PDB-7m3w: Crystal Structure of enoyl-CoA hydratase EchA15 protein from Myco...

ID or keywords:

Entry

Database: PDB / ID: 7m3w

Title

Crystal Structure of enoyl-CoA hydratase EchA15 protein from Mycolicibacterium paratuberculosis

Components

Enoyl-CoA hydratase EchA15

Keywords

LYASE / SSGCID /

structural genomics / seattle structural genomics center for infectious disease

Function / homology

Enoyl-CoA hydratase, C-terminal /

enoyl-CoA hydratase activity / Enoyl-CoA hydratase/isomerase, conserved site / Enoyl-CoA hydratase/isomerase signature. / Enoyl-CoA hydratase/isomerase / Enoyl-CoA hydratase/isomerase / ClpP/crotonase-like domain superfamily / EchA15

Function and homology information

Biological species

Mycolicibacterium paratuberculosis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.9 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: to be published
Title: Crystal Structure of enoyl-CoA hydratase EchA15 protein from Mycolicibacterium paratuberculosis
Authors: Abendroth, J. / Sankaran, B. / Lorimer, D.D. / Horanyi, P.S. / Edwards, T.E.

History

Deposition	Mar 19, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 7, 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	7m3w.cif.gz	371.1 KB	Display	PDBx/mmCIF format
PDB format	pdb7m3w.ent.gz	253.7 KB	Display	PDB format
PDBx/mmJSON format	7m3w.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/m3/7m3w ftp://data.pdbj.org/pub/pdb/validation_reports/m3/7m3w	HTTPS FTP

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Related structure data

Related structure data	3qk8S S: Starting model for refinement
Similar structure data	3qk8-d 1wz8-d 3q1t-d 3sll-d 2iex-2 2uzf-1 5aez-1 3h81-1 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

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Links

PDB pages	PDBj / wwPDB / NCBI

Deposited unit

A: Enoyl-CoA hydratase EchA15

B: Enoyl-CoA hydratase EchA15

C: Enoyl-CoA hydratase EchA15

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

1

A: Enoyl-CoA hydratase EchA15

B: Enoyl-CoA hydratase EchA15

C: Enoyl-CoA hydratase EchA15

A: Enoyl-CoA hydratase EchA15

B: Enoyl-CoA hydratase EchA15

C: Enoyl-CoA hydratase EchA15

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

Unit cell

Length a, b, c (Å)	131.600, 131.600, 107.810
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	94
Space group name H-M	P4₂2₁2
Space group name Hall	P4n2n
Symmetry operation	#1: x,y,z #2: -y+1/2,x+1/2,z+1/2 #3: y+1/2,-x+1/2,z+1/2 #4: x+1/2,-y+1/2,-z+1/2 #5: -x+1/2,y+1/2,-z+1/2 #6: -x,-y,z #7: y,x,-z #8: -y,-x,-z

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
d_1	ens_1	(chain "A" and (resid 3 through 10 or resid 12...
d_2	ens_1	(chain "B" and (resid 3 through 10 or resid 12...
d_3	ens_1	(chain "C" and (resid 3 through 10 or resid 12...

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	VAL	TYR	A	1 - 8
d_1	2	ens_1	ASP	VAL	A	10 - 99
d_1	3	ens_1	ASN	ALA	A	101 - 212
d_1	4	ens_1	HIS	ARG	A	214 - 228
d_1	5	ens_1	MET	THR	A	230 - 266
d_2	1	ens_1	VAL	TYR	B	2 - 9
d_2	2	ens_1	ASP	VAL	B	11 - 100
d_2	3	ens_1	ASN	ALA	B	102 - 213
d_2	4	ens_1	HIS	ARG	B	215 - 229
d_2	5	ens_1	MET	THR	B	231 - 267
d_3	1	ens_1	VAL	TYR	C	2 - 9
d_3	2	ens_1	ASP	VAL	C	11 - 100
d_3	3	ens_1	ASN	ALA	C	102 - 213
d_3	4	ens_1	HIS	ARG	C	215 - 229
d_3	5	ens_1	MET	THR	C	231 - 267

NCS oper:

ID	Code	Matrix	Vector
1	given	(-0.499645192123, -0.864480852359, -0.0550230669241), (0.866218767874, -0.498955334651, -0.0266199212316), (-0.00444164057462, -0.0609625288937, 0.998130172823)	-20.0329613441, 74.9003838186, 1.7919225729
2	given	(-0.498653777104, 0.866799780922, -0.00159698895225), (-0.866022871756, -0.498283205947, -0.0414515653083), (-0.0367259605031, -0.0192869506493, 0.999139238224)	-74.9571608337, 19.9414273888, -0.516791316116

#1: Protein	Enoyl-CoA hydratase EchA15 Mass: 31561.902 Da / Num. of mol.: 3 / Fragment: MypaA.00829.a.B1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycolicibacterium paratuberculosis (bacteria) Strain: ATCC BAA-968 / K-10 / Gene: echA15, MAP_2800 / Plasmid: MypaA.00829.a.A1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q73W60, enoyl-CoA hydratase
#2: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 43 / Source method: isolated from a natural source / Formula: H₂O

#1: Protein

Enoyl-CoA hydratase EchA15

Mass: 31561.902 Da / Num. of mol.: 3 / Fragment: MypaA.00829.a.B1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.)

Mycolicibacterium paratuberculosis (bacteria)
Strain: ATCC BAA-968 / K-10 / Gene: echA15, MAP_2800 / Plasmid: MypaA.00829.a.A1 / Production host:

Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q73W60,

enoyl-CoA hydratase

#2: Water

ChemComp-HOH / water /

Water

Mass: 18.015 Da / Num. of mol.: 43 / 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: 2.47 Å³/Da / Density % sol: 50.2 %
Crystal grow	Temperature: 287 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: Rigaku Reagents JCSG+ screen, optimized condition B4: 10% (w/V) PEG 8000, 8% (V/V) ethylene glycol, 100mM HEPES pH 7.5: MypaA.00829.b.A1.PS00774 at 52.8 mg/ml: tray 220508a7: cryo: 25% EG: puck ebk5-13.

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Data collection

Diffraction

Mean temperature: 100 K / Serial crystal experiment: N

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.9774 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Mar 26, 2011

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9774 Å / Relative weight: 1

Reflection

Resolution: 2.9→50 Å / Num. obs: 21541 / % possible obs: 99.7 % / Redundancy: 10.339 % / B_iso Wilson estimate: 61.301 Å² / CC_1/2: 0.999 / R_merge(I) obs: 0.074 / R_rim(I) all: 0.078 / Χ²: 0.928 / Net I/σ(I): 27.02

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
2.9-2.98	10.67	0.577	4.04	1559	0.867	0.608	99.9
2.98-3.06	10.627	0.473	4.86	1519	0.916	0.498	99.9
3.06-3.15	10.605	0.38	6.13	1497	0.947	0.4	100
3.15-3.24	10.575	0.302	7.69	1430	0.962	0.318	100
3.24-3.35	10.621	0.228	10.39	1400	0.976	0.24	100
3.35-3.47	10.386	0.184	13	1377	0.984	0.194	99.9
3.47-3.6	10.489	0.125	18.36	1294	0.994	0.132	100
3.6-3.74	10.223	0.109	21.77	1265	0.994	0.116	99.7
3.74-3.91	10.225	0.1	23.37	1214	0.995	0.106	99.8
3.91-4.1	10.374	0.067	32.41	1169	0.998	0.071	99.9
4.1-4.32	10.285	0.049	42.16	1107	0.999	0.051	99.8
4.32-4.59	10.32	0.046	43.58	1061	0.999	0.049	99.8
4.59-4.9	10.191	0.046	44.67	1009	0.999	0.048	99.7
4.9-5.29	10.217	0.046	44.3	917	0.999	0.049	99.8
5.29-5.8	10.148	0.051	40.75	865	0.999	0.053	99.5
5.8-6.48	9.963	0.045	44.05	783	0.999	0.047	99.4
6.48-7.49	9.78	0.032	57.24	703	0.999	0.034	98.9
7.49-9.17	10.113	0.021	77.01	603	1	0.023	99
9.17-12.97	9.679	0.017	82.91	483	1	0.018	98.6
12.97-50	8.759	0.015	80.87	286	1	0.016	93.2

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: pdb entry 3qk8 as per Morda

3qk8

Resolution: 2.9→46.64 Å / SU ML: 0.3422 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 23.1127
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2335	1915	8.9 %	0
R_work	0.1778	19591	-	-
obs	0.1827	21506	99.74 %	-

Solvent computation

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

Displacement parameters

B_iso mean: 64.28 Å²

Refinement step

Cycle: LAST / Resolution: 2.9→46.64 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5896	0	0	43	5939

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.0046	6077
X-RAY DIFFRACTION	f_angle_d	0.7026	8293
X-RAY DIFFRACTION	f_chiral_restr	0.0499	961
X-RAY DIFFRACTION	f_plane_restr	0.0069	1087
X-RAY DIFFRACTION	f_dihedral_angle_d	12.5338	2150

Refine LS restraints NCS

Ens-ID	Dom-ID	Auth asym-ID	Refine-ID	Type	Rms dev position (Å)
ens_1	d_2	A	X-RAY DIFFRACTION	Torsion NCS	0.337670216599
ens_1	d_3	A	X-RAY DIFFRACTION	Torsion NCS	0.432902482125

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 (%)
2.9-2.97	0.3177	132	0.263	1371	X-RAY DIFFRACTION	99.93
2.97-3.05	0.3171	138	0.2338	1368	X-RAY DIFFRACTION	99.93
3.05-3.14	0.3034	137	0.2324	1366	X-RAY DIFFRACTION	100
3.14-3.24	0.2811	148	0.2207	1365	X-RAY DIFFRACTION	100
3.24-3.36	0.2885	140	0.215	1388	X-RAY DIFFRACTION	100
3.36-3.49	0.2921	130	0.2318	1377	X-RAY DIFFRACTION	99.93
3.49-3.65	0.2524	138	0.1886	1390	X-RAY DIFFRACTION	99.87
3.65-3.85	0.2311	144	0.1739	1375	X-RAY DIFFRACTION	99.87
3.85-4.09	0.2479	132	0.1638	1396	X-RAY DIFFRACTION	100
4.09-4.4	0.1664	122	0.1371	1411	X-RAY DIFFRACTION	99.93
4.4-4.84	0.1994	127	0.1404	1419	X-RAY DIFFRACTION	99.87
4.85-5.54	0.2068	137	0.1521	1417	X-RAY DIFFRACTION	99.68
5.55-6.98	0.2225	141	0.1828	1437	X-RAY DIFFRACTION	99.5
6.98-46.64	0.2092	149	0.1712	1511	X-RAY DIFFRACTION	98.22

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	0.912208999332	-1.02160845637	0.578832618007	3.45481875897	-2.55078508763	1.99907454362	-0.0693979169503	-0.448081521976	-0.167567204618	-0.656363176754	0.46453413646	1.12787423477	0.0558564610727	-0.990840232147	-0.318452902398	0.658435300951	-0.0987249983945	0.203383174041	0.937615669722	-0.22110064489	1.05076421597	-65.7998213603	24.6437700345	10.0194149657
2	3.30754006054	0.19520852816	-0.640617400874	1.45998394514	0.16831278385	2.21214047656	0.0274885033464	-0.237969127351	0.00210603099647	0.398290674738	-0.0902796909013	0.511551962978	0.305961387898	-0.229682900918	0.0634933563732	0.52204259262	-0.0523106347604	0.157470485117	0.377567850343	-0.0335529736574	0.444683047687	-46.4602223226	19.0706705891	14.7888907062
3	7.12111062506	3.99548612684	3.29174887067	2.39897405812	1.85454645375	1.66039802972	0.0560266495931	0.626807666636	-1.33099678052	0.8370639746	0.438561818655	-0.577908595607	0.763154596259	1.03693518208	-0.603757450287	0.820271229655	0.28267300383	-0.219969952296	0.640844314349	-0.0610531872829	0.863799313241	-9.19803729642	4.69126105509	9.92103062032
4	2.14046741952	0.32627832725	-1.11653645117	3.35095642216	0.278820142137	2.38214121347	-0.00190169570384	-0.366667786423	-0.385278099072	0.658293928039	-0.0373878125739	-0.691553080091	0.393821029344	0.617595782982	0.159347416535	0.64967610098	0.161383527277	-0.14803944264	0.483816371635	0.00986876438368	0.48776216176	-9.72250150677	13.7805833373	14.1593175058
5	1.75877261924	0.82500331096	-0.50152631471	2.56131139874	0.340715863688	1.67384543506	-0.0070423400017	-0.332862461429	0.0602006773099	0.536540178775	-0.133819496263	-0.393545600922	0.180879207418	0.36841630786	0.0901941946725	0.499433576831	0.0578481920839	-0.131527141713	0.462773643926	0.0381237324965	0.316225423147	-13.0399725822	27.3639684105	14.8856806633
6	2.69997578329	0.579662393092	-0.414248051952	1.45581768254	0.427155774692	1.85365331285	0.0551048107688	-0.327250163407	-0.117695164411	0.685249861213	-0.0591244677002	-0.00824348659074	0.240392250434	0.105784821168	0.0156271263846	0.598964480309	0.042624451923	-0.061196095675	0.369636325523	0.0257816908568	0.303687422973	-21.8277040413	22.3033576742	16.4745265138
7	4.89532453869	-0.676671688829	1.87777671719	2.26769393686	1.02631609767	5.3566165223	-0.0373646625888	-0.0524727315172	-0.105896819219	0.171730582893	0.3037486437	-0.167760206138	0.385601557411	-0.24200566134	-0.213674322096	0.485140360734	-0.12476509154	-0.156047788872	0.883083432343	-0.0263471954451	0.619450541526	0.0485856957353	42.0871910456	18.9191451308
8	8.20021742016	-1.6258617521	-3.25391593325	1.8006833024	2.13363059776	2.78361387993	0.569932258507	-0.133476164499	2.06214578777	0.241679527598	0.2016308004	0.0990016607566	-0.851862120391	0.530743320539	-0.70078956575	0.93950575215	-0.147163376326	0.00912150432902	0.497872344089	-0.0483493302548	1.12255022625	-19.8161973493	64.0926144766	11.0153267787
9	2.58387785891	0.895021125849	0.171269256124	1.53661162046	0.330286014839	1.593759613	0.0251783129855	-0.183731212085	0.838815516841	0.523695288466	-0.156995138961	0.528738190968	-0.372065263165	-0.218578470785	0.100278027918	0.618855732384	0.02141455118	0.112870748675	0.352844456575	-0.100703866519	0.756980379523	-34.978123534	50.077949114	15.6194694444

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 24 )	A	A	3 - 24	1 - 22
2	2	chain 'A' and (resid 25 through 268 )	A	A	25 - 268	23 - 266
3	3	chain 'B' and (resid 2 through 24 )	B	B	2 - 24	1 - 23
4	4	chain 'B' and (resid 25 through 66 )	B	B	25 - 66	24 - 65
5	5	chain 'B' and (resid 67 through 175 )	B	B	67 - 175	66 - 174
6	6	chain 'B' and (resid 176 through 248 )	B	B	176 - 248	175 - 247
7	7	chain 'B' and (resid 249 through 268 )	B	B	249 - 268	248 - 267
8	8	chain 'C' and (resid 2 through 24 )	C	C	2 - 24	1 - 23
9	9	chain 'C' and (resid 25 through 268 )	C	C	25 - 268	24 - 267

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Yorodumi