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Summary document	3ckn_validation.pdf.gz	861.5 KB	Display	wwPDB validaton report
Full document	3ckn_full_validation.pdf.gz	864.5 KB	Display
Data in XML	3ckn_validation.xml.gz	12.9 KB	Display
Data in CIF	3ckn_validation.cif.gz	17.1 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ck/3ckn ftp://data.pdbj.org/pub/pdb/validation_reports/ck/3ckn	HTTPS FTP

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Related structure data

Related structure data	3ckjC 3ckoC 3ckqC 3ckvC C: citing same article (ref.)
Similar structure data	3cko-1 4nl1-1 3ckj-1 4y9x-1 5juc-1 5dmn-d 4y6u-1 6y9k-1 3ckv-1 6shs-d 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

35.4 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
70.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	86.862, 86.862, 104.243
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-MN / MANGANESE (II) ION Mass: 54.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mn
#3: Chemical	ChemComp-SO4 / SULFATE ION Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO₄
#4: Chemical	ChemComp-UDP / URIDINE-5'-DIPHOSPHATE Type: RNA linking / Mass: 404.161 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₉H₁₄N₂O₁₂P₂ / Comment: UDP*YM
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 36 / 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: 2.82 Å³/Da / Density % sol: 56.43 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7 Details: 1 M Ammonium sulphate, 0.1 M HEPES pH 7.0, 20 mM Manganese chloride, 1 mM Sodium thiosulphate, 100 mM uridine-5 -diphosphate, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 1.0053 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 16, 2006
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.0053 Å / Relative weight: 1
Reflection	Resolution: 2.2→100 Å / Num. all: 20557 / Num. obs: 19867 / Redundancy: 9.7 % / R_sym value: 0.068 / Net I/σ(I): 5.9
Reflection shell	Highest resolution: 2.2 Å / R_sym value: 0.554

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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: 2.2→50 Å / Cor.coef. F_o:F_c: 0.953 / Cor.coef. F_o:F_c free: 0.935 / SU B: 10.211 / SU ML: 0.139 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.216 / ESU R Free: 0.178 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23243	667	3.2 %	RANDOM
R_work	0.20569	-	-	-
obs	0.20657	19867	98.38 %	-

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: 30.916 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.12 Å²	0 Å²	0 Å²
2-	-	0.12 Å²	0 Å²
3-	-	-	-0.24 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2231	0	31	36	2298

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.009	0.022	2339
X-RAY DIFFRACTION	r_bond_other_d
X-RAY DIFFRACTION	r_angle_refined_deg	1.158	2.005	3218
X-RAY DIFFRACTION	r_angle_other_deg
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.217	5	310
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.961	22.874	87
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.321	15	350
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.251	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.073	0.2	381
X-RAY DIFFRACTION	r_gen_planes_refined	0.003	0.02	1772
X-RAY DIFFRACTION	r_gen_planes_other
X-RAY DIFFRACTION	r_nbd_refined	0.186	0.2	1005
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined	0.302	0.2	1564
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined	0.153	0.2	94
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	0.187	0.2	51
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined	0.135	0.2	7
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	0.459	1.5	1544
X-RAY DIFFRACTION	r_mcbond_other
X-RAY DIFFRACTION	r_mcangle_it	0.767	2	2440
X-RAY DIFFRACTION	r_scbond_it	1.115	3	892
X-RAY DIFFRACTION	r_scangle_it	1.843	4.5	772
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.2→2.257 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.343	54	-
R_work	0.25	1445	-
obs	-	-	99.67 %

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	3.2726	4.1089	6.0717	5.1588	7.6232	11.2647	-1.0693	0.0272	-0.3562	2.2389	1.7072	-0.9217	1.983	2.5803	-0.6379	1.4838	0.6154	0.1685	0.0016	0.4476	0.6307	26.6767	7.3714	22.6807
2	1.7646	-2.4687	2.8659	3.4537	-4.0094	4.6546	-0.7506	-2.2656	-0.4942	2.1393	1.5726	-0.8375	1.4751	2.1726	-0.8221	1.5868	0.3994	0.3167	0.5623	0.3111	0.4074	23.4874	14.1886	34.8279
3	1.9676	-1.353	-1.2864	5.0426	0.5362	3.7717	-0.4398	-0.485	-0.2947	1.3704	0.1386	1.3522	0.5944	-0.5206	0.3012	0.6203	-0.053	0.4261	0.1764	0.0113	0.5025	7.0816	26.6604	25.1732
4	2.429	-0.7652	-1.8254	4.5991	-0.399	7.2972	-0.4089	-0.5716	-0.5388	1.3705	0.2768	0.3554	1.312	0.5152	0.1321	0.7778	0.1716	0.132	0.1846	0.1087	0.3592	21.3758	16.5832	20.2926
5	2.1772	-0.9736	-1.2097	3.5768	1.4513	4.2101	-0.2529	-0.4434	-0.0854	0.783	0.1904	0.111	0.49	0.4311	0.0624	0.3614	0.0404	-0.0129	0.1265	0.0131	0.2357	23.437	25.031	14.7774
6	10.0203	4.1263	-3.3336	8.097	-0.7586	5.4768	-0.4111	-0.7592	-0.2336	1.4474	0.3418	-0.2714	0.7321	1.2713	0.0693	0.697	0.2668	-0.1037	0.2728	0.0645	0.1723	28.1132	21.0031	21.3164
7	4.8806	-5.7942	17.0818	6.8788	-20.2794	59.7856	0.2667	0.5686	-1.2682	0.5387	0.1468	1.8806	1.509	-1.0818	-0.4135	0.6594	-0.3157	0.2242	0.1885	0.1076	0.9087	8.2528	14.9474	11.0828
8	4.2271	-0.6117	0.9444	3.673	1.0486	5.4278	0.1154	0.2784	-0.2385	-0.0624	-0.1721	0.445	0.0826	-0.3489	0.0568	0.1695	0.0043	-0.035	0.1506	-0.0446	0.329	15.0947	27.6213	-1.7761
9	6.6031	3.9078	6.4325	5.5132	5.8294	9.3635	0.1512	0.2663	0.0188	-0.1112	-0.3102	0.6745	-0.3618	-0.5749	0.159	0.1723	0.0365	-0.103	0.2767	-0.0812	0.4269	8.8736	30.6916	-3.8491
10	7.4419	-1.2148	-0.2393	8.3229	1.3737	9.6637	-0.1065	-0.9705	0.406	1.2699	0.2274	0.0089	-0.3892	0.4691	-0.1209	0.5268	-0.0298	0.0411	0.1749	-0.1156	0.3612	18.9761	41.2228	21.7786

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 - 27	15 - 27
2	X-RAY DIFFRACTION	2	A	A	28 - 48	28 - 48
3	X-RAY DIFFRACTION	3	A	A	49 - 154	49 - 154
4	X-RAY DIFFRACTION	4	A	A	155 - 193	155 - 193
5	X-RAY DIFFRACTION	5	A	A	194 - 245	194 - 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 - 307	270 - 307
9	X-RAY DIFFRACTION	9	A	A	308 - 317	308 - 317
10	X-RAY DIFFRACTION	10	A	A	318 - 329	318 - 329

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