PDB-5c9g: Crystal Structure of a Putative enoyl-CoA hydratase/isomerase fam...

ID or keywords:

Entry

Database: PDB / ID: 5c9g

Title

Crystal Structure of a Putative enoyl-CoA hydratase/isomerase family protein from Hyphomonas neptunium

Components

Enoyl-CoA hydratase/isomerase family protein

Keywords

ISOMERASE /

Structural Genomics / PSI-Biology / New York Structural Genomics Research Consortium / NYSGRC

Function / homology

Function and homology information

isomerase activity
Similarity search - Function

Biological species

Hyphomonas neptunium (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.1 Å

Authors

Szlachta, K. / Cooper, D.R. / Chapman, H.C. / Cymbrowski, M.T. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Bonanno, J. / Seidel, R. / Almo, S.C. ...

Citation

Journal: to be published
Title: Crystal Structure of a Putative enoyl-CoA hydratase/isomerase family protein from Hyphomonas neptunium
Authors: Szlachta, K. / Cooper, D.R. / Chapman, H.C. / Cymbrowski, M.T. / Stead, M. / Hillerich, B.S. / Ahmed, M. / Bonanno, J. / Seidel, R. / Almo, S.C. / Minor, W. / Hammonds, J. / New York ...

History

Deposition	Jun 26, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 14, 2015	Provider: repository / Type: Initial release
Revision 1.1	Apr 13, 2022	Group: Database references / Derived calculations / Structure summary Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_oper_list Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2	Sep 27, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id
Revision 1.3	Nov 15, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	5c9g.cif.gz	591.3 KB	Display	PDBx/mmCIF format
PDB format	pdb5c9g.ent.gz	485.5 KB	Display	PDB format
PDBx/mmJSON format	5c9g.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/c9/5c9g ftp://data.pdbj.org/pub/pdb/validation_reports/c9/5c9g	HTTPS FTP

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Related structure data

Related structure data	4olqSC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4olq-1 4olq-2 6b4s-d 3gz6-d 6gpx-d 6jqf-d 3o2x-d 3ljz-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) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search
Other databases	TargetTrack: NYSGRC-028317

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#154 - Oct 2012 Citric Acid Cycle similarity (1) #21 - Sep 2001 Antibodies similarity (1)

Deposited unit

A: Enoyl-CoA hydratase/isomerase family protein

B: Enoyl-CoA hydratase/isomerase family protein

C: Enoyl-CoA hydratase/isomerase family protein

D: Enoyl-CoA hydratase/isomerase family protein

E: Enoyl-CoA hydratase/isomerase family protein

F: Enoyl-CoA hydratase/isomerase family protein

hetero molecules

182 kDa, 6 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

A: Enoyl-CoA hydratase/isomerase family protein

B: Enoyl-CoA hydratase/isomerase family protein

C: Enoyl-CoA hydratase/isomerase family protein

defined by author&software
90.7 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

D: Enoyl-CoA hydratase/isomerase family protein

E: Enoyl-CoA hydratase/isomerase family protein

F: Enoyl-CoA hydratase/isomerase family protein

hetero molecules

defined by author&software
91 kDa, 3 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	63.479, 128.120, 209.646
Angle α, β, γ (deg.)	90.000, 90.000, 90.000
Int Tables number	19
Space group name H-M	P2₁2₁2₁

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: 0 / Refine code: 0

Dom-ID	Ens-ID	Beg auth comp-ID	Beg label comp-ID	End auth comp-ID	End label comp-ID	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	SER	SER	TYR	TYR	A	A	0 - 259	22 - 281
2	1	SER	SER	TYR	TYR	B	B	0 - 259	22 - 281
1	2	THR	THR	TYR	TYR	A	A	2 - 259	24 - 281
2	2	THR	THR	TYR	TYR	C	C	2 - 259	24 - 281
1	3	GLY	GLY	ARG	ARG	A	A	-12 - 260	10 - 282
2	3	GLY	GLY	ARG	ARG	D	D	-12 - 260	10 - 282
1	4	THR	THR	TYR	TYR	A	A	2 - 259	24 - 281
2	4	THR	THR	TYR	TYR	E	E	2 - 259	24 - 281
1	5	GLN	GLN	TYR	TYR	A	A	-1 - 259	21 - 281
2	5	GLN	GLN	TYR	TYR	F	F	-1 - 259	21 - 281
1	6	THR	THR	TYR	TYR	B	B	2 - 259	24 - 281
2	6	THR	THR	TYR	TYR	C	C	2 - 259	24 - 281
1	7	SER	SER	TYR	TYR	B	B	0 - 259	22 - 281
2	7	SER	SER	TYR	TYR	D	D	0 - 259	22 - 281
1	8	THR	THR	TYR	TYR	B	B	2 - 259	24 - 281
2	8	THR	THR	TYR	TYR	E	E	2 - 259	24 - 281
1	9	SER	SER	TYR	TYR	B	B	0 - 259	22 - 281
2	9	SER	SER	TYR	TYR	F	F	0 - 259	22 - 281
1	10	THR	THR	TYR	TYR	C	C	2 - 259	24 - 281
2	10	THR	THR	TYR	TYR	D	D	2 - 259	24 - 281
1	11	THR	THR	ARG	ARG	C	C	2 - 260	24 - 282
2	11	THR	THR	ARG	ARG	E	E	2 - 260	24 - 282
1	12	THR	THR	TYR	TYR	C	C	2 - 259	24 - 281
2	12	THR	THR	TYR	TYR	F	F	2 - 259	24 - 281
1	13	THR	THR	TYR	TYR	D	D	2 - 259	24 - 281
2	13	THR	THR	TYR	TYR	E	E	2 - 259	24 - 281
1	14	GLN	GLN	TYR	TYR	D	D	-1 - 259	21 - 281
2	14	GLN	GLN	TYR	TYR	F	F	-1 - 259	21 - 281
1	15	THR	THR	TYR	TYR	E	E	2 - 259	24 - 281
2	15	THR	THR	TYR	TYR	F	F	2 - 259	24 - 281

NCS ensembles :

ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15

#1: Protein	Enoyl-CoA hydratase/isomerase family protein Mass: 30233.537 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Hyphomonas neptunium (strain ATCC 15444) (bacteria) Strain: ATCC 15444 / Gene: HNE_1107 / Plasmid: pSGC-His / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 (DE3) RIL / References: UniProt: Q0C365
#2: Chemical	ChemComp-PG4 / TETRAETHYLENE GLYCOL / Polyethylene glycol Mass: 194.226 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C₈H₁₈O₅ / Comment: precipitant*YM
#3: Chemical	ChemComp-MLT / D-MALATE / (2R)-2-HYDROXYBUTANEDIOIC ACID / 2-HYDROXY-SUCCINIC ACID / Malic acid Mass: 134.087 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₄H₆O₅
#4: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 1153 / 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: 2.37 Å³/Da / Density % sol: 48.06 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2 ul of 17.6 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of (the JCSG+ condition #G8) 0.15M DL-Malic acid, 19% ...Details: 0.2 ul of 17.6 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of (the JCSG+ condition #G8) 0.15M DL-Malic acid, 19% PEG 3350 and equilibrated against 1.5 M NaCl solution in 96 Well 3 drop Crystallization Plate (Swissci).

Crystal

Density Matthews: 2.37 Å³/Da / Density % sol: 48.06 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.2 ul of 17.6 mg/ml protein in 20 mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5 mM TCEP were mixed with 0.2 ul of (the JCSG+ condition #G8) 0.15M DL-Malic acid, 19% ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

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

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 24, 2014 / 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: 2.1→40 Å / Num. obs: 98973 / % possible obs: 97.7 % / Redundancy: 7.3 % / R_merge(I) obs: 0.135 / R_pim(I) all: 0.055 / R_rim(I) all: 0.14 / Χ²: 1.159 / Net I/av σ(I): 14.857 / Net I/σ(I): 4.8 / Num. measured all: 726544

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	Num. unique all	CC_1/2	R_pim(I) all	Χ²	% possible all	R_merge(I) obs	R_rim(I) all
2.1-2.14	6.9	4779	0.747	0.472	0.664	95.2
2.14-2.18	7.1	4763	0.79	0.434	0.65	95.6
2.18-2.22	7.1	4775	0.841	0.377	0.672	95.9	0.981
2.22-2.26	7.2	4809	0.884	0.243	0.689	95.9	0.635	0.682
2.26-2.31	7.2	4822	0.9	0.272	0.696	96.7	0.71	0.762
2.31-2.37	7.2	4840	0.925	0.225	0.717	96.2	0.587	0.63
2.37-2.42	7.2	4851	0.946	0.199	0.723	97.3	0.518	0.556
2.42-2.49	7.2	4871	0.952	0.173	0.734	97.3	0.451	0.484
2.49-2.56	7.2	4901	0.961	0.153	0.779	96.9	0.399	0.428
2.56-2.65	7.2	4873	0.972	0.125	0.8	97.2	0.326	0.35
2.65-2.74	7.2	4917	0.98	0.106	0.842	97.8	0.276	0.297
2.74-2.85	7.3	4912	0.985	0.086	0.903	97.5	0.225	0.241
2.85-2.98	7.3	4937	0.99	0.073	0.945	97.9	0.189	0.203
2.98-3.14	7.3	4968	0.992	0.06	1.051	98.2	0.156	0.167
3.14-3.33	7.4	5031	0.995	0.047	1.24	98.8	0.124	0.133
3.33-3.59	7.5	5049	0.996	0.039	1.525	99.7	0.103	0.11
3.59-3.95	7.7	5115	0.995	0.037	2.067	100	0.096	0.103
3.95-4.52	7.9	5140	0.997	0.033	2.573	100	0.087	0.093
4.52-5.7	8	5190	0.997	0.029	2.191	100	0.079	0.084
5.7-40	7.6	5430	0.999	0.02	1.891	99.9	0.053	0.057

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0107	refinement
HKL-3000		data scaling
PDB_EXTRACT	3.15	data extraction
HKL-3000		data collection
MOLREP		phasing
HKL-3000		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 4OLQ

4olq

Resolution: 2.1→40 Å / Cor.coef. F_o:F_c: 0.959 / Cor.coef. F_o:F_c free: 0.943 / WR_factor R_free: 0.2091 / WR_factor R_work: 0.177 / FOM work R set: 0.8058 / SU B: 10.332 / SU ML: 0.14 / SU R Cruickshank DPI: 0.2367 / SU R_free: 0.1855 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.237 / ESU R Free: 0.186
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2321	4923	5 %	RANDOM
R_work	0.1984	-	-	-
obs	0.2	93373	97.65 %	-

Solvent computation

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

Displacement parameters

B_iso max: 97.38 Å² / B_iso mean: 33.663 Å² / B_iso min: 15.47 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-1.19 Å²	-0 Å²	0 Å²
2-	-	1.29 Å²	-0 Å²
3-	-	-	-0.1 Å²

Refinement step

Cycle: final / Resolution: 2.1→40 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	11687	0	22	1153	12862
B_iso mean	-	-	66.59	37.01	-
Num. residues	-	-	-	-	1587

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	11916
X-RAY DIFFRACTION	r_bond_other_d	0.009	0.02	11648
X-RAY DIFFRACTION	r_angle_refined_deg	1.489	1.974	16147
X-RAY DIFFRACTION	r_angle_other_deg	1.576	3	26678
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.653	5	1583
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	34.604	23.547	468
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	14.683	15	1834
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	14.683	15	93
X-RAY DIFFRACTION	r_chiral_restr	0.075	0.2	1841
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.021	13704
X-RAY DIFFRACTION	r_gen_planes_other	0.008	0.02	2613
X-RAY DIFFRACTION	r_mcbond_it	1.29	2.845	6344
X-RAY DIFFRACTION	r_mcbond_other	1.29	2.845	6343
X-RAY DIFFRACTION	r_mcangle_it	2.128	4.261	7920

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-ID	Dom-ID	Auth asym-ID	Number	Rms dev position (Å)
1	1	A	28946	0.08
1	2	B	28946	0.08
2	1	A	28684	0.08
2	2	C	28684	0.08
3	1	A	31100	0.04
3	2	D	31100	0.04
4	1	A	28872	0.09
4	2	E	28872	0.09
5	1	A	28776	0.08
5	2	F	28776	0.08
6	1	B	29552	0.08
6	2	C	29552	0.08
7	1	B	29744	0.08
7	2	D	29744	0.08
8	1	B	29696	0.08
8	2	E	29696	0.08
9	1	B	30214	0.07
9	2	F	30214	0.07
10	1	C	29552	0.08
10	2	D	29552	0.08
11	1	C	30438	0.05
11	2	E	30438	0.05
12	1	C	29416	0.09
12	2	F	29416	0.09
13	1	D	29656	0.09
13	2	E	29656	0.09
14	1	D	29616	0.08
14	2	F	29616	0.08
15	1	E	29396	0.09
15	2	F	29396	0.09

LS refinement shell

Resolution: 2.1→2.154 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.294	348	-
R_work	0.291	6593	-
all	-	6941	-
obs	-	-	95.59 %

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	0.2877	-0.1712	0.1993	0.129	-0.1256	0.1437	-0.0319	-0.0466	-0.0693	0.015	0.066	0.0261	-0.0323	-0.0446	-0.0341	0.0255	0.0093	0.0086	0.0608	0.0005	0.0422	-9.537	21.3597	15.6612
2	0.2549	-0.047	0.1673	0.1339	-0.062	0.361	-0.0398	-0.0143	0.0293	0.0142	0.0009	-0.0107	-0.0388	0.0292	0.0389	0.0313	0.0095	-0.0093	0.0347	-0.0104	0.0098	21.3774	33.1338	24.3619
3	0.3581	0.2649	0.0765	0.3444	-0.0619	0.2146	-0.0062	0.0198	-0.0046	0.0247	0.0319	0.0153	0.0456	0.0156	-0.0256	0.0496	0.0233	-0.0019	0.0244	-0.0068	0.007	12.1294	4.529	37.5844
4	0.0346	0.013	0.0737	0.0741	0.0314	0.1672	0.0014	0.0043	-0.0084	-0.0101	0.0194	0.0078	0.0035	0.0308	-0.0208	0.0149	-0.0071	-0.0003	0.0505	-0.0071	0.0303	29.9363	21.4049	88.4303
5	0.4976	-0.2085	0.0959	0.313	-0.0276	0.1356	0.0252	0.002	-0.0276	-0.0067	-0.0007	-0.0017	0.0567	-0.02	-0.0244	0.0367	-0.018	-0.01	0.0215	0.0024	0.0052	8.4116	4.8766	67.1701
6	0.3306	0.0915	0.1542	0.2054	0.0947	0.1991	-0.0412	0.0206	0.052	-0.0227	0.0168	0.016	-0.0045	-0.0072	0.0244	0.0274	-0.0084	-0.0032	0.0311	0.0115	0.0117	-1.2847	33.5362	80.5854

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	-12 - 260
2	X-RAY DIFFRACTION	2	B	-10 - 260
3	X-RAY DIFFRACTION	3	C	2 - 260
4	X-RAY DIFFRACTION	4	D	-12 - 260
5	X-RAY DIFFRACTION	5	E	2 - 260
6	X-RAY DIFFRACTION	6	F	-3 - 260

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