PDB-4mys: 1.4 Angstrom Crystal Structure of 2-succinyl-6-hydroxy-2,4-cycloh...

ID or keywords:

Entry

Database: PDB / ID: 4mys

Title

1.4 Angstrom Crystal Structure of 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase with SHCHC and Pyruvate

Components

2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase

Keywords

LYASE / alpha/beta hydrolase fold / 2-succinyl-6-hydroxy-2 / 4-cyclohexadiene-1-carboxylate synthase

Function / homology

Function and homology information

2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase / 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase activity / menaquinone biosynthetic process / cytosol
Similarity search - Function

Biological species

Escherichia coli (E. coli)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.423 Å

Authors

Sun, Y. / Yin, S. / Feng, Y. / Li, J. / Zhou, J. / Liu, C. / Zhu, G. / Guo, Z.

Citation

Journal: J.Biol.Chem. / Year: 2014
Title: Molecular basis of the general base catalysis of an alpha / beta-hydrolase catalytic triad.
Authors: Sun, Y. / Yin, S. / Feng, Y. / Li, J. / Zhou, J. / Liu, C. / Zhu, G. / Guo, Z.

History

Deposition	Sep 28, 2013	Deposition site: RCSB / Processing site: PDBJ
Revision 1.0	Apr 23, 2014	Provider: repository / Type: Initial release
Revision 1.1	May 7, 2014	Group: Database references
Revision 1.2	Aug 24, 2022	Group: Database references / Derived calculations / Category: citation / database_2 / struct_site Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.0	Nov 15, 2023	Group: Atomic model / Data collection Category: atom_site / atom_site_anisotrop ...atom_site / atom_site_anisotrop / chem_comp_atom / chem_comp_bond Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _atom_site_anisotrop.pdbx_auth_atom_id / _atom_site_anisotrop.pdbx_label_atom_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4mys.cif.gz	396 KB	Display	PDBx/mmCIF format
PDB format	pdb4mys.ent.gz	333.1 KB	Display	PDB format
PDBx/mmJSON format	4mys.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4mys_validation.pdf.gz	490.1 KB	Display	wwPDB validaton report
Full document	4mys_full_validation.pdf.gz	503.4 KB	Display
Data in XML	4mys_validation.xml.gz	38.8 KB	Display
Data in CIF	4mys_validation.cif.gz	61.3 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/my/4mys ftp://data.pdbj.org/pub/pdb/validation_reports/my/4mys	HTTPS FTP

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Related structure data

Related structure data	4mxdC 4mydC C: citing same article (ref.)
Similar structure data	4myd-1 4gdm-1 4geg-2 3amq-4 4gdm-3 4ke6-3 3vhn-5 3vho-1 3e0x-2 2f91-d Search similar-shape structures by Omokage search (details) 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

Related structure data

4mxdC

4mydC

C: citing same article (ref.)

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#102 - Jun 2008 Lactate Dehydrogenase similarity (1) #263 - Nov 2021 Acetohydroxyacid Synthase similarity (1) #165 - Sep 2013 Designed Protein Cages similarity (1) #220 - Apr 2018 Dehalogenases similarity (1)

Deposited unit

A: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase

B: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase

C: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase

hetero molecules

83.8 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase

hetero molecules

defined by author&software
28 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase

hetero molecules

defined by author&software
28 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

C: 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase

defined by author&software
27.7 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	122.000, 122.000, 46.940
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	144
Space group name H-M	P3₁

#1: Protein	2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase / SHCHC synthase Mass: 27713.338 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Escherichia coli (E. coli) / Strain: K12 / Gene: b2263, JW2258, menH, yfbB / Plasmid: pETM / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 References: UniProt: P37355, 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase
#2: Chemical	ChemComp-164 / 2-(3-CARBOXYPROPIONYL)-6-HYDROXY-CYCLOHEXA-2,4-DIENE CARBOXYLIC ACID Mass: 240.209 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₁H₁₂O₆
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Chemical	ChemComp-PYR / PYRUVIC ACID Mass: 88.062 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₄O₃
#5: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 827 / 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: 2.43 Å³/Da / Density % sol: 49.3 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.8 Details: 1.6M K/Na phosphate, pH 6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.97 Å
Detector	Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 15, 2012
Radiation	Monochromator: Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97 Å / Relative weight: 1
Reflection	Resolution: 1.42→37.201 Å / Num. all: 145860 / Num. obs: 145860 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 5 % / B_iso Wilson estimate: 13.2 Å² / R_merge(I) obs: 0.1 / Net I/σ(I): 10.6
Reflection shell	Resolution: 1.42→1.5 Å / Redundancy: 4.6 % / % possible all: 94.4

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASES		phasing
PHENIX	(phenix.refine: 1.8.2_1309)	refinement
MOSFLM		data reduction
SCALA		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 1.423→35.089 Å / Occupancy max: 1 / Occupancy min: 0.49 / SU ML: 0.13 / σ(F): 1.97 / Phase error: 17.12 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection
R_free	0.1819	7310	5.01 %
R_work	0.1584	-	-
obs	0.1595	145825	99.5 %
all	-	145838	-

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso max: 133.36 Å² / B_iso mean: 25.8655 Å² / B_iso min: 6.79 Å²

Refinement step

Cycle: LAST / Resolution: 1.423→35.089 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5801	0	46	827	6674

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	7998
X-RAY DIFFRACTION	f_angle_d	1.058	10881
X-RAY DIFFRACTION	f_dihedral_angle_d	14.336	2831
X-RAY DIFFRACTION	f_chiral_restr	0.044	1174
X-RAY DIFFRACTION	f_plane_restr	0.005	1453

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 30

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.423-1.4392	0.2503	238	0.233	4273	4511	94
1.4392-1.4561	0.2496	221	0.2268	4668	4889	98
1.4561-1.4739	0.2552	220	0.2056	4615	4835	100
1.4739-1.4925	0.2304	234	0.1901	4624	4858	100
1.4925-1.5122	0.1946	264	0.1715	4691	4955	100
1.5122-1.5329	0.1859	255	0.1719	4549	4804	100
1.5329-1.5548	0.1828	241	0.1649	4717	4958	100
1.5548-1.578	0.1949	240	0.1615	4629	4869	100
1.578-1.6026	0.1842	248	0.1622	4627	4875	100
1.6026-1.6289	0.1705	244	0.1611	4625	4869	100
1.6289-1.657	0.1839	255	0.159	4632	4887	100
1.657-1.6871	0.1799	245	0.1552	4603	4848	100
1.6871-1.7196	0.2009	253	0.161	4665	4918	100
1.7196-1.7547	0.1658	244	0.1543	4614	4858	100
1.7547-1.7928	0.1856	257	0.1602	4702	4959	100
1.7928-1.8345	0.2033	253	0.1634	4619	4872	100
1.8345-1.8804	0.2083	239	0.166	4659	4898	100
1.8804-1.9313	0.1757	234	0.1623	4587	4821	100
1.9313-1.9881	0.1992	242	0.1602	4628	4870	100
1.9881-2.0522	0.1743	271	0.1599	4645	4916	100
2.0522-2.1256	0.1768	242	0.161	4629	4871	100
2.1256-2.2107	0.1789	258	0.1562	4629	4887	100
2.2107-2.3113	0.1825	262	0.1575	4593	4855	100
2.3113-2.4331	0.1633	223	0.151	4693	4916	100
2.4331-2.5855	0.1794	230	0.1549	4665	4895	100
2.5855-2.785	0.2001	270	0.1547	4631	4901	100
2.785-3.0652	0.1809	251	0.1593	4598	4849	100
3.0652-3.5083	0.1784	207	0.1498	4663	4870	100
3.5083-4.4188	0.1427	247	0.1249	4579	4826	99
4.4188-35.1001	0.1931	222	0.1772	4463	4685	96

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	3.7376	0.4659	0.2484	1.1977	-0.2527	1.5462	0.0378	-0.308	-0.0573	0.2573	0.0244	-0.248	0.0185	0.1574	-0.0369	0.1579	-0.0246	-0.0541	0.1403	-0.017	0.1221	0.31	52.2295	2.7605
2	1.4495	0.3676	0.1976	1.3813	0.1996	1.0275	0.0013	0.0095	0.0678	0.0715	0.0378	-0.0843	-0.0636	0.063	-0.0301	0.1085	-0.0181	-0.0223	0.1019	-0.0031	0.0678	-7.0248	55.0595	-4.0292
3	1.4548	0.1668	-0.3049	1.0548	0.2928	1.015	-0.0123	0.1268	0.0819	-0.0622	0.0133	0.1122	-0.0171	-0.0782	0.0009	0.1036	-0.0118	-0.0275	0.1206	0.0131	0.0434	-24.2083	46.3716	-9.0109
4	1.5831	-0.0359	-0.3946	1.5743	-0.3336	1.9848	0.0501	0.2111	0.315	-0.2813	-0.0228	-0.1765	-0.2294	0.1259	-0.0502	0.1971	-0.0297	0.0275	0.1471	0.0493	0.1565	-9.9848	63.0641	-16.0858
5	3.4795	-0.4379	1.4837	1.7131	0.8628	1.8651	0.0609	0.6531	0.1268	-0.76	-0.0028	-0.192	-0.3369	0.3292	-0.0099	0.2937	-0.0391	0.0456	0.2934	0.0011	0.127	-5.9522	49.86	-21.2604
6	3.9075	-0.2395	0.122	2.0381	-0.2354	1.8256	0.0531	0.0844	-0.1326	-0.1712	0.0237	-0.3179	-0.0321	0.3377	-0.0707	0.1122	-0.0015	0.0099	0.1976	-0.0383	0.1182	-1.2725	42.477	-13.6441
7	1.4666	-0.899	0.2629	3.4569	-0.0915	1.5071	0.0667	0.25	0.1715	-0.3184	0.0019	0.1723	-0.1049	-0.0919	-0.0622	0.1634	-0.0173	-0.0163	0.1306	0.0541	0.1167	45.0791	26.3665	-10.6397
8	1.0884	0.1574	-0.1269	1.6373	-0.2485	1.0047	-0.0007	0.0698	0.1056	0.0025	0.0404	-0.0097	-0.0805	0.0179	-0.0303	0.117	-0.0114	-0.0082	0.0918	0.0235	0.0685	51.0784	21.5186	-3.8518
9	2.0236	0.5244	0.7719	1.9313	1.3863	2.4203	-0.0053	-0.143	0.052	0.5997	0.0825	-0.4367	0.2262	0.279	-0.1052	0.2311	0.0187	-0.0779	0.1647	0.0071	0.1508	61.8141	2.797	5.1482
10	0.7665	-0.2684	-0.1122	1.098	0.2413	1.2209	-0.0151	-0.0369	-0.07	0.0203	0.0034	0.0228	0.1013	-0.0302	0.0199	0.1156	-0.0049	-0.011	0.0928	0.0168	0.0466	47.8558	1.6773	-0.8316
11	2.5182	-0.3776	0.19	2.0167	1.0579	2.8033	0.055	-0.3001	0.3496	0.2073	-0.0439	-0.191	-0.1537	0.0272	-0.0139	0.1654	-0.0322	-0.0227	0.1515	-0.0405	0.1501	59.9133	22.5254	8.0798
12	2.6745	-0.2529	-0.3687	2.4422	-1.3035	0.7971	0.0636	-0.7672	0.1802	0.5625	-0.0007	-0.0022	-0.4393	0.1329	-0.0109	0.3147	-0.0152	0.0212	0.2637	-0.028	0.1136	45.8512	19.4613	13.4533
13	2.7772	-0.7921	0.2058	2.9956	-0.069	1.6046	0.0757	-0.1738	0.2312	0.1169	0.0113	0.301	-0.3271	-0.1379	-0.0961	0.1868	0.039	0.0375	0.1389	0.01	0.1258	37.34	20.569	5.8352
14	0.0308	-0.0213	0.0058	0.0145	-0.0026	0.0035	-0.0252	0.0106	-0.0836	-0.0061	-0.0221	0.0352	0.0196	-0.0054	-0.0305	0.0687	0.039	0.0755	0.0768	-0.0374	0.3694	16.2807	28.1843	-3.9312
15	0.0544	0.0056	0.0025	0.0274	-0.0195	0.0391	-0.032	-0.0125	-0.0308	-0.0203	-0.0347	-0.0233	0.0758	-0.0342	-0.04	-0.0152	0.0999	-0.0072	0.0564	-0.0019	0.5786	13.9744	24.1923	-3.9417
16	0.0103	0.0022	0.0093	0.0122	-0.0019	0.0037	-0.0088	0.0039	-0.0616	0.0111	-0.0022	0.046	0.0249	-0.0224	-0.0011	0.1639	-0.0447	0.0367	0.1138	0.0015	0.7068	4.3749	7.565	-3.9353
17	0.008	0.0169	-0.0027	0.0177	0.0015	0.0192	0.0142	-0.0331	-0.1298	-0.0209	-0.0235	0.0588	0.1088	-0.0525	0.0003	0.1463	0.0221	0.0436	0.1592	-0.0066	0.4984	7.3653	12.7581	-3.9382
18	0.019	0.0099	-0.0178	0.0153	0.0044	0.0346	-0.0038	0.0207	-0.0413	0.0324	0.0364	0.0178	0.0374	-0.0262	-0.0009	0.1731	0.0675	-0.0204	0.2331	0.0122	0.5807	13.1402	22.7535	-3.9621
19	0.0066	-0.0053	-0.0009	0.0032	0.0006	-0	0.0551	0.006	-0.0513	0.0286	0.0767	0.0394	-0.0187	0.0044	0	0.2037	0.0295	-0.0524	0.2497	0.0019	0.3335	12.391	21.4779	-3.9493
20	0.0122	-0.0131	0.0087	0.0063	-0.0051	0.0007	-0.0297	0.0108	-0.0406	0.0335	0.0159	0.0377	-0.017	0.0011	-0.0082	0.0973	0.0075	-0.0026	0.1083	0.0099	0.2735	15.3067	26.5137	-3.9391

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	chain 'A' and (resid 1:20)	A	1 - 20
2	X-RAY DIFFRACTION	2	chain 'A' and (resid 21:117)	A	21 - 117
3	X-RAY DIFFRACTION	3	chain 'A' and (resid 118:182)	A	118 - 182
4	X-RAY DIFFRACTION	4	chain 'A' and (resid 183:200)	A	183 - 200
5	X-RAY DIFFRACTION	5	chain 'A' and (resid 201:227)	A	201 - 227
6	X-RAY DIFFRACTION	6	chain 'A' and (resid 228:252)	A	228 - 252
7	X-RAY DIFFRACTION	7	chain 'B' and (resid 1:20)	B	1 - 20
8	X-RAY DIFFRACTION	8	chain 'B' and (resid 21:117)	B	21 - 117
9	X-RAY DIFFRACTION	9	chain 'B' and (resid 118:135)	B	118 - 135
10	X-RAY DIFFRACTION	10	chain 'B' and (resid 136:182)	B	136 - 182
11	X-RAY DIFFRACTION	11	chain 'B' and (resid 183:200)	B	183 - 200
12	X-RAY DIFFRACTION	12	chain 'B' and (resid 201:227)	B	201 - 227
13	X-RAY DIFFRACTION	13	chain 'B' and (resid 228:252)	B	228 - 252
14	X-RAY DIFFRACTION	14	chain 'C' and (resid 2:60)	C	2 - 60
15	X-RAY DIFFRACTION	15	chain 'C' and (resid 61:128)	C	61 - 128
16	X-RAY DIFFRACTION	16	chain 'C' and (resid 129:157)	C	129 - 157
17	X-RAY DIFFRACTION	17	chain 'C' and (resid 158:182)	C	158 - 182
18	X-RAY DIFFRACTION	18	chain 'C' and (resid 183:210)	C	183 - 210
19	X-RAY DIFFRACTION	19	chain 'C' and (resid 211:227)	C	211 - 227
20	X-RAY DIFFRACTION	20	chain 'C' and (resid 228:252)	C	228 - 252

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