PDB-3nav: Crystal structure of an alpha subunit of tryptophan synthase from...

ID or keywords:

Entry

Database: PDB / ID: 3nav

Title

Crystal structure of an alpha subunit of tryptophan synthase from Vibrio cholerae O1 biovar El Tor str. N16961

Components

Tryptophan synthase alpha chain

Keywords

LYASE / Tryptophan synthase / alpha subunit / STRUCTURAL GENOMICS / CSGID / Center for Structural Genomics of Infectious Diseases

Function / homology

Function and homology information

tryptophan synthase / tryptophan synthase activity / tryptophan biosynthetic process / cytosol
Similarity search - Function

Biological species

Vibrio cholerae O1 biovar El Tor (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Nocek, B. / Makowska-Grzyska, M. / Kwon, K. / Anderson, A. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: Crystal structure of an alpha subunit of tryptophan synthase from Vibrio cholerae O1 biovar El Tor str. N16961
Authors: Nocek, B. / Makowska-Grzyska, M. / Kwon, K. / Anderson, W. / Joachimiak, A. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jun 2, 2010	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jun 30, 2010	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Version format compliance
Revision 1.2	Sep 6, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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	3nav.cif.gz	218.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3nav.ent.gz	177.3 KB	Display	PDB format
PDBx/mmJSON format	3nav.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	3nav_validation.pdf.gz	446.1 KB	Display	wwPDB validaton report
Full document	3nav_full_validation.pdf.gz	448.6 KB	Display
Data in XML	3nav_validation.xml.gz	23.8 KB	Display
Data in CIF	3nav_validation.cif.gz	35.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/na/3nav ftp://data.pdbj.org/pub/pdb/validation_reports/na/3nav	HTTPS FTP

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Related structure data

Related structure data	1xc4S S: Starting model for refinement
Similar structure data	2abw-d 6skr-d 1k57-2 2nn7-d 2foy-d 2hp6-d 1k56-2 1k6s-d 2hpb-d 2nn1-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	TargetDB: idp04160

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#228 - Dec 2018 Directed Evolution of Enzymes similarity (6)

Deposited unit

A: Tryptophan synthase alpha chain

B: Tryptophan synthase alpha chain

hetero molecules

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

1

Idetical with deposited unit
defined by software

Unit cell

Length a, b, c (Å)	57.594, 60.380, 141.197
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	19
Space group name H-M	P2₁2₁2₁

#1: Protein	Tryptophan synthase alpha chain Mass: 28788.865 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria) Strain: N16961 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 magic References: UniProt: C3LLL5, UniProt: Q9KST7*PLUS, tryptophan synthase
#2: Chemical	ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₂H₆O₂
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 381 / 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: 2.13 Å³/Da / Density % sol: 42.31 %
Crystal grow	Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 M Ammonium flouride 20% Peg 3350, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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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: May 18, 2010 / 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: 2.1→40 Å / Num. all: 29900 / Num. obs: 29864 / % possible obs: 99.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / B_iso Wilson estimate: 31 Å² / R_merge(I) obs: 0.091 / Net I/σ(I): 10
Reflection shell	Resolution: 2.1→2.14 Å / Redundancy: 5.2 % / R_merge(I) obs: 0.38 / Mean I/σ(I) obs: 8.3 / Num. unique all: 1465 / % possible all: 100

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Processing

Software

Name	Version	Classification
SBC-Collect		data collection
MOLREP		phasing
REFMAC	5.5.0109	refinement
HKL-3000		data reduction
HKL-3000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1XC4

1xc4

Resolution: 2.1→40 Å / Cor.coef. F_o:F_c: 0.949 / Cor.coef. F_o:F_c free: 0.916 / SU B: 11.182 / SU ML: 0.134 / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / ESU R Free: 0.196 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.23304	1491	5.1 %	RANDOM
R_work	0.17914	-	-	-
obs	0.18201	27827	99.32 %	-
all	-	29318	-	-

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: 23.31 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.91 Å²	0 Å²	0 Å²
2-	-	-1 Å²	0 Å²
3-	-	-	0.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.1→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3882	0	4	381	4267

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.02	0.022	3965
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	2634
X-RAY DIFFRACTION	r_angle_refined_deg	1.668	1.979	5396
X-RAY DIFFRACTION	r_angle_other_deg	1.17	3	6483
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.231	5	517
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.029	25.273	165
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.876	15	632
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	20.284	15	19
X-RAY DIFFRACTION	r_chiral_restr	0.097	0.2	628
X-RAY DIFFRACTION	r_gen_planes_refined	0.009	0.021	4456
X-RAY DIFFRACTION	r_gen_planes_other	0.001	0.02	731
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	1.03	1.5	2597
X-RAY DIFFRACTION	r_mcbond_other	0.201	1.5	1034
X-RAY DIFFRACTION	r_mcangle_it	1.889	2	4157
X-RAY DIFFRACTION	r_scbond_it	2.645	3	1368
X-RAY DIFFRACTION	r_scangle_it	4.429	4.5	1238
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.277	104	-
R_work	0.193	2028	-
obs	-	-	99.58 %

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	5.2696	0.5861	3.5762	0.3159	-0.5421	2.2062	-0.0953	0.1292	0.3951	-0.0729	-0.0478	0.1078	-0.0506	0.2334	0.1431	0.4348	-0.0226	0.0623	0.1272	-0.0151	0.1986	15.7165	17.6073	18.5461
2	0.7552	-0.1566	0.3761	2.5201	-1.7015	1.5979	0.0385	-0.016	0.0292	-0.2394	0.0239	0.0975	-0.0165	-0.0994	-0.0624	0.2609	0.0055	-0.0043	0.2033	-0.0005	0.1972	8.1701	10.3718	14.2814
3	0.5274	0.1307	0.3464	1.0091	-0.2778	1.0616	-0.0105	0.0694	0.007	-0.0204	-0.032	-0.0933	0.0854	0.1017	0.0425	0.2096	0.0085	0.0016	0.2115	-0.0057	0.2038	19.9746	-1.8249	24.4572
4	0.6982	-0.0409	-0.7716	0.6814	0.3228	0.4433	0.0166	-0.0086	0.0379	0.0841	0.0192	-0.0027	0.006	-0.0314	-0.0358	0.2174	0.0078	-0.0115	0.226	0.02	0.2096	14.6035	-0.3579	39.8796
5	0.4657	0.3192	0.3023	1.1855	-0.066	0.2824	0.0089	-0.0584	-0.0483	0.026	-0.0147	-0.0518	0.0136	-0.0069	0.0059	0.201	0.0084	-0.001	0.2118	-0.0019	0.2065	23.1149	-1.3012	37.3743
6	0.4889	1.0113	-0.404	1.3221	0.4622	1.0688	0.0088	0.027	-0.034	-0.0882	0.0316	-0.1039	-0.0662	0.1142	-0.0404	0.2027	0.0081	0.0363	0.2579	0.0044	0.2042	24.6324	6.9624	21.3382
7	0.765	0.3238	0.3426	0.9001	0.2867	1.0456	-0.0114	-0.0541	0.0145	0.0277	-0.0032	-0.0609	-0.0202	-0.0159	0.0146	0.2187	0.0025	0.002	0.1998	0.001	0.2046	22.4233	13.3881	36.6816
8	0.982	-0.0328	-0.6277	0.4192	-0.1152	1.2013	0.0256	0.0237	0.0099	0.0726	0.014	-0.0138	-0.0489	-0.0904	-0.0397	0.2246	0.0067	0.0088	0.196	0.0052	0.2031	14.0984	17.4874	36.1836
9	9.6221	3.773	-0.751	1.1558	-0.002	-0.1202	0.023	-0.1713	0.2013	-0.0225	-0.0462	0.1282	-0.0351	0.0336	0.0232	0.2301	0.0042	-0.0033	0.2105	0.0092	0.2137	16.0097	19.5537	30.669
10	3.9158	-2.243	-3.0532	3.2007	1.5275	2.3573	0.0788	-0.0547	0.0505	-0.0109	-0.0465	-0.0415	0.0403	-0.0692	-0.0323	0.201	0.0095	-0.0396	0.2047	0.0169	0.2106	2.6359	20.388	32.5312
11	-1.7639	-3.2112	-0.8133	-3.3511	2.7612	3.1988	0.4942	-0.5707	0.5576	0.0015	-0.0284	-0.0463	0.9667	-0.3466	-0.4658	0.3549	-0.2971	-0.054	0.3868	-0.0269	0.4232	-3.306	8.3072	30.1621
12	2.0254	-1.1494	-0.3146	4.8228	-0.0127	1.055	-0.0164	0.2065	0.0897	-0.2923	0.0878	0.3048	0.1196	-0.1788	-0.0714	0.1981	-0.0018	-0.0463	0.2432	0.0151	0.2047	-1.9654	17.2483	25.4422
13	-0.1913	0.2507	-0.0148	3.6534	0.8461	1.5457	-0.0084	0.0085	-0.0503	-0.1296	-0.0226	0.0442	-0.035	-0.132	0.031	0.2059	0.0065	-0.0025	0.217	-0.0014	0.1946	0.5714	2.2871	22.8498
14	3.6745	-1.3368	-1.0626	1.9926	-0.022	1.8949	0.0761	-0.1609	-0.3137	-0.067	-0.0514	0.0223	0.2834	0.0029	-0.0247	0.2458	0.0053	-0.0291	0.1743	-0.0056	0.2363	15.1928	-12.3611	27.6759
15	2.9963	-1.7272	0.0808	2.3445	-0.5921	0.7148	0.1069	0.0896	-0.0749	-0.2156	-0.0337	0.0455	0.1606	-0.0666	-0.0732	0.258	0.0024	-0.0169	0.1888	-0.029	0.2033	9.2162	-4.969	16.9316
16	0.9288	-0.8595	-1.7976	4.9177	-1.7834	1.5932	-0.0608	-0.1352	0.1832	0.3047	0.0131	-0.3634	-0.0133	0.0784	0.0477	0.2372	-0.0048	-0.0337	0.2461	-0.0281	0.2341	16.5988	2.5995	73.2768
17	2.5716	2.4323	3.487	3.3468	1.2774	5.5539	0.1497	-0.0219	-0.0689	0.0139	0.1351	-0.1864	-0.0381	-0.1109	-0.2848	0.239	0.0132	-0.0034	0.2222	0.0194	0.1832	11.6634	-6.1275	78.3317
18	0.5468	-0.262	0.3971	0.7377	-0.4936	0.8583	-0.0347	-0.0195	0.0018	0.065	0.0413	0.023	-0.0417	-0.09	-0.0065	0.2147	-0.0025	0.0076	0.2026	-0.0031	0.1954	1.3323	5.8184	63.7419
19	0.6146	0.2915	0.1347	0.3813	0.8174	1.117	-0.0146	0.0742	-0.0303	0.0639	0.0349	-0.0583	0.0574	0.0576	-0.0203	0.2283	0.0036	-0.0107	0.2253	-0.0002	0.2183	4.0768	5.5185	44.6428
20	1.6402	0.4159	0.7716	1.2238	-0.236	0.3233	-0.0648	0.1828	-0.0524	-0.1062	0.1138	0.0377	-0.0424	0.0649	-0.049	0.2306	0.0018	0.0012	0.2117	0.003	0.1946	0.6176	14.1116	51.2288
21	1.348	-0.0944	-0.598	1.3379	0.3286	1.2454	-0.035	-0.0846	0.0506	0.1196	0.0907	0.074	-0.131	-0.0751	-0.0557	0.2352	0.0077	0.0033	0.2178	-0.0066	0.1884	5.8555	13.8693	68.6986
22	1.0411	0.0986	-0.3267	0.7851	-0.3637	0.9286	-0.0299	-0.0251	0.0068	0.0123	-0.0085	-0.0303	-0.0885	0.0947	0.0384	0.2137	-0.0127	-0.0098	0.219	-0.0102	0.1823	15.5353	13.3334	58.014
23	2.3206	0.2881	0.7566	1.2967	0.8665	2.046	0.0008	0.2933	-0.0211	0.03	0.1427	-0.0472	0.0602	0.4334	-0.1435	0.19	0.0036	-0.0215	0.2833	-0.0052	0.1869	23.9757	6.2868	53.0824
24	2.4274	2.8281	0.5601	9.038	1.9587	1.9377	-0.0295	-0.0606	-0.1409	0.1396	-0.0097	-0.1318	0.1152	0.3213	0.0391	0.1929	0.0093	-0.0294	0.2696	0.026	0.1614	21.5239	5.9049	60.9693
25	-2.6027	0.9825	-7.1949	19.3443	-4.8245	3.4694	-0.6423	-1.0185	-0.6811	-1.7051	-1.473	-0.8249	0.0712	1.0623	2.1153	0.0701	0.2944	0.1654	0.3426	0.2312	0.5967	27.1479	-6.1654	56.5572
26	0.5661	0.1208	-0.3112	1.1345	-1.3376	2.7426	0.0408	0.1212	-0.1527	-0.0555	-0.0203	0.0013	0.0845	0.0986	-0.0205	0.2107	0.0332	-0.0055	0.2109	-0.009	0.2494	15.4776	-5.3664	60.0243
27	16.9483	19.9924	6.3752	13.6652	0.3971	8.7507	-0.0138	-1.4497	0.4325	-0.534	-1.6849	-0.4911	3.071	1.2679	1.6987	0.5875	0.4914	0.2307	0.0568	0.0722	0.3257	22.8433	-13.9338	62.2115
28	1.7233	-0.5157	0.6063	0.8645	-0.4066	0.5323	0.0824	0.0536	-0.0515	-0.0317	-0.0181	0.0061	0.2117	-0.0342	-0.0643	0.2557	-0.011	-0.0124	0.1882	-0.0138	0.2039	5.4104	-7.839	60.9968
29	-0.3478	-0.6425	0.513	3.4561	-0.2782	3.9571	0.0425	-0.0707	-0.1334	-0.1352	-0.0223	0.4651	0.0495	-0.2253	-0.0202	0.1517	-0.0364	0.007	0.2685	0.0232	0.2864	-11.3556	3.0591	61.0396
30	8.2456	-5.4479	6.2328	5.0383	-3.3654	6.1646	0.1128	-0.4695	-0.1526	0.1264	0.129	0.1483	0.1519	-0.3001	-0.2419	0.2475	-0.0331	0.0052	0.197	0.0296	0.1917	0.3545	-8.1936	69.9204

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	0 - 4
2	X-RAY DIFFRACTION	2	A	5 - 21
3	X-RAY DIFFRACTION	3	A	22 - 48
4	X-RAY DIFFRACTION	4	A	49 - 64
5	X-RAY DIFFRACTION	5	A	65 - 82
6	X-RAY DIFFRACTION	6	A	83 - 97
7	X-RAY DIFFRACTION	7	A	98 - 120
8	X-RAY DIFFRACTION	8	A	121 - 142
9	X-RAY DIFFRACTION	9	A	143 - 153
10	X-RAY DIFFRACTION	10	A	154 - 173
11	X-RAY DIFFRACTION	11	A	174 - 193
12	X-RAY DIFFRACTION	12	A	194 - 211
13	X-RAY DIFFRACTION	13	A	212 - 235
14	X-RAY DIFFRACTION	14	A	236 - 250
15	X-RAY DIFFRACTION	15	A	251 - 268
16	X-RAY DIFFRACTION	16	B	0 - 8
17	X-RAY DIFFRACTION	17	B	9 - 15
18	X-RAY DIFFRACTION	18	B	16 - 52
19	X-RAY DIFFRACTION	19	B	53 - 64
20	X-RAY DIFFRACTION	20	B	65 - 80
21	X-RAY DIFFRACTION	21	B	81 - 95
22	X-RAY DIFFRACTION	22	B	96 - 127
23	X-RAY DIFFRACTION	23	B	128 - 143
24	X-RAY DIFFRACTION	24	B	144 - 155
25	X-RAY DIFFRACTION	25	B	156 - 170
26	X-RAY DIFFRACTION	26	B	171 - 180
27	X-RAY DIFFRACTION	27	B	192 - 204
28	X-RAY DIFFRACTION	28	B	205 - 242
29	X-RAY DIFFRACTION	29	B	243 - 257
30	X-RAY DIFFRACTION	30	B	258 - 268

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