PDB-7mcm: Crystal Structure of Enoyl-CoA hydratase from Mycolicibacterium s...

ID or keywords:

Entry

Database: PDB / ID: 7mcm

Title

Crystal Structure of Enoyl-CoA hydratase from Mycolicibacterium smegmatis

Components

Enoyl-CoA hydratase

Keywords

LYASE / SSGCID / MSMEG_3390 / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease

Function / homology

Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / enoyl-CoA hydratase activity / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily / Enoyl-CoA hydratase

Function and homology information

Biological species

Mycolicibacterium smegmatis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.05 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of Enoyl-CoA hydratase from Mycolicibacterium smegmatis
Authors: Abendroth, J. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Apr 2, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 14, 2021	Provider: repository / Type: Initial release
Revision 1.1	Oct 18, 2023	Group: Data collection / Database references / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	7mcm.cif.gz	216.4 KB	Display	PDBx/mmCIF format
PDB format	pdb7mcm.ent.gz	142.7 KB	Display	PDB format
PDBx/mmJSON format	7mcm.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	7mcm_validation.pdf.gz	440.4 KB	Display	wwPDB validaton report
Full document	7mcm_full_validation.pdf.gz	441.7 KB	Display
Data in XML	7mcm_validation.xml.gz	19.2 KB	Display
Data in CIF	7mcm_validation.cif.gz	27.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/mc/7mcm ftp://data.pdbj.org/pub/pdb/validation_reports/mc/7mcm	HTTPS FTP

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Related structure data

Related structure data	3qmjS 4jcsS 4kd6S 4mi2S 6l3oS S: Starting model for refinement
Similar structure data	3pe8-1 6rud-d 5xzd-d 3qyr-1 6paa-2 6v29-2 6ruf-d 1jja-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	TargetTrack: MysmA.00358.n

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Enoyl-CoA hydratase

B: Enoyl-CoA hydratase

hetero molecules

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

1

A: Enoyl-CoA hydratase

B: Enoyl-CoA hydratase

hetero molecules

A: Enoyl-CoA hydratase

B: Enoyl-CoA hydratase

hetero molecules

A: Enoyl-CoA hydratase

B: Enoyl-CoA hydratase

hetero molecules

defined by author
Evidence: gel filtration
165 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	104.130, 104.130, 83.750
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	173
Space group name H-M	P6₃
Space group name Hall	P6c
Symmetry operation	#1: x,y,z #2: x-y,x,z+1/2 #3: y,-x+y,z+1/2 #4: -y,x-y,z #5: -x+y,-x,z #6: -x,-y,z+1/2

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 3 through 50 or resid 52...
d_2	ens_1	(chain "B" and (resid 3 through 50 or resid 52...

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Beg label comp-ID	End label comp-ID	Label asym-ID	Label seq-ID
d_1	1	ens_1	THR	ILE	A	1 - 48
d_1	2	ens_1	VAL	ALA	A	50 - 107
d_1	3	ens_1	SER	PRO	A	109 - 132
d_1	4	ens_1	ALA	GLY	A	134 - 136
d_1	5	ens_1	ALA	ASN	A	138 - 162
d_1	6	ens_1	VAL	GLU	A	164 - 198
d_1	7	ens_1	THR	GLN	A	201 - 215
d_2	1	ens_1	THR	ILE	C	2 - 49
d_2	2	ens_1	VAL	ALA	C	51 - 108
d_2	3	ens_1	SER	PRO	C	110 - 133
d_2	4	ens_1	ALA	GLY	C	135 - 137
d_2	5	ens_1	ALA	ASN	C	139 - 163
d_2	6	ens_1	VAL	GLU	C	165 - 199
d_2	7	ens_1	THR	GLN	C	202 - 216

NCS oper: (Code: givenMatrix: (0.855036581672, 0.517960936195, -0.0250781294816), (0.517934539195, -0.855382439705, -0.00804331723991), (-0.0256175157069, -0.00611149895884, -0.999653136077)Vector: - ...

#1: Protein	Enoyl-CoA hydratase Mass: 27519.193 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium smegmatis (bacteria) / Strain: ATCC 700084 / mc(2)155 / Gene: MSMEG_3390 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: A0QXQ8, enoyl-CoA hydratase
#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.: 253 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	N

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.38 Å³/Da / Density % sol: 48.4 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7 Details: Rigaku Reagents JCSG+ screen, condition B8: 200mM magnesium chloride, 100mM Tris / HCl pH 7.0, 10% (w/v) PEG 8000: MysmA.00358.n.a1.PS00566 at 8.7mg/ml: tray 319818 B8: cryo: 20% EG: puck ACC1-3

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97872 Å

Detector

Type: RAYONIX MX-300 / Detector: CCD / Date: Mar 4, 2021 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97872 Å / Relative weight: 1

Reflection

Resolution: 2.05→50 Å / Num. obs: 32467 / % possible obs: 100 % / Redundancy: 8.819 % / B_iso Wilson estimate: 40.877 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.063 / R_rim(I) all: 0.067 / Χ²: 0.9 / Net I/σ(I): 21.54

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Mean I/σ(I) obs	Num. unique obs	CC_1/2	R_rim(I) all	% possible all
2.05-2.1	8.839	0.633	4.03	2379	0.933	0.672	100
2.1-2.16	8.836	0.488	5.22	2351	0.963	0.518	100
2.16-2.22	8.84	0.435	5.78	2250	0.974	0.461	100
2.22-2.29	8.875	0.308	8.05	2189	0.985	0.327	100
2.29-2.37	8.805	0.263	8.94	2148	0.99	0.279	100
2.37-2.45	8.858	0.217	10.86	2048	0.99	0.231	100
2.45-2.54	8.819	0.175	12.96	2007	0.994	0.186	100
2.54-2.65	8.831	0.151	14.48	1913	0.995	0.161	100
2.65-2.76	8.812	0.111	18.37	1852	0.997	0.118	100
2.76-2.9	8.827	0.082	23.29	1775	0.998	0.088	100
2.9-3.06	8.794	0.072	26.81	1671	0.998	0.077	100
3.06-3.24	8.861	0.06	32.01	1579	0.998	0.063	100
3.24-3.47	8.826	0.048	37.96	1499	0.999	0.051	100
3.47-3.74	8.822	0.043	42.18	1390	0.999	0.046	100
3.74-4.1	8.877	0.039	45.56	1273	0.999	0.042	100
4.1-4.58	8.806	0.038	49.13	1176	0.999	0.041	100
4.58-5.29	8.779	0.034	49.62	1022	0.999	0.037	100
5.29-6.48	8.812	0.033	48.73	878	0.999	0.035	99.9
6.48-9.17	8.661	0.033	52.57	681	0.999	0.036	100
9.17-50	8.083	0.033	53.12	386	0.999	0.035	97.7

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Processing

Software

Name	Version	Classification
XDS		data reduction
XSCALE		data scaling
PHENIX	1.19 4175	refinement
PDB_EXTRACT	3.27	data extraction
MoRDa		phasing
MR-Rosetta		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: MR-rosetta based on top5 models from HHPRED: 4jcs, 4kd6, 6l3o, 3qmj, 4mi2

Resolution: 2.05→39.7 Å / SU ML: 0.1899 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.218
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.199	1904	5.87 %	0
R_work	0.1661	30538	-	-
obs	0.1681	32442	99.96 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 41.15 Å²

Refinement step

Cycle: LAST / Resolution: 2.05→39.7 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3129	0	4	253	3386

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.007	3251
X-RAY DIFFRACTION	f_angle_d	0.8733	4446
X-RAY DIFFRACTION	f_chiral_restr	0.0582	530
X-RAY DIFFRACTION	f_plane_restr	0.0069	588
X-RAY DIFFRACTION	f_dihedral_angle_d	12.1375	1149

Refine LS restraints NCS

Type: Torsion NCS / Rms dev position: 0.47518560528 Å

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
2.05-2.1	0.23	122	0.1907	2176	X-RAY DIFFRACTION	100
2.1-2.16	0.18	147	0.1718	2165	X-RAY DIFFRACTION	100
2.16-2.22	0.2279	111	0.1992	2211	X-RAY DIFFRACTION	99.91
2.22-2.29	0.2339	140	0.1741	2140	X-RAY DIFFRACTION	99.91
2.29-2.38	0.2548	114	0.194	2213	X-RAY DIFFRACTION	100
2.38-2.47	0.2367	147	0.1869	2163	X-RAY DIFFRACTION	99.96
2.47-2.58	0.2657	141	0.1992	2145	X-RAY DIFFRACTION	99.91
2.58-2.72	0.24	146	0.1943	2177	X-RAY DIFFRACTION	99.96
2.72-2.89	0.2341	140	0.1943	2173	X-RAY DIFFRACTION	100
2.89-3.11	0.2707	126	0.1866	2191	X-RAY DIFFRACTION	100
3.11-3.43	0.2175	133	0.1841	2184	X-RAY DIFFRACTION	100
3.43-3.92	0.1873	150	0.1485	2170	X-RAY DIFFRACTION	100
3.92-4.94	0.1431	159	0.1278	2188	X-RAY DIFFRACTION	99.96
4.94-39.7	0.1667	128	0.1503	2242	X-RAY DIFFRACTION	99.87

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	0.246225973754	-0.892310246038	-0.149071340699	3.19845228004	-0.0886415089522	3.10718104455	-0.31181671481	-0.294398403136	-0.693866527308	0.516501014962	0.343572902468	1.90832506659	0.382962098073	-0.437913474359	-0.0126638583309	0.284397505671	0.0109655915161	0.113635134319	0.417056105808	0.0196841224633	0.830502971942	21.0961074809	26.0696438668	40.0513548181
2	3.86885141114	0.468569160699	1.55066289837	6.95203579154	-1.03797039605	4.70008606071	0.0636781014661	-0.0413417839319	-0.63876591429	-0.175486402159	-0.0937095129984	1.32836882956	0.333972205911	-0.299024033339	-0.0102815375223	0.197765048939	0.026133963786	0.0694005026141	0.315935150707	-0.0446065110737	0.632952682407	26.0512134368	20.4634821403	36.3518788093
3	4.23438113288	-1.892220378	-0.951373628327	4.45353820121	0.725190948757	0.532532668861	-0.158825357822	-0.256556404552	-0.148795441851	0.274504186098	0.0947884400414	0.317663569812	0.150755033678	-0.0977855822096	0.0800744483891	0.266191600358	0.00700766388863	0.0401938336055	0.233127125281	0.0333825111551	0.223673271771	40.6730688072	20.115707915	40.1633884132
4	1.58160141349	0.958000771246	-1.02136638624	4.18914445599	-4.55733569901	6.41919550333	0.0110525859849	-0.635183672661	-0.116122792755	1.61543357183	0.286583633997	1.1470664637	-0.319996334496	-0.188188749279	-0.418345962323	0.50234321962	0.0777681643183	0.184396078066	0.485985780025	-0.046810850046	0.560435345157	29.4375855376	32.6121967856	49.655514929
5	3.07708038719	0.0162810756505	-0.0882378327339	9.0861285428	-1.71302780779	5.21121097763	0.218863749008	0.0143196792302	0.0941988579075	-1.04099575644	0.109096498462	-0.00408383220394	0.0260878191823	0.376702462094	-0.126073395976	0.283260365718	0.0307426297247	-0.0244750255499	0.244236638927	-0.0612903227779	0.217127223363	36.2247021417	38.4012632978	31.8621304213
6	9.94396183163	5.3167659538	3.78416225185	7.53313423041	-0.79689745845	8.8576407531	0.114238603296	0.326769993185	0.493794219476	-0.36939719587	0.0490174292456	0.0154606901869	-0.776869032629	0.319350024014	-0.126749180052	0.381877559576	0.02893807731	0.0196442466637	0.351698262118	-0.0114062568316	0.198371906462	44.190096596	43.5371488644	24.0452456243
7	6.11730003989	-2.70724997808	0.474817832921	4.43044089896	0.492792950773	5.15008885018	-0.0991489611184	-0.0189262417382	-1.06864719896	-0.588214063951	0.392989894725	1.74439386834	0.264109149155	-0.721356874848	-0.273667863704	0.295977950633	-0.105905705593	-0.0607945300355	0.420555505439	0.103075474385	0.631126402946	22.8707716129	17.9406852479	2.01594595257
8	4.68397576574	-1.74243712663	-0.0656737756263	5.13424645048	-1.62941975168	5.68712081351	-0.140431806295	-0.0995899612697	-0.237862683905	0.227563714256	0.21073001488	0.774452715958	0.0222617440884	-0.522872338282	-0.0921512065151	0.220809016638	-0.0429543249507	0.0338368595185	0.259367254121	0.0247273565642	0.389280766397	24.805427689	22.7007204019	6.86706284648
9	3.642962464	0.821134135143	3.59531095161	7.0797429408	2.98211805598	4.52698150469	0.0960483786317	-0.206341569043	0.886692932537	-0.332907921326	-0.157392217062	0.566764956129	-1.12204915551	-1.21036434809	0.223173038787	0.364384465783	0.0558589545734	-0.0468480507871	0.42525517116	0.0314886669339	0.49310013217	24.9395552047	33.4545299743	-0.773930617251
10	1.82793563662	-0.148934778977	0.131689080745	5.33891068338	0.552103411253	0.0733410896633	-0.0263715630305	-0.033925740641	0.0252528824082	0.13507357667	-0.0105307488812	0.312015879589	0.033942325711	-0.0988671475755	0.071833559745	0.220729988009	0.00961291575529	-0.0225548374866	0.25491133571	-0.000123791418199	0.235451739204	33.4590806376	31.0862922918	3.42778894203
11	2.07010826453	1.20230180046	0.0603103770203	6.18411596152	2.28364905171	4.48291814217	-0.0568873076011	0.119916342166	-0.0101823296942	-0.105980181991	0.0270050368002	-0.166541472348	0.19342857904	0.0531750869829	0.0200620822377	0.200914230836	0.0522326772238	0.00994438427657	0.253687091702	0.0202318389302	0.241934750507	42.2867062398	34.6509830485	-2.01393688108
12	9.20066142714	-6.95352390761	5.0834258082	9.23104414299	-5.99009755681	4.05509664946	0.442384254075	0.645186717521	-0.472135448543	-1.41112569609	-0.210360430193	0.870573154529	0.705355865254	-0.327134968947	-0.269598846753	0.443316610918	-0.00283272058105	-0.108751945108	0.354783396867	-0.139280107097	0.408217204893	33.6074530179	16.1305139229	-8.31544218275
13	2.36514520298	3.38031196397	2.18823348182	5.86342833252	2.04887109773	7.26270270624	-0.128471346968	-0.303482935004	-0.132366213776	0.472642331814	0.387714896576	0.134109959172	-0.469406747719	0.15206155882	-0.132128161274	0.39510139852	0.058418343213	0.0132684741764	0.290337224479	-0.0300563767164	0.296755614468	42.5808791812	13.768774258	9.45948945566
14	9.63938803294	-4.20748787898	-0.259376537472	7.10233548008	0.614526769625	2.18107049674	-0.126767666921	-0.233880421245	-0.348970088748	0.430171002593	0.222467041709	0.141776413306	0.429180423419	-0.213923818389	-0.0542069198733	0.401090937298	-0.0272991207556	0.0251382593407	0.365223395964	-0.0175073908372	0.166982664761	51.3569297623	14.513210119	17.0336683308

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 3 through 19 )	A	A	3 - 19	1 - 17
2	2	chain 'A' and (resid 20 through 91 )	A	A	20 - 91	18 - 66
3	3	chain 'A' and (resid 92 through 191 )	A	A	92 - 191	67 - 166
4	4	chain 'A' and (resid 192 through 207 )	A	A	192 - 207	167 - 182
5	5	chain 'A' and (resid 208 through 226 )	A	A	208 - 226	183 - 201
6	6	chain 'A' and (resid 227 through 240 )	A	A	227 - 240	202 - 215
7	7	chain 'B' and (resid 2 through 19 )	B	C	2 - 19	1 - 18
8	8	chain 'B' and (resid 20 through 57 )	B	C	20 - 57	19 - 56
9	9	chain 'B' and (resid 58 through 91 )	B	C	58 - 91	57 - 67
10	10	chain 'B' and (resid 92 through 151 )	B	C	92 - 151	68 - 127
11	11	chain 'B' and (resid 152 through 191 )	B	C	152 - 191	128 - 167
12	12	chain 'B' and (resid 192 through 207 )	B	C	192 - 207	168 - 183
13	13	chain 'B' and (resid 208 through 225 )	B	C	208 - 225	184 - 201
14	14	chain 'B' and (resid 226 through 241 )	B	C	226 - 241	202 - 217

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About Yorodumi

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Yorodumi