PDB-4eit: Crystal structure of an enoyl-(acyl carrier protein) reductase fr...

ID or keywords:

Entry

Database: PDB / ID: 4eit

Title

Crystal structure of an enoyl-(acyl carrier protein) reductase from Bartonella henselae

Components

Enoyl-[acyl-carrier-protein] reductase [NADH]

Keywords

OXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / selenomethionine-labeled / acyl-carrier protein / NAD+dependent / fatty acid biosynthesis

Function / homology

Function and homology information

enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity / enoyl-[acyl-carrier-protein] reductase (NADH) / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function

Biological species

Bartonella henselae (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.4 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal structure of an enoyl-(acyl carrier protein) reductase from Bartonella henselae
Authors: Edwards, T.E. / Craig, T.K. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

History

Deposition	Apr 5, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 18, 2012	Provider: repository / Type: Initial release
Revision 1.1	Sep 13, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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 / _struct_ref_seq_dif.details
Revision 1.2	Dec 6, 2023	Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.3	Nov 6, 2024	Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	4eit.cif.gz	550.3 KB	Display	PDBx/mmCIF format
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Validation report

Summary document	4eit_validation.pdf.gz	467.3 KB	Display	wwPDB validaton report
Full document	4eit_full_validation.pdf.gz	477.2 KB	Display
Data in XML	4eit_validation.xml.gz	51.1 KB	Display
Data in CIF	4eit_validation.cif.gz	70.7 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ei/4eit ftp://data.pdbj.org/pub/pdb/validation_reports/ei/4eit	HTTPS FTP

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Related structure data

Related structure data	3grkS S: Starting model for refinement
Similar structure data	3ek2-d 5trt-d 5i7f-2 5i7s-1 5i7v-1 4bnn-1 4nk4-4 5i8w-1 5i9m-2 5i9n-1 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: BaheA.00010.b

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (3) #77 - May 2006 Glucose Oxidase similarity (1)

Deposited unit

A: Enoyl-[acyl-carrier-protein] reductase [NADH]

B: Enoyl-[acyl-carrier-protein] reductase [NADH]

C: Enoyl-[acyl-carrier-protein] reductase [NADH]

D: Enoyl-[acyl-carrier-protein] reductase [NADH]

E: Enoyl-[acyl-carrier-protein] reductase [NADH]

F: Enoyl-[acyl-carrier-protein] reductase [NADH]

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

1

A: Enoyl-[acyl-carrier-protein] reductase [NADH]

B: Enoyl-[acyl-carrier-protein] reductase [NADH]

C: Enoyl-[acyl-carrier-protein] reductase [NADH]

D: Enoyl-[acyl-carrier-protein] reductase [NADH]

defined by author&software
120 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

E: Enoyl-[acyl-carrier-protein] reductase [NADH]

F: Enoyl-[acyl-carrier-protein] reductase [NADH]

E: Enoyl-[acyl-carrier-protein] reductase [NADH]

F: Enoyl-[acyl-carrier-protein] reductase [NADH]

defined by author&software
120 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	122.360, 76.860, 171.950
Angle α, β, γ (deg.)	90.000, 107.990, 90.000
Int Tables number	5
Space group name H-M	C121

Noncrystallographic symmetry (NCS)

NCS domain:
NCS domain segments:

Component-ID: _ / Refine code: _

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	GLY	GLY	ALA	ALA	A	A	6 - 261	10 - 265
2	1	GLY	GLY	ALA	ALA	B	B	6 - 261	10 - 265
1	2	GLY	GLY	LYS	LYS	A	A	6 - 260	10 - 264
2	2	GLY	GLY	LYS	LYS	C	C	6 - 260	10 - 264
1	3	GLY	GLY	ALA	ALA	A	A	6 - 261	10 - 265
2	3	GLY	GLY	ALA	ALA	D	D	6 - 261	10 - 265
1	4	GLY	GLY	LYS	LYS	A	A	6 - 260	10 - 264
2	4	GLY	GLY	LYS	LYS	E	E	6 - 260	10 - 264
1	5	GLY	GLY	VAL	VAL	A	A	6 - 262	10 - 266
2	5	GLY	GLY	VAL	VAL	F	F	6 - 262	10 - 266
1	6	GLY	GLY	ALA	ALA	B	B	4 - 261	8 - 265
2	6	GLY	GLY	ALA	ALA	C	C	4 - 261	8 - 265
1	7	GLY	GLY	ALA	ALA	B	B	6 - 261	10 - 265
2	7	GLY	GLY	ALA	ALA	D	D	6 - 261	10 - 265
1	8	ASN	ASN	ALA	ALA	B	B	5 - 261	9 - 265
2	8	ASN	ASN	ALA	ALA	E	E	5 - 261	9 - 265
1	9	GLY	GLY	ALA	ALA	B	B	6 - 261	10 - 265
2	9	GLY	GLY	ALA	ALA	F	F	6 - 261	10 - 265
1	10	GLY	GLY	LYS	LYS	C	C	6 - 260	10 - 264
2	10	GLY	GLY	LYS	LYS	D	D	6 - 260	10 - 264
1	11	ASN	ASN	ALA	ALA	C	C	5 - 261	9 - 265
2	11	ASN	ASN	ALA	ALA	E	E	5 - 261	9 - 265
1	12	GLY	GLY	LYS	LYS	C	C	6 - 260	10 - 264
2	12	GLY	GLY	LYS	LYS	F	F	6 - 260	10 - 264
1	13	GLY	GLY	ALA	ALA	D	D	6 - 261	10 - 265
2	13	GLY	GLY	ALA	ALA	E	E	6 - 261	10 - 265
1	14	GLY	GLY	LYS	LYS	D	D	6 - 260	10 - 264
2	14	GLY	GLY	LYS	LYS	F	F	6 - 260	10 - 264
1	15	GLY	GLY	ALA	ALA	E	E	6 - 261	10 - 265
2	15	GLY	GLY	ALA	ALA	F	F	6 - 261	10 - 265

NCS ensembles :

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

#1: Protein	Enoyl-[acyl-carrier-protein] reductase [NADH] Mass: 30076.152 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bartonella henselae (bacteria) / Strain: Houston-1 / Gene: BH04310, fabI2, fabl2 / Production host: Escherichia coli (E. coli) References: UniProt: Q6G4D5, UniProt: A0A0H3M2Q2*PLUS, enoyl-[acyl-carrier-protein] reductase (NADH)
#2: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 199 / Source method: isolated from a natural source / Formula: H₂O
Has protein modification	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.13 Å³/Da / Density % sol: 42.27 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8 Details: BaheA.00010.b.A1 PW26981 selenomethionine-labeled at 27.5 mg/mL against PACT screen condition B5, 0.1 M MIB pH 8.0, 25% PEG 1500 with 15% ethylene glycol as cryo-protectant, crystal tracking ...Details: BaheA.00010.b.A1 PW26981 selenomethionine-labeled at 27.5 mg/mL against PACT screen condition B5, 0.1 M MIB pH 8.0, 25% PEG 1500 with 15% ethylene glycol as cryo-protectant, crystal tracking ID 232038b5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal

Density Matthews: 2.13 Å³/Da / Density % sol: 42.27 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8
Details: BaheA.00010.b.A1 PW26981 selenomethionine-labeled at 27.5 mg/mL against PACT screen condition B5, 0.1 M MIB pH 8.0, 25% PEG 1500 with 15% ethylene glycol as cryo-protectant, crystal tracking ...

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-D / Wavelength: 1.07806 Å

Detector

Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 28, 2012

Radiation

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

Radiation wavelength

Wavelength: 1.07806 Å / Relative weight: 1

Reflection

Resolution: 2.4→50 Å / Num. all: 59634 / Num. obs: 59084 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Redundancy: 3.8 % / B_iso Wilson estimate: 44.808 Å² / R_merge(I) obs: 0.089 / Net I/σ(I): 10.42

Reflection shell

Diffraction-ID: 1

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Num. measured obs	Num. unique obs	% possible all
2.4-2.46		0.441	3.14	16632	4292	98.6
2.46-2.53		0.399	3.45	16215	4182	98.7
2.53-2.6		0.327	4.15	16047	4140	98.7
2.6-2.68		0.28	4.75	15498	4009	98.9
2.68-2.77		0.24	5.47	15096	3896	98.9
2.77-2.87		0.205	6.31	14350	3706	98.9
2.87-2.98		0.155	7.94	14069	3642	99
2.98-3.1		0.14	8.8	13358	3466	99.3
3.1-3.24		0.116	10.17	12973	3379	99.1
3.24-3.39		0.097	12.04	12282	3209	99.3
3.39-3.58		0.081	13.95	11615	3050	99.3
3.58-3.79		0.076	15.2	11090	2916	99.2
3.79-4.06		0.065	17.07	10296	2724	99.5
4.06-4.38		0.062	18.61	9500	2535	99.5
4.38-4.8		0.061	19.19	8957	2378	99.5
4.8-5.37		0.057	19.06	7979	2111	99.8
5.37-6.2		0.061	18.62	7084	1881	99.2
6.2-7.59		0.058	19.52	6021	1610	99.6
7.59-10.73		0.054	21.65	4658	1261	99.8
	10.73	0.05	20.88	2383	697	96.1

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	47.83 Å
Translation	2.5 Å	47.83 Å

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
PHASER	2.3.0	phasing
REFMAC		refinement
PDB_EXTRACT	3.11	data extraction
XDS		data reduction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3grk

3grk

Resolution: 2.4→50 Å / Cor.coef. F_o:F_c: 0.941 / Cor.coef. F_o:F_c free: 0.925 / WR_factor R_free: 0.2279 / WR_factor R_work: 0.1971 / Occupancy max: 1 / Occupancy min: 0.4 / FOM work R set: 0.8647 / SU B: 14.653 / SU ML: 0.166 / SU R Cruickshank DPI: 0.4758 / SU R_free: 0.2474 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.476 / ESU R Free: 0.247 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.2262	2994	5.1 %	RANDOM
R_work	0.1956	-	-	-
obs	0.1972	59083	99.13 %	-

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: 104.87 Å² / B_iso mean: 37.2283 Å² / B_iso min: 11.64 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.14 Å²	0 Å²	-1.21 Å²
2-	-	0.79 Å²	0 Å²
3-	-	-	-1.68 Å²

Refinement step

Cycle: LAST / Resolution: 2.4→50 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	10961	0	0	199	11160

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	11185
X-RAY DIFFRACTION	r_bond_other_d	0.007	0.02	7039
X-RAY DIFFRACTION	r_angle_refined_deg	1.484	1.968	15214
X-RAY DIFFRACTION	r_angle_other_deg	1.349	3	17223
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.554	5	1489
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.691	23.904	415
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	13.094	15	1562
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.216	15	47
X-RAY DIFFRACTION	r_chiral_restr	0.082	0.2	1794
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	12716
X-RAY DIFFRACTION	r_gen_planes_other	0.006	0.02	2299

Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: LOCAL / Weight: 0.05

LS refinement shell

Resolution: 2.4→2.462 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.282	226	-
R_work	0.265	3932	-
all	-	4158	-
obs	-	-	98.65 %

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	0.5622	-0.1065	0.527	0.2553	-0.2108	0.5715	-0.2811	0.2432	0.1748	0.0061	0.0715	0.0271	-0.2612	0.1878	0.2095	0.2468	-0.1906	-0.1079	0.1599	0.1046	0.1493	-29.9182	30.1173	-39.9279
2	0.7226	-0.0142	0.5883	0.292	-0.3737	0.9638	0.0885	0.0785	-0.1591	-0.0157	0.0162	0.0128	0.1253	0.08	-0.1047	0.1817	-0.0286	0.0187	0.0913	-0.0094	0.0915	-23.8677	-7.842	-22.7535
3	0.5518	-0.2281	0.6885	0.1158	-0.2593	0.8892	-0.1638	0.1639	0.1112	0.1043	-0.0415	-0.0042	-0.1948	0.2247	0.2052	0.1708	-0.1182	-0.0024	0.1919	0.068	0.115	-10.447	18.0093	-17.3219
4	0.7206	-0.1713	0.3356	0.1961	-0.3507	0.6345	-0.0296	-0.0555	0.0176	-0.0531	0.0543	0.0148	0.1166	-0.1309	-0.0247	0.1414	-0.1282	0.019	0.1477	-0.0135	0.0677	-49.7573	9.0707	-32.1176
5	0.3739	0.2549	-0.3587	0.261	-0.0864	0.9244	0.1273	-0.0053	0.0627	0.0376	-0.0656	0.0496	-0.1025	-0.1162	-0.0617	0.0932	0.0312	0.0177	0.1658	0.0001	0.1176	-49.4514	17.9843	-75.5537
6	0.6356	-0.0301	-0.1779	0.0518	-0.0861	0.6217	0.0422	-0.0696	-0.0677	0.0221	-0.0055	0.0205	0.1597	-0.0715	-0.0367	0.1348	-0.0672	-0.022	0.1414	0.0351	0.1115	-44.7729	-11.1587	-69.589

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	6 - 262
2	X-RAY DIFFRACTION	2	B	4 - 261
3	X-RAY DIFFRACTION	3	C	4 - 261
4	X-RAY DIFFRACTION	4	D	6 - 261
5	X-RAY DIFFRACTION	5	E	5 - 261
6	X-RAY DIFFRACTION	6	F	6 - 262

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