PDB-4mxd: 1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2...

ID or keywords:

Entry

Database: PDB / ID: 4mxd

Title

1.45 angstronm crystal structure of E.coli 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase (MenH)

Components

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

Keywords

LYASE / Open Conformation /

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: 1.45 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 26, 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 ...citation / database_2 / struct_ref_seq_dif / 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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3	Nov 8, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4mxd.cif.gz	128.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4mxd.ent.gz	100 KB	Display	PDB format
PDBx/mmJSON format	4mxd.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/mx/4mxd ftp://data.pdbj.org/pub/pdb/validation_reports/mx/4mxd	HTTPS FTP

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Related structure data

Related structure data	4mydC 4mysC 1r3dS C: citing same article (ref.) S: Starting model for refinement
Similar structure data	5f2z-4 6nj3-d 6t81-d 5frd-2 1va4-6 5oce-4 6h34-d 4gdm-2 5v79-1 5gwx-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

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#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

hetero molecules

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

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	72.163, 72.163, 112.583
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	152
Space group name H-M	P3₁21

Components on special symmetry positions

ID	Model	Components
1	1	A-638- HOH
2	1	A-742- HOH

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Protein , 1 types, 1 molecules A

#1: Protein	2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate synthase / / SHCHC synthase Mass: 27944.545 Da / Num. of mol.: 1 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

#1: Protein

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

/ SHCHC synthase

Mass: 27944.545 Da / Num. of mol.: 1
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

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Non-polymers , 5 types, 355 molecules

#2: Chemical	ChemComp-SO4 / SULFATE ION / Sulfate Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO₄
#3: Chemical	ChemComp-PEG / DI(HYDROXYETHYL)ETHER / Diethylene glycol Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₁₀O₃
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Chemical	ChemComp-PGE / TRIETHYLENE GLYCOL / Polyethylene glycol Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₆H₁₄O₄
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 349 / 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: 3.03 Å³/Da / Density % sol: 59.38 %
Crystal grow	Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 9 Details: 0.2M Li2SO4, 0.1M Tris buffer (pH 9.0), 30% v/v glycerol, 17% PEG 3350, 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: 1.45→50 Å / Num. all: 60722 / Num. obs: 60673 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 10.8 % / B_iso Wilson estimate: 14.47 Å² / R_merge(I) obs: 0.091

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.45-1.5	10.9	0.592	5.5	1	100
1.5-1.56	10.9	0.425		1	100
1.56-1.63	10.9	0.318		1	100
1.63-1.72	10.9	0.235		1	100
1.72-1.83	10.9	0.176		1	100
1.83-1.97	11	0.127		1	100

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Processing

Software

Name	Version	Classification
HKL-2000		data collection
PHASES		phasing
PHENIX	(phenix.refine: 1.8.1_1168)	refinement
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 1R3D

1r3d

Resolution: 1.45→41.826 Å / Occupancy max: 1 / Occupancy min: 0.31 / FOM work R set: 0.9101 / SU ML: 0.1 / σ(F): 0 / Phase error: 15.33 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.168	1983	3.34 %	RANDOM
R_work	0.1551	-	-	-
all	0.1555	60673	-	-
obs	0.1555	59422	97.83 %	-

Solvent computation

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

Displacement parameters

B_iso max: 81.79 Å² / B_iso mean: 22.9859 Å² / B_iso min: 7.46 Å²

Refinement step

Cycle: LAST / Resolution: 1.45→41.826 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	1969	0	38	349	2356

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.006	2162
X-RAY DIFFRACTION	f_angle_d	1.11	2947
X-RAY DIFFRACTION	f_dihedral_angle_d	15.062	781
X-RAY DIFFRACTION	f_chiral_restr	0.08	307
X-RAY DIFFRACTION	f_plane_restr	0.004	398

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 14

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.4502-1.4864	0.2031	136	0.1895	3863	3999	93
1.4864-1.5266	0.2076	135	0.1748	3899	4034	94
1.5266-1.5715	0.1498	139	0.1607	3956	4095	96
1.5715-1.6223	0.1471	134	0.1518	3999	4133	97
1.6223-1.6802	0.1771	138	0.1492	4081	4219	98
1.6802-1.7475	0.174	139	0.1514	4057	4196	98
1.7475-1.8271	0.1797	141	0.1547	4077	4218	98
1.8271-1.9234	0.1527	141	0.1513	4118	4259	99
1.9234-2.0439	0.1405	146	0.1495	4138	4284	99
2.0439-2.2017	0.1569	145	0.1491	4186	4331	100
2.2017-2.4232	0.1586	145	0.1522	4182	4327	100
2.4232-2.7738	0.2224	147	0.1592	4245	4392	100
2.7738-3.4945	0.1719	143	0.1625	4257	4400	100
3.4945-41.8432	0.1569	154	0.1503	4381	4535	99

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	1.7312	0.2029	1.688	2.0313	-0.6682	4.1381	0.3087	-0.5873	-0.2576	0.4229	-0.0007	-0.5534	0.2957	0.7924	0.2197	0.3289	0.0249	0.0088	0.3076	0.0595	0.1809	39.2323	18.302	21.5319
2	4.3642	-0.7755	3.7356	0.5854	-0.3599	3.3724	0.1431	-0.6602	-0.3486	0.1717	0.0721	0.2099	0.291	-0.5258	-0.0942	0.227	-0.0364	0.0337	0.2505	0.0584	0.1502	22.559	23.052	12.4231
3	2.5168	-0.1594	0.9284	0.5477	-0.0401	1.18	0.0033	-0.1654	0.0097	0.0882	0.0199	0.0212	0.0541	-0.0613	-0.0247	0.123	0.0027	0.0079	0.1207	0.0108	0.06	29.6267	28.3148	7.8773
4	2.4863	-0.5062	2.1953	3.6079	-2.5087	3.2298	0.0515	-0.1985	-0.2441	0.1673	-0.1306	-0.2436	0.4611	0.3832	-0.0184	0.1779	0.0222	-0.0245	0.2015	-0.003	0.0816	41.851	27.4839	17.0235
5	5.3153	1.7986	-2.1766	2.1112	-0.8588	3.4815	-0.0939	-0.1953	-0.3808	0.0798	0.0383	-0.1677	0.5169	0.2291	0.0013	0.2596	0.0633	-0.0387	0.154	0.0221	0.099	40.9823	16.2327	11.5146
6	0.3642	-0.1804	0.0851	0.1646	-0.5715	3.548	0.0795	-0.1659	-0.2556	-0.0707	0.065	0.1064	0.9153	-0.3003	0.0558	0.3152	-0.0678	-0.0136	0.1722	0.0604	0.1392	26.8208	15.7698	7.989
7	4.0553	-0.7091	0.264	2.1733	0.6815	2.4679	0.0614	-0.0267	-0.1466	-0.032	0.0114	-0.0096	0.3061	0.2084	-0.0887	0.1367	0.0305	-0.0005	0.1324	0.0134	0.0576	39.6877	21.6755	1.163
8	4.4048	0.704	-0.9491	4.1997	-5.6353	7.5668	0.0414	-0.1199	-0.6213	-0.2476	-0.0358	-0.015	0.7483	-0.2889	0.0724	0.2624	-0.0246	-0.0192	0.1251	0.0185	0.1665	31.3482	17.1012	0.1322
9	2.2512	-1.7014	1.8663	3.7177	-0.7461	2.2049	0.0077	0.2659	-0.0849	-0.1125	0.0574	-0.2628	-0.0244	0.4776	-0.1619	0.1128	0.007	0.0091	0.1885	-0.0195	0.0888	43.8976	26.2876	-6.0544
10	1.7477	-0.4235	-1.3792	4.4047	4.3157	4.7777	-0.2175	1.4165	-0.4205	-0.4965	0.5845	-0.2203	-0.1517	0.9331	-0.152	0.2144	-0.0892	0.0304	0.673	-0.1682	0.3796	57.4145	27.905	-2.8039
11	3.8191	-1.4368	0.4015	4.8581	0.9717	0.4428	-0.0168	0.1394	0.0025	0.4264	-0.1661	-0.0395	-0.3499	0.2499	0.0651	0.2176	-0.0723	-0.0352	0.2657	-0.0212	0.1727	54.6439	38.6689	10.7135
12	2.5349	-0.1961	2.908	1.9198	-0.9669	3.6193	-0.4025	1.072	0.6803	-0.589	0.271	0.264	-0.5233	0.4255	0.0648	0.3484	-0.1004	-0.0303	0.4248	0.0967	0.2952	46.3606	42.9825	1.5361
13	3.9104	-1.1241	0.1937	2.8603	1.4621	2.6609	-0.2154	-0.2096	0.7523	-0.0507	0.1869	-0.1468	-0.7477	0.0215	0.0081	0.3275	-0.0281	-0.0351	0.2263	0.0049	0.2942	42.3176	43.2831	10.1213
14	0.2926	0.5926	0.1995	1.5638	1.3744	2.5927	-0.0278	0.0744	-0.1164	0.0719	0.2051	-0.2078	0.1172	0.624	-0.1838	0.1229	0.0494	-0.0031	0.2606	-0.0228	0.1179	49.5526	22.9658	1.4046
15	2.3064	-0.7239	-2.9814	3.3591	2.5804	4.7264	-0.2202	-0.1388	-0.3561	0.0009	0.1231	0.094	0.2619	0.1325	-0.0212	0.228	0.0385	-0.008	0.1307	-0.0021	0.108	36.8184	13.6594	-8.1835
16	2.4357	0.0783	-1.1841	6.2305	0.5306	2.6863	0.1033	0.1043	0.1513	-0.2187	-0.0283	-0.012	-0.153	0.1141	-0.097	0.1505	0.02	0.0304	0.1321	0.0136	0.0743	34.1636	31.5187	-9.4407
17	1.0839	-0.1161	-0.4249	6.7112	1.9464	2.9821	0.1056	0.1181	0.1026	-0.1294	0.0003	-0.1597	-0.0706	0.2134	-0.1215	0.1563	0.0155	0.0386	0.2007	-0.0024	0.0751	40.3992	28.2315	-12.6775
18	3.1652	0.1869	0.1447	2.0198	2.4364	3.3424	0.0607	0.2627	0.1404	-0.4573	-0.006	0.0585	-0.15	-0.0696	-0.0665	0.1674	0.0433	0.0039	0.1544	0.0274	0.0719	30.0148	32.9808	-11.5326
19	1.4195	-0.4194	0.2224	1.868	0.1113	4.0425	0.0551	0.003	0.1604	-0.0212	-0.1087	-0.2227	-0.1554	0.2565	0.035	0.0937	0.0082	0.0125	0.0961	0.0197	0.0767	30.9699	37.179	-2.8084
20	7.33	-1.7268	-1.2844	3.1922	-1.9045	3.9174	0.1399	0.151	-0.3166	-0.3216	-0.0861	0.1209	0.3046	-0.0128	0.0046	0.1547	0.0162	-0.015	0.1272	-0.0262	0.092	21.2361	25.0849	-5.5777

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 -2:3)	A	-2 - 3
2	X-RAY DIFFRACTION	2	(chain A and resid 4:14)	A	4 - 14
3	X-RAY DIFFRACTION	3	(chain A and resid 15:49)	A	15 - 49
4	X-RAY DIFFRACTION	4	(chain A and resid 50:56)	A	50 - 56
5	X-RAY DIFFRACTION	5	(chain A and resid 57:74)	A	57 - 74
6	X-RAY DIFFRACTION	6	(chain A and resid 75:82)	A	75 - 82
7	X-RAY DIFFRACTION	7	(chain A and resid 83:99)	A	83 - 99
8	X-RAY DIFFRACTION	8	(chain A and resid 100:108)	A	100 - 108
9	X-RAY DIFFRACTION	9	(chain A and resid 109:116)	A	109 - 116
10	X-RAY DIFFRACTION	10	(chain A and resid 117:129)	A	117 - 129
11	X-RAY DIFFRACTION	11	(chain A and resid 130:143)	A	130 - 143
12	X-RAY DIFFRACTION	12	(chain A and resid 144:156)	A	144 - 156
13	X-RAY DIFFRACTION	13	(chain A and resid 157:176)	A	157 - 176
14	X-RAY DIFFRACTION	14	(chain A and resid 177:193)	A	177 - 193
15	X-RAY DIFFRACTION	15	(chain A and resid 194:201)	A	194 - 201
16	X-RAY DIFFRACTION	16	(chain A and resid 202:210)	A	202 - 210
17	X-RAY DIFFRACTION	17	(chain A and resid 211:222)	A	211 - 222
18	X-RAY DIFFRACTION	18	(chain A and resid 223:229)	A	223 - 229
19	X-RAY DIFFRACTION	19	(chain A and resid 230:244)	A	230 - 244
20	X-RAY DIFFRACTION	20	(chain A and resid 245:252)	A	245 - 252

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