PDB-3l84: High resolution crystal structure of transketolase from Campyloba...

ID or keywords:

Entry

Database: PDB / ID: 3l84

Title

High resolution crystal structure of transketolase from Campylobacter jejuni subsp. jejuni NCTC 11168

Components

Transketolase

Keywords

TRANSFERASE / transketolase / tkt / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID

Function / homology

Function and homology information

transketolase / transketolase activity / metal ion binding
Similarity search - Function

Biological species

Campylobacter jejuni (Campylobacter)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

SAD / Resolution: 1.36 Å

Authors

Nocek, B. / Makowska-Grzyska, M. / Maltseva, N. / Grimshaw, S. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: High resolution crystal structure of transketolase from Campylobacter jejuni subsp. jejuni NCTC 11168
Authors: Nocek, B. / Makowska-Grzysa, M. / Maltseva, N. / Grimshaw, S. / Anderson, W.F. / Joachimiak, A.

History

Deposition	Dec 29, 2009	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 9, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Advisory / Version format compliance
Revision 1.2	Feb 22, 2012	Group: Structure summary
Revision 1.3	Nov 6, 2024	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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	3l84.cif.gz	155 KB	Display	PDBx/mmCIF format
PDB format	pdb3l84.ent.gz	121.3 KB	Display	PDB format
PDBx/mmJSON format	3l84.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3l84_validation.pdf.gz	443.1 KB	Display	wwPDB validaton report
Full document	3l84_full_validation.pdf.gz	449.3 KB	Display
Data in XML	3l84_validation.xml.gz	35.8 KB	Display
Data in CIF	3l84_validation.cif.gz	52.9 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/l8/3l84 ftp://data.pdbj.org/pub/pdb/validation_reports/l8/3l84	HTTPS FTP

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Related structure data

Similar structure data	3m34-1 5i51-1 6jml-2 3m6l-1 1itz-2 6m1w-1 6bb1-2 5xt0-1 5xvt-1 3m7i-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
Other databases	TargetDB: idp90564

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#153 - Sep 2012 Pyruvate Dehydrogenase Complex similarity (6) #154 - Oct 2012 Citric Acid Cycle similarity (4) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1)

Deposited unit

A: Transketolase

hetero molecules

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

1

A: Transketolase

hetero molecules

A: Transketolase

hetero molecules

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

Unit cell

Length a, b, c (Å)	129.493, 71.181, 69.416
Angle α, β, γ (deg.)	90.00, 109.77, 90.00
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-920- HOH
2	1	A-953- HOH
3	1	A-1230- HOH

Details

likely dimer

#1: Protein	Transketolase Mass: 70148.406 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: subsp. jejuni NCTC 11168 / Gene: tkt, Cj1645 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Magic / References: UniProt: Q0P7Y3, transketolase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Chemical	ChemComp-ACT / ACETATE ION Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₃O₂
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 737 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.68 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Tacsimate, Hepes, 10 % 5000 PEGMMe, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9794 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2009 / Details: mirrors
Radiation	Monochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.9794 Å / Relative weight: 1
Reflection	Resolution: 1.35→40 Å / Num. all: 128010 / Num. obs: 127117 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / B_iso Wilson estimate: 23.2 Å² / R_merge(I) obs: 0.07 / Net I/σ(I): 35.8
Reflection shell	Resolution: 1.35→1.37 Å / Redundancy: 4.6 % / R_merge(I) obs: 0.69 / Mean I/σ(I) obs: 2.3 / Num. unique all: 6289 / % possible all: 98.2

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
HKL-3000		phasing
REFMAC	5.5.0102	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

SAD / Resolution: 1.36→40 Å / Cor.coef. F_o:F_c: 0.981 / Cor.coef. F_o:F_c free: 0.976 / SU B: 1.52 / SU ML: 0.028 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R: 0.044 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.15171	6369	5 %	RANDOM
R_work	0.13167	-	-	-
all	0.1327	128010	-	-
obs	0.13268	120713	99.08 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK

Displacement parameters

B_iso mean: 8.444 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.25 Å²	0 Å²	-0.21 Å²
2-	-	0.19 Å²	0 Å²
3-	-	-	-0.08 Å²

Refinement step

Cycle: LAST / Resolution: 1.36→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4901	0	16	737	5654

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.014	0.022	5142
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	3512
X-RAY DIFFRACTION	r_angle_refined_deg	1.501	1.964	6963
X-RAY DIFFRACTION	r_angle_other_deg	0.933	3	8639
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.794	5	672
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.987	25.294	238
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	12.242	15	911
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	13.81	15	16
X-RAY DIFFRACTION	r_chiral_restr	0.09	0.2	759
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	5804
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	1016
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	0.799	1.5	3196
X-RAY DIFFRACTION	r_mcbond_other	0.248	1.5	1313
X-RAY DIFFRACTION	r_mcangle_it	1.393	2	5116
X-RAY DIFFRACTION	r_scbond_it	2.447	3	1946
X-RAY DIFFRACTION	r_scangle_it	3.88	4.5	1826
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.356→1.391 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.233	433	-
R_work	0.219	8673	-
obs	-	-	96.13 %

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	9.1027	1.9514	4.9501	7.2283	-3.3684	6.3434	0.2631	-0.2316	-0.7305	-0.1143	-0.018	-0.2364	0.3579	-0.3295	-0.2451	0.1049	-0.0329	-0.0333	0.0895	-0.0365	0.1677	31.4773	10.3728	-15.6556
2	0.6941	0.4683	-0.0503	1.1929	0.2999	0.4303	-0.0276	0.1227	-0.1094	-0.1309	0.0396	-0.0052	-0.0108	-0.0321	-0.012	0.0726	0.0047	-0.0158	0.0803	-0.0286	0.0647	40.4493	24.3575	-18.523
3	0.5425	-0.0339	-0.3361	0.7661	0.1598	1.1647	0.0558	0.0243	-0.0751	-0.0213	-0.0589	0.0338	0.0466	-0.1234	0.0031	0.058	-0.0241	-0.021	0.0666	-0.0074	0.1053	33.0502	20.3952	-1.5116
4	0.565	0.2285	-0.2459	0.1531	-0.1083	0.6399	0.0186	0.0507	-0.0278	-0.013	-0.0077	0.05	-0.0021	-0.0403	-0.0109	0.0661	0.0009	-0.0098	0.0742	-0.0122	0.084	38.3593	31.399	-7.8157
5	1.0188	0.3684	-0.4775	0.5251	-0.7009	1.4053	0.0196	-0.0124	-0.1332	-0.0112	-0.018	0.0312	0.0162	-0.0743	-0.0016	0.0667	-0.0225	-0.002	0.0618	0.0071	0.0965	45.3668	24.2671	7.6742
6	0.5899	0.1191	0.1544	0.1637	0.0779	0.1403	0.0498	0.0247	-0.2058	-0.0148	-0.0185	-0.0089	0.0425	0.0083	-0.0312	0.0714	-0.0021	-0.017	0.0382	-0.0094	0.1345	55.6101	16.1802	-4.0331
7	1.9332	1.4706	-0.0966	2.0332	0.4106	7.121	0.0392	-0.0157	-0.24	-0.0353	-0.0329	0.0472	0.3117	-0.1919	-0.0063	0.0905	-0.0114	-0.0355	0.0366	-0.0311	0.1989	40.683	6.6687	-8.2856
8	0.4864	0.0911	0.133	0.5753	-0.335	2.5724	0.0852	0.0947	-0.2215	-0.0934	0.0061	-0.0449	0.1855	0.001	-0.0913	0.0701	0.0033	-0.0111	0.0508	-0.0418	0.1511	48.8037	13.4358	-11.7922
9	6.1466	2.0216	2.0293	1.7542	1.3912	2.9219	-0.163	0.4634	-0.1898	-0.3343	0.1802	-0.1037	-0.0796	0.0475	-0.0172	0.1062	0.0008	0.0022	0.1112	-0.0611	0.0443	41.6149	23.5083	-28.2705
10	1.2482	0.3582	-0.9637	0.6311	-0.2198	3.0888	0.0009	0.2007	-0.1181	-0.0602	-0.0116	0.15	0.1177	-0.3877	0.0107	0.0847	-0.0078	-0.0269	0.1496	-0.0395	0.0849	27.5204	22.7375	-17.2247
11	2.1667	1.3628	1.1763	1.159	0.4731	7.2192	0.0477	-0.0551	-0.0584	0.0277	-0.0502	0.0512	0.1498	-0.0412	0.0025	0.049	-0.026	0.0125	0.077	0.0069	0.0972	27.33	20.7699	12.3615
12	2.4785	3.0106	1.0751	4.3142	0.5751	1.4429	0.0739	-0.2476	0.3098	0.0567	-0.1989	0.4385	-0.0374	-0.1359	0.125	0.0877	-0.042	0.0162	0.1459	-0.0114	0.1315	36.9574	34.6723	21.6412
13	2.9724	0.162	-0.9577	1.1427	-0.1966	1.6392	0.0057	-0.1016	0.014	0.0713	0.0287	0.0363	-0.0677	-0.004	-0.0344	0.0837	-0.0205	0.0205	0.1373	-0.0163	0.0067	54.9675	47.5394	30.1197
14	3.4368	1.6636	0.2642	1.0179	0.4158	0.7188	0.1583	-0.2649	-0.1024	0.1667	-0.1237	-0.0166	0.0448	-0.0628	-0.0346	0.0951	-0.0368	0.0198	0.124	0.0126	0.0513	55.9455	39.1852	25.3342
15	0.6298	0.0774	0.1165	0.3055	0.1208	0.3432	0.0516	-0.0765	-0.0746	0.0408	-0.0389	0.0156	0.0211	-0.0279	-0.0126	0.0665	-0.0211	0.0037	0.0737	0.0136	0.0688	56.532	32.5401	12.6714
16	0.3712	0.0439	0.0302	0.1586	-0.0275	0.2373	0.0516	-0.0694	0.0071	0.015	-0.0304	-0.0058	0.0139	-0.01	-0.0212	0.0752	-0.0222	0.0109	0.0824	-0.0018	0.053	63.3443	46.0026	12.9289
17	2.5569	0.7921	0.8802	0.5878	0.3626	1.6437	0.1106	-0.1117	-0.1589	0.0488	-0.0296	-0.0202	-0.016	-0.0095	-0.081	0.0757	-0.0216	0.0143	0.077	-0.0019	0.0498	59.7058	45.2435	16.3927
18	2.2393	0.2021	0.9611	0.9652	-0.2957	2.0839	0.083	-0.2788	0.2286	0.106	0.0055	0.1187	-0.0636	-0.1131	-0.0884	0.0753	-0.0135	0.049	0.0885	-0.0521	0.0698	57.8212	60.7562	21.8612
19	2.0593	0.2266	0.0575	1.3713	0.0701	0.974	0.044	-0.1269	0.3755	0.0164	0.0208	0.035	-0.1389	0.027	-0.0648	0.0838	-0.0234	0.0462	0.0491	-0.0385	0.0965	63.7463	65.3827	15.6009
20	0.7673	-0.3388	0.1762	0.7315	-0.0057	0.3455	0.0427	-0.0136	0.1332	0.0085	-0.0511	-0.0811	-0.0405	0.0219	0.0084	0.0753	-0.0252	0.0236	0.0625	-0.0046	0.0738	75.2471	57.2668	10.5908

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	1 - 8
2	X-RAY DIFFRACTION	2	A	9 - 40
3	X-RAY DIFFRACTION	3	A	41 - 53
4	X-RAY DIFFRACTION	4	A	54 - 106
5	X-RAY DIFFRACTION	5	A	107 - 143
6	X-RAY DIFFRACTION	6	A	144 - 215
7	X-RAY DIFFRACTION	7	A	216 - 225
8	X-RAY DIFFRACTION	8	A	226 - 253
9	X-RAY DIFFRACTION	9	A	254 - 274
10	X-RAY DIFFRACTION	10	A	275 - 294
11	X-RAY DIFFRACTION	11	A	295 - 313
12	X-RAY DIFFRACTION	12	A	314 - 326
13	X-RAY DIFFRACTION	13	A	327 - 337
14	X-RAY DIFFRACTION	14	A	338 - 356
15	X-RAY DIFFRACTION	15	A	357 - 439
16	X-RAY DIFFRACTION	16	A	440 - 487
17	X-RAY DIFFRACTION	17	A	488 - 502
18	X-RAY DIFFRACTION	18	A	503 - 521
19	X-RAY DIFFRACTION	19	A	522 - 580
20	X-RAY DIFFRACTION	20	A	581 - 632

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