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- PDB-2x62: CRYSTAL STRUCTURE OF THE SIALYLTRANSFERASE CST-II Y81F IN COMPLEX... -

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Open data

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Basic information

Entry

Database: PDB / ID: 2x62

Title

CRYSTAL STRUCTURE OF THE SIALYLTRANSFERASE CST-II Y81F IN COMPLEX WITH CMP

Components

ALPHA-2,3-/2,8-SIALYLTRANSFERASE

Keywords

TRANSFERASE / GLYCOSYLTRANSFERASE / GTA

Function / homology

Function and homology information

glycosyltransferase activity
Similarity search - Function

Biological species

CAMPYLOBACTER JEJUNI (Campylobacter)

Method

X-RAY DIFFRACTION /

MOLECULAR REPLACEMENT / Resolution: 2.2 Å

Authors

Lee, H.J. / Lairson, L.L. / Rich, J.R. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J.

Citation

Journal: J.Biol.Chem. / Year: 2011
Title: Structural and Kinetic Analysis of Substrate Binding to the Sialyltransferase Cst-II from Campylobacter Jejuni.
Authors: Lee, H.J. / Lairson, L.L. / Rich, J.R. / Lameignere, E. / Wakarchuk, W.W. / Withers, S.G. / Strynadka, N.C.J.

History

Deposition	Feb 14, 2010	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Feb 23, 2011	Provider: repository / Type: Initial release
Revision 1.1	Sep 28, 2011	Group: Database references / Version format compliance
Revision 1.2	Oct 19, 2011	Group: Database references
Revision 1.3	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewer	Molecule: MolmilJmol/JSmol

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Downloads & links

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Download

PDBx/mmCIF format	2x62.cif.gz	227 KB	Display	PDBx/mmCIF format
PDB format	pdb2x62.ent.gz	185 KB	Display	PDB format
PDBx/mmJSON format	2x62.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	2x62_validation.pdf.gz	1.1 MB	Display	wwPDB validaton report
Full document	2x62_full_validation.pdf.gz	1.1 MB	Display
Data in XML	2x62_validation.xml.gz	23.4 KB	Display
Data in CIF	2x62_validation.cif.gz	32.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/x6/2x62 ftp://data.pdbj.org/pub/pdb/validation_reports/x6/2x62	HTTPS FTP

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Related structure data

Related structure data	2x61C 2x63C 1ro8S 1ro7 S: Starting model for refinement C: citing same article (ref.)
Similar structure data	2x61-2 2x61-1 1ro7-d 2x63-1 1ro8-1 2drj-1 5zbm-2 6a4h-1 5zbm-1 1al7-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI

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Assembly

Deposited unit

A: ALPHA-2,3-/2,8-SIALYLTRANSFERASE

B: ALPHA-2,3-/2,8-SIALYLTRANSFERASE

hetero molecules

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

1

A: ALPHA-2,3-/2,8-SIALYLTRANSFERASE

hetero molecules

A: ALPHA-2,3-/2,8-SIALYLTRANSFERASE

hetero molecules

A: ALPHA-2,3-/2,8-SIALYLTRANSFERASE

hetero molecules

A: ALPHA-2,3-/2,8-SIALYLTRANSFERASE

hetero molecules

defined by author&software
124 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: ALPHA-2,3-/2,8-SIALYLTRANSFERASE

hetero molecules

B: ALPHA-2,3-/2,8-SIALYLTRANSFERASE

hetero molecules

B: ALPHA-2,3-/2,8-SIALYLTRANSFERASE

hetero molecules

B: ALPHA-2,3-/2,8-SIALYLTRANSFERASE

hetero molecules

defined by author&software
124 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	116.617, 116.617, 46.836
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	75
Space group name H-M	P4

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Components

#1: Protein	ALPHA-2,3-/2,8-SIALYLTRANSFERASE / ALPHA-2\ / 3/8-SIALYLTRANSFERASE / SIALYLTRANSFERASE CST-II Mass: 30501.633 Da / Num. of mol.: 2 / Fragment: RESIDUES 1-259 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) CAMPYLOBACTER JEJUNI (Campylobacter) / Strain: OH4384 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q9LAK3, Transferases; Glycosyltransferases; Transferring other glycosyl groups
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Chemical	ChemComp-CH / N3-PROTONATED CYTIDINE-5'-MONOPHOSPHATE Type: RNA linking / Mass: 324.204 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₉H₁₅N₃O₈P
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, ILE 53 TO SER ENGINEERED RESIDUE IN CHAIN A, TYR 81 TO PHE ...ENGINEERED RESIDUE IN CHAIN A, ILE 53 TO SER ENGINEERED RESIDUE IN CHAIN A, TYR 81 TO PHE ENGINEERED RESIDUE IN CHAIN A, GLU 222 TO GLY ENGINEERED RESIDUE IN CHAIN B, ILE 53 TO SER ENGINEERED RESIDUE IN CHAIN B, TYR 81 TO PHE ENGINEERED RESIDUE IN CHAIN B, GLU 222 TO GLY

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Experimental details

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.49 Å³/Da / Density % sol: 50 % / Description: NONE
Crystal grow	pH: 7.5 Details: 100 MM HEPES5, PH 7.5, 8% (W/V) POLYETHYLENE GLYCOL 6000, AND 5% (V/V) 2-METHYL-2, 4-PENTANEDIOL

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: ROTATING ANODE / Wavelength: 1.5418
Detector	Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 26, 2009 / Details: MIRRORS
Radiation	Monochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1.5418 Å / Relative weight: 1
Reflection	Resolution: 2.2→35 Å / Num. obs: 30500 / % possible obs: 94.2 % / Observed criterion σ(I): 2.5 / Redundancy: 2.3 % / R_merge(I) obs: 0.05 / Net I/σ(I): 17.7
Reflection shell	Resolution: 2.2→2.28 Å / Redundancy: 1.8 % / R_merge(I) obs: 0.25 / Mean I/σ(I) obs: 2.7 / % possible all: 87.7

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0066	refinement
HKL-2000		data reduction
SCALEPACK		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1RO8

Resolution: 2.2→40 Å / Cor.coef. F_o:F_c: 0.961 / Cor.coef. F_o:F_c free: 0.939 / SU B: 12.09 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.258 / ESU R Free: 0.205 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.22787	1547	5.1 %	RANDOM
R_work	0.17679	-	-	-
obs	0.17939	28950	94.13 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å

Displacement parameters

B_iso mean: 41.42 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.69 Å²	0 Å²	0 Å²
2-	-	-1.69 Å²	0 Å²
3-	-	-	3.39 Å²

Refinement step

Cycle: LAST / Resolution: 2.2→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4236	0	50	191	4477

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	4411
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	3748
X-RAY DIFFRACTION	r_angle_refined_deg	1.228	1.96	5949
X-RAY DIFFRACTION	r_angle_other_deg	1.126	3.001	8775
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.911	5	504
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.049	24.936	233
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.301	15	756
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	12.136	15	6
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	612
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	4845
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	961
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	0.529	1.5	2529
X-RAY DIFFRACTION	r_mcbond_other	0.116	1.5	1023
X-RAY DIFFRACTION	r_mcangle_it	0.983	2	4073
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.478	3	1882
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	2.291	4.5	1875
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
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	0.274	96	-
R_work	0.237	1927	-
obs	-	-	86.01 %

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	2.5932	0.2253	0.1783	3.5878	-1.234	1.7184	-0.1046	-0.3244	-0.0918	0.3487	0.156	0.4108	-0.1276	-0.1956	-0.0514	0.0482	0.0159	0.0605	0.0952	-0.0035	0.0861	26.0716	47.764	-2.2493
2	1.4818	-1.3318	0.3933	2.99	-0.6381	0.9564	-0.0062	-0.0102	0.0469	0.0639	0.0053	-0.1586	-0.0456	0.076	0.0009	0.0286	-0.0133	0.0018	0.0785	-0.0113	0.0724	45.1231	50.0751	-6.9004
3	2.5393	-0.6671	0.203	1.9764	-0.1535	0.5706	0.0031	0.0637	-0.3515	0.0065	0.015	0.31	0.0828	-0.0241	-0.0181	0.0569	-0.0338	0.0099	0.0439	0.0097	0.0964	34.7702	38.21	-7.5917
4	5.8277	-5.027	3.9013	4.3609	-3.369	2.6201	0.5699	0.2642	0.0992	-0.7456	-0.417	-0.1648	0.5534	0.1545	-0.1529	0.7038	0.0208	0.0499	0.5739	-0.001	0.7395	32.4471	38.4093	-17.7528
5	7.5868	0.6718	2.1016	3.6427	0.3805	5.2046	0.1957	-0.0999	-0.768	0.4202	0.047	0.2009	0.6445	-0.0017	-0.2426	0.1363	-0.0072	0.0241	0.0553	0.0529	0.1962	40.5069	30.6136	2.0735
6	4.2051	-1.6481	-1.8678	0.7905	1.0706	2.7972	0.0545	-0.0399	-0.4501	0.1626	-0.0163	0.2892	0.2369	-0.4056	-0.0382	0.2703	-0.0441	0.184	0.2305	0.161	0.3927	22.8107	32.5299	5.0637
7	7.3326	3.0936	-1.196	4.8531	-2.5853	4.4388	-0.208	0.4682	0.0367	-0.3915	0.1956	0.3433	0.1543	-0.1342	0.0124	0.0993	0.0243	-0.0526	0.0557	-0.0195	0.0606	28.0335	56.9186	-16.0397
8	4.612	-0.7999	0.362	5.6659	0.2417	9.9827	0.0707	-0.2956	0.477	0.209	0.0814	0.0054	0.6919	0.272	-0.1521	0.0563	0.019	0.0089	0.041	0.0232	0.3193	-6.3816	34.8802	-10.6023
9	3.5879	-0.8356	-1.1373	3.2781	0.5022	1.0677	0.0212	-0.0871	0.8259	-0.1406	0.046	-0.1211	-0.0939	0.1192	-0.0672	0.0677	-0.0115	-0.0026	0.0602	0.059	0.3115	2.0482	34.9232	-16.625
10	3.4371	0.4366	-0.8085	1.6899	-0.6886	0.4034	-0.0102	0.2194	0.1618	-0.2403	0.0498	0.0627	0.0816	-0.0413	-0.0395	0.1187	-0.0124	-0.0043	0.1179	0.0719	0.1269	0.7561	17.8657	-19.8913
11	1.9985	0.61	0.3133	3.2031	0.5783	2.1595	-0.0453	0.0415	0.454	-0.1816	0.0358	0.4337	-0.0724	-0.0656	0.0095	0.0298	0.0125	-0.0273	0.0542	0.067	0.2072	-13.7926	22.334	-15.4925
12	2.7895	-0.1543	0.463	0.5945	0.0054	0.1905	0.209	0.8043	0.4127	-0.5843	-0.0547	0.1726	-0.0618	0.0378	-0.1543	0.6343	0.075	-0.0042	0.4298	0.2444	0.5498	-6.3138	35.333	-29.8188
13	1.6818	0.0775	-0.9378	4.2531	-0.3267	1.5417	0.0995	-0.1108	0.5905	0.0431	0.0538	0.6311	-0.1753	0.1137	-0.1533	0.0442	0.016	0.0251	0.0492	0.008	0.3932	-15.4592	36.0962	-9.972
14	3.1702	-1.3023	-1.7678	6.1526	2.1875	4.6397	-0.0487	0.5932	0.4825	-1.1736	-0.0402	-0.1377	-0.1597	0.0759	0.089	0.2731	-0.0031	0.0404	0.2513	0.2444	0.2685	9.2307	28.5216	-29.264

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 79
2	X-RAY DIFFRACTION	2	A	80 - 116
3	X-RAY DIFFRACTION	3	A	117 - 173
4	X-RAY DIFFRACTION	4	A	174 - 190
5	X-RAY DIFFRACTION	5	A	191 - 207
6	X-RAY DIFFRACTION	6	A	208 - 234
7	X-RAY DIFFRACTION	7	A	235 - 259
8	X-RAY DIFFRACTION	8	B	1 - 12
9	X-RAY DIFFRACTION	9	B	13 - 70
10	X-RAY DIFFRACTION	10	B	71 - 108
11	X-RAY DIFFRACTION	11	B	109 - 151
12	X-RAY DIFFRACTION	12	B	152 - 188
13	X-RAY DIFFRACTION	13	B	189 - 234
14	X-RAY DIFFRACTION	14	B	235 - 259

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