PDB-3sef: 2.4 Angstrom resolution crystal structure of shikimate 5-dehydrog...

ID or keywords:

Entry

Database: PDB / ID: 3sef

Title

2.4 Angstrom resolution crystal structure of shikimate 5-dehydrogenase (aroE) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with shikimate and NADPH

Components

Shikimate 5-dehydrogenase

Keywords

OXIDOREDUCTASE /

Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID /

shikimate / alpha/beta domain /

Rossmann fold

Function / homology

Function and homology information

shikimate dehydrogenase (NADP+) / shikimate metabolic process / shikimate 3-dehydrogenase (NADP+) activity / chorismate biosynthetic process / aromatic amino acid family biosynthetic process / amino acid biosynthetic process /

NADP binding /

cytosol
Similarity search - Function

Biological species

Vibrio cholerae O1 biovar El Tor (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.4 Å

Authors

Halavaty, A.S. / Light, S.H. / Minasov, G. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: To be Published
Title: 2.4 Angstrom resolution crystal structure of shikimate 5-dehydrogenase (aroE) from Vibrio cholerae O1 biovar eltor str. N16961 in complex with shikimate and NADPH
Authors: Halavaty, A.S. / Light, S.H. / Minasov, G. / Shuvalova, L. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)

History

Deposition	Jun 10, 2011	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Jul 27, 2011	Provider: repository / Type: Initial release
Revision 1.1	Aug 10, 2011	Group: Data collection
Revision 1.2	Nov 8, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	Sep 13, 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	3sef.cif.gz	416.8 KB	Display	PDBx/mmCIF format
PDB format	pdb3sef.ent.gz	343 KB	Display	PDB format
PDBx/mmJSON format	3sef.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

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

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Related structure data

Related structure data	3pgjS 3o8q S: Starting model for refinement
Similar structure data	4n6h-d 4rwa-2 2r00-1 2o1w-4 2hww-d 1zyc-2 2o1w-5 4rwd-2 1zxe-2 5lp4-2 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
Other databases	TargetDB: IDP90792

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#34 - Oct 2002 Dihydrofolate Reductase similarity (1) #57 - Sep 2004 Catalase similarity (1)

Deposited unit

A: Shikimate 5-dehydrogenase

B: Shikimate 5-dehydrogenase

C: Shikimate 5-dehydrogenase

D: Shikimate 5-dehydrogenase

hetero molecules

134 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Shikimate 5-dehydrogenase

D: Shikimate 5-dehydrogenase

hetero molecules

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

2

B: Shikimate 5-dehydrogenase

C: Shikimate 5-dehydrogenase

hetero molecules

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

Unit cell

Length a, b, c (Å)	76.030, 86.079, 81.018
Angle α, β, γ (deg.)	90.00, 92.85, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	Shikimate 5-dehydrogenase Mass: 33024.414 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae O1 biovar El Tor (bacteria) Strain: N16961 / Gene: aroE, VC_0056 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21/Magic References: UniProt: Q9KVT3, shikimate dehydrogenase (NADP+)
#2: Chemical	ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / Nicotinamide adenine dinucleotide phosphate Mass: 745.421 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₁H₃₀N₇O₁₇P₃
#3: Chemical	ChemComp-SKM / (3R,4S,5R)-3,4,5-TRIHYDROXYCYCLOHEX-1-ENE-1-CARBOXYLIC ACID / SHIKIMATE / Shikimic acid Mass: 174.151 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₇H₁₀O₅
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 134 / 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 Å³/Da / Density % sol: 38.64 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Protein: 6.8 mg/mL in 10 mM Tris/HCl pH 8.3, 0.25 M NaCl, 5 mM BME. Soak: 5 mM NADPH, 5 mM dehydroshikimate. Crystallization: PEGsII (B11: 0.2 M Na acetate, 0.1 M HEPES pH 7.5, 20 % (w/v) ...Details: Protein: 6.8 mg/mL in 10 mM Tris/HCl pH 8.3, 0.25 M NaCl, 5 mM BME. Soak: 5 mM NADPH, 5 mM dehydroshikimate. Crystallization: PEGsII (B11: 0.2 M Na acetate, 0.1 M HEPES pH 7.5, 20 % (w/v) PEG3000, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal

Density Matthews: 2 Å³/Da / Density % sol: 38.64 %

Crystal grow

Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: Protein: 6.8 mg/mL in 10 mM Tris/HCl pH 8.3, 0.25 M NaCl, 5 mM BME. Soak: 5 mM NADPH, 5 mM dehydroshikimate. Crystallization: PEGsII (B11: 0.2 M Na acetate, 0.1 M HEPES pH 7.5, 20 % (w/v) ...

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97872 Å
Detector	Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 8, 2010 / Details: Be-Lenses
Radiation	Monochromator: C(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97872 Å / Relative weight: 1
Reflection	Resolution: 2.4→30 Å / Num. all: 41040 / Num. obs: 41040 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / R_merge(I) obs: 0.055 / Net I/σ(I): 18.92
Reflection shell	Resolution: 2.4→2.44 Å / Redundancy: 3.8 % / R_merge(I) obs: 0.57 / Mean I/σ(I) obs: 2.31 / % possible all: 100

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Processing

Software

Name	Version	Classification
Blu-Ice	Max	data collection
PHASER		phasing
REFMAC	5.5.0102	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 3PGJ

3pgj

Resolution: 2.4→29.48 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.915 / SU B: 24.191 / SU ML: 0.252 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.712 / ESU R Free: 0.312 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2756	2059	5 %	RANDOM
R_work	0.23459	-	-	-
obs	0.23666	38956	99.7 %	-
all	-	38956	-	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 57.938 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-0.19 Å²	0 Å²	1.04 Å²
2-	-	1.64 Å²	0 Å²
3-	-	-	-1.36 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→29.48 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	8076	0	120	134	8330

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.005	0.022	8400
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	5658
X-RAY DIFFRACTION	r_angle_refined_deg	1.267	1.977	11374
X-RAY DIFFRACTION	r_angle_other_deg	0.797	3	13787
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	0.45	5	1057
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	9.844	24.409	381
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	2.834	15	1409
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	1.965	15	55
X-RAY DIFFRACTION	r_chiral_restr	0.117	0.2	1274
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.02	9431
X-RAY DIFFRACTION	r_gen_planes_other	0	0.02	1707
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	0.573	1.5	5231
X-RAY DIFFRACTION	r_mcbond_other	0.084	1.5	2182
X-RAY DIFFRACTION	r_mcangle_it	1.087	2	8332
X-RAY DIFFRACTION	r_scbond_it	1.481	3	3169
X-RAY DIFFRACTION	r_scangle_it	2.49	4.5	3042
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 2.396→2.458 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.38	141	-
R_work	0.295	2840	-
obs	-	-	97.74 %

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	1.663	-0.7734	-0.4486	2.3167	0.3936	1.8933	-0.0498	-0.1101	-0.1261	0.1187	0.1933	0.04	0.0632	0.0855	-0.1435	0.0072	0.0127	0	0.0477	0.0263	0.0464	4.7694	-10.5212	35.6029
2	0.2469	0.3563	-0.1551	1.1875	-0.4652	0.409	-0.0039	0.0388	-0.0341	-0.0745	0.0203	0.0556	0.0365	-0.0131	-0.0164	0.0235	-0.0103	-0.0214	0.0888	-0.002	0.0614	10.3263	-1.9173	20.5795
3	1.0579	0.3234	0.0714	2.2575	0.5809	1.3333	-0.0208	0.0007	-0.0613	0.0343	-0.0142	-0.2977	0.1304	0.0855	0.0351	0.0142	0.0037	0.0045	0.074	0.0176	0.0849	26.5407	1.2985	18.4548
4	1.3805	0.426	-0.0033	0.5589	-0.3479	0.4326	0.0032	-0.0527	0.0688	0.1055	-0.0128	-0.0318	-0.0772	0.0324	0.0096	0.0337	-0.0171	-0.0251	0.0844	-0.0082	0.0559	18.7599	11.3326	26.9888
5	4.4324	1.1985	1.2604	1.913	-0.0774	1.0995	-0.1424	-0.173	0.4429	-0.0919	0.0016	0.3514	-0.1394	-0.1437	0.1408	0.0474	0.0233	-0.0188	0.0597	0.0032	0.1101	1.74	6.4246	34.3809
6	1.7785	0.0238	-0.1812	2.4651	1.0227	2.1343	-0.0274	0.1223	0.0607	-0.352	0.0326	0.1241	-0.1115	-0.1132	-0.0053	0.0575	-0.0201	-0.0326	0.0385	0.0311	0.0436	-36.3402	15.8752	-3.5895
7	0.9547	-0.4456	0.3445	0.3736	-0.0493	1.0007	-0.0299	-0.1493	0.0308	0.0529	0.0276	0.0888	0.0529	-0.104	0.0023	0.0129	-0.0116	0.0158	0.0635	-0.0103	0.0865	-29.4492	14.4783	15.1963
8	4.9562	0.0571	-0.7993	2.3897	-0.2601	2.0406	-0.184	-0.3948	0.2346	0.3553	0.1262	-0.0524	0.0346	-0.0856	0.0578	0.062	0.0284	-0.0133	0.0593	-0.0345	0.0203	-17.5882	16.3575	27.697
9	1.3192	0.7036	0.0827	0.9783	0.518	1.1988	-0.0525	-0.0996	0.0122	0.0123	-0.0162	-0.0913	0.0544	0.0189	0.0687	0.0313	0.0299	-0.0102	0.0467	0.0056	0.0708	-11.0796	8.4112	14.4028
10	1.6739	-0.2316	0.8944	0.3984	-0.2416	1.171	-0.0748	-0.1181	-0.1641	-0.0107	0.0663	0.0295	0.1692	0.01	0.0085	0.0811	0.0257	0.021	0.0379	0.0118	0.0886	-22.0391	3.4644	4.7706
11	0.6676	0.8378	-0.5451	2.0973	-0.4023	3.3276	0.0714	-0.1304	-0.0502	0.0811	-0.1897	-0.0331	-0.057	0.3221	0.1183	0.0222	-0.031	-0.0285	0.065	0.0423	0.0426	-26.0917	14.2581	-19.5947
12	2.3555	0.2841	0.6104	0.1271	-0.0943	1.6446	-0.0244	0.1359	0.0091	0.0126	0.0618	-0.005	-0.0231	0.0072	-0.0374	0.0444	-0.0247	-0.0485	0.0659	0.0175	0.0738	-35.6136	20.3752	-39.9779
13	4.1745	-0.5357	0.4937	2.7092	-0.4071	2.342	-0.0172	0.2194	0.4776	0.1203	0.0712	-0.0156	-0.598	0.1308	-0.054	0.1957	-0.036	-0.023	0.0235	0.0327	0.1236	-34.8662	33.1097	-41.4777
14	2.4656	-2.1577	2.273	2.4314	-2.3003	2.7738	0.0106	-0.2883	0.1638	-0.0873	0.0757	0.0822	-0.0336	-0.2134	-0.0863	0.0542	0.0039	-0.0448	0.1239	-0.0484	0.1657	-44.2888	23.2635	-34.3745
15	5.0625	-1.9701	-0.394	3.0458	-0.8803	2.1737	-0.1362	0.3418	-0.4709	0.03	0.0298	0.43	0.4028	-0.1605	0.1064	0.1159	-0.0477	0.0343	0.0581	-0.0049	0.1018	-41.3385	7.73	-24.8804
16	1.6557	-0.702	0.7063	1.2886	-1.1052	2.8629	0.2374	0.201	0.1305	0.0722	-0.1897	-0.1855	-0.3709	0.1798	-0.0477	0.1248	0.0127	0.037	0.04	0.0341	0.0571	4.7433	-1.7318	56.182
17	0.8808	0.4028	-0.3604	0.4759	0.0752	1.1246	0.0621	-0.0759	0.1465	0.0375	-0.0337	-0.0039	-0.2677	-0.0163	-0.0284	0.1383	0.0117	0.0105	0.0096	-0.0174	0.07	-3.2749	-3.8046	72.3782
18	1.0112	-0.2373	0.2337	1.9008	0.4185	1.011	-0.0221	-0.0538	-0.0927	0.2118	0.022	-0.1274	0.0006	0.0707	0	0.0686	-0.0199	-0.0152	0.0604	0.0011	0.0264	-1.9863	-18.938	80.5002
19	0.6448	0.4487	-0.8465	2.1302	-0.8998	1.2687	0.1334	0.1115	0.0297	0.1291	-0.0305	0.1653	-0.125	-0.1362	-0.1029	0.0744	0.0257	0.0088	0.0663	0.0101	0.0555	-13.1679	-17.1874	69.9153
20	3.8625	0.5866	-0.2266	4.5626	-1.6071	2.7609	0.0883	-0.1201	0.39	-0.4147	0.1041	0.7245	-0.3247	-0.5423	-0.1924	0.1613	0.1259	-0.044	0.1805	0.0349	0.1738	-12.4272	-3.6221	57.0299
21	0.3312	2.2487	1.6048	15.2937	10.9068	7.7819	0.0642	-0.1096	0.1251	0.4255	-0.6993	0.8536	0.2783	-0.5047	0.6351	0.2178	0.0135	-0.0184	0.2682	0.0638	0.2126	23.9367	-1.0475	30.4739
22	2.7687	-1.8164	-0.2584	2.4191	-0.1991	0.1356	0.1843	0.6417	0.0235	-0.4211	-0.1357	0.1645	0.0667	-0.143	-0.0486	0.1912	-0.0182	-0.0556	0.2603	-0.0166	0.1515	-16.445	18.9392	10.4679
23	84.9734	-17.0694	-11.2714	4.6213	9.8605	49.9075	-0.9652	-1.1456	-0.7467	-0.0771	-0.0201	0.2893	-1.3928	-1.1015	0.9852	1.1274	0.1974	0.1722	0.0702	-0.0105	0.3821	-27.0579	14.7799	3.0191
24	29.7508	48.5398	35.2535	79.1953	57.5181	41.775	-0.7282	0.9632	-0.8253	-1.3053	1.6481	-1.353	-0.9604	1.1315	-0.9199	0.2439	0.2154	0.1766	0.4267	0.0209	0.2376	-34.4354	19.0188	-22.458

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	5 - 85
2	X-RAY DIFFRACTION	2	A	86 - 152
3	X-RAY DIFFRACTION	3	A	153 - 201
4	X-RAY DIFFRACTION	4	A	202 - 253
5	X-RAY DIFFRACTION	5	A	254 - 276
6	X-RAY DIFFRACTION	6	B	5 - 60
7	X-RAY DIFFRACTION	7	B	61 - 158
8	X-RAY DIFFRACTION	8	B	159 - 183
9	X-RAY DIFFRACTION	9	B	184 - 222
10	X-RAY DIFFRACTION	10	B	223 - 276
11	X-RAY DIFFRACTION	11	C	5 - 103
12	X-RAY DIFFRACTION	12	C	104 - 152
13	X-RAY DIFFRACTION	13	C	153 - 193
14	X-RAY DIFFRACTION	14	C	202 - 252
15	X-RAY DIFFRACTION	15	C	253 - 275
16	X-RAY DIFFRACTION	16	D	5 - 86
17	X-RAY DIFFRACTION	17	D	87 - 152
18	X-RAY DIFFRACTION	18	D	153 - 203
19	X-RAY DIFFRACTION	19	D	204 - 253
20	X-RAY DIFFRACTION	20	D	254 - 276
21	X-RAY DIFFRACTION	21	A	279
22	X-RAY DIFFRACTION	22	B	279
23	X-RAY DIFFRACTION	23	B	280
24	X-RAY DIFFRACTION	24	C	279

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-Structure viewers

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-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

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-Assembly

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-Experimental details

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-Data collection

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+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

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Movie

-
Structure viewers

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Viewer log

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This page

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This web site

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Options

+
Open data

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Basic information

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Structure visualization

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Downloads & links

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Download

-
Validation report

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Related structure data

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Links

-
Assembly

-
Components

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Experimental details

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Experiment

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Sample preparation

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Data collection

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Processing

+
About Yorodumi

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News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

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Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

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Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

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Jul 12, 2017. Major update of PDB

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Yorodumi