PDB-4b0i: Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehyd...

ID or keywords:

Entry

Database: PDB / ID: 4b0i

Title

Crystal Structure of 3-hydroxydecanoyl-Acyl Carrier Protein Dehydratase (FabA) mutant (H70N) from Pseudomonas aeruginosa in complex with 3-hydroxydecanoyl-N-acetyl cysteamine

Components

3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE

Keywords

LYASE / FATTY ACID BIOSYNTHESIS / BACTERIAL VIRULENCE / DRUG DISCOVERY

Function / homology

Function and homology information

trans-2-decenoyl-[acyl-carrier protein] isomerase / trans-2-decenoyl-acyl-carrier-protein isomerase activity / unsaturated fatty acid biosynthetic process / : / 3-hydroxyacyl-[acyl-carrier-protein] dehydratase / cytoplasm
Similarity search - Function

Biological species

PSEUDOMONAS AERUGINOSA (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 2.03 Å

Authors

Moynie, L. / McMahon, S.A. / Leckie, S.M. / Duthie, F.G. / Koehnke, A. / Naismith, J.H.

Citation

Journal: J.Mol.Biol. / Year: 2013
Title: Structural Insights Into the Mechanism and Inhibition of the Beta-Hydroxydecanoyl-Acyl Carrier Protein Dehydratase from Pseudomonas Aeruginosa
Authors: Moynie, L. / Leckie, S.M. / Mcmahon, S.A. / Duthie, F.G. / Koehnke, A. / Taylor, J.W. / Alphey, M.S. / Brenk, R. / Smith, A.D. / Naismith, J.H.

History

Deposition	Jul 2, 2012	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Nov 28, 2012	Provider: repository / Type: Initial release
Revision 1.1	Jan 16, 2013	Group: Database references
Revision 1.2	Dec 20, 2023	Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_sheet / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Remark 700

SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ...

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4b0i.cif.gz	349.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4b0i.ent.gz	291.1 KB	Display	PDB format
PDBx/mmJSON format	4b0i.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4b0i_validation.pdf.gz	1.4 MB	Display	wwPDB validaton report
Full document	4b0i_full_validation.pdf.gz	1.4 MB	Display
Data in XML	4b0i_validation.xml.gz	36.4 KB	Display
Data in CIF	4b0i_validation.cif.gz	50.4 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/b0/4b0i ftp://data.pdbj.org/pub/pdb/validation_reports/b0/4b0i	HTTPS FTP

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Related structure data

Related structure data	4b0bC 4b0cC 4b0jC 4b8uC 4fq9SC C: citing same article (ref.) S: Starting model for refinement
Similar structure data	4cl6-1 3fmu-d 4b8u-1 4fq9-3 4b8u-2 4b0j-8 4cl6-2 4b0j-7 4fq9-5 3tjm-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) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

Related structure data

4fq9SC

C: citing same article (ref.)

S: Starting model for refinement

Similar structure data

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (4)

Deposited unit

A: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE

B: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE

C: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE

D: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE

E: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE

hetero molecules

95.2 kDa, 5 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

C: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE

D: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE

hetero molecules

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

2

A: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE

B: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE

hetero molecules

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

3

E: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE

hetero molecules

E: 3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE

hetero molecules

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

Unit cell

Length a, b, c (Å)	110.791, 169.686, 108.300
Angle α, β, γ (deg.)	90.00, 90.00, 90.00
Int Tables number	20
Space group name H-M	C222₁

Components on special symmetry positions

ID	Model	Components
1	1	E-2009- HOH

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	E

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	2	A	26 - 60
2	1	1	2	E	26 - 60
1	2	1	2	A	64 - 134
2	2	1	2	E	64 - 134
1	3	1	5	A	135 - 138
2	3	1	5	E	135 - 138
1	4	1	2	A	139 - 171
2	4	1	2	E	139 - 171

NCS oper:

ID	Code	Matrix	Vector
1	given	(0.8177, -0.5677, -0.0951), (0.0297, -0.0951), (0.0297, -0.995)	6.1088, 29.5215, -61.2506
2	given	(0.331, 0.943, 0.0339), (-0.9418, 0.328, 0.0733), (0.058, -0.0562, 0.9967)	-68.1135, -28.3795, 4.6588
3	given	(0.8013, 0.5878, -0.1113), (0.5863, -0.8086, -0.0494), (-0.119, -0.0256, -0.9926)	-33.9203, 91.7643, -60.1804
4	given	(0.3075, -0.9511, 0.0285), (0.95, 0.3052, -0.0667), (0.0547, 0.0476, 0.9974)	-6.2526, 74.0216, 0.8203

#1: Protein	3-HYDROXYDECANOYL-[ACYL-CARRIER-PROTEIN] DEHYDRATASE / BETA-HYDROXYDECANOYL THIOESTER DEHYDRASE Mass: 18744.488 Da / Num. of mol.: 5 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PA01 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): STAR / References: UniProt: O33877, EC: 4.2.1.60
#2: Chemical	ChemComp-KBP / S-[2-(acetylamino)ethyl] (3R)-3-hydroxydecanethioate / 3-hydroxydecanoyl-N-acetylcysteamine Mass: 289.434 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C₁₄H₂₇NO₃S
#3: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H₂O
Compound details	ENGINEERED RESIDUE IN CHAIN A, HIS 70 TO ASN ENGINEERED RESIDUE IN CHAIN B, HIS 70 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, HIS 70 TO ASN ENGINEERED RESIDUE IN CHAIN B, HIS 70 TO ASN ENGINEERED RESIDUE IN CHAIN C, HIS 70 TO ASN ENGINEERED RESIDUE IN CHAIN D, HIS 70 TO ASN ENGINEERED RESIDUE IN CHAIN E, HIS 70 TO ASN

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.69 Å³/Da / Density % sol: 54.36 % / Description: NONE
Crystal grow	pH: 4.5 Details: 13% PEG MME 5000, 0.09 M LITHIUM SULPHATE, 0.1 M SODIUM CITRATE PH 4.5

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.99189
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 18, 2010
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.99189 Å / Relative weight: 1
Reflection	Resolution: 2.03→54.15 Å / Num. obs: 64767 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 4.5 % / R_merge(I) obs: 0.06 / Net I/σ(I): 15.23
Reflection shell	Resolution: 2.03→2.15 Å / Redundancy: 4.5 % / R_merge(I) obs: 0.46 / Mean I/σ(I) obs: 2.68 / % possible all: 99.5

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Processing

Software

Name	Version	Classification
REFMAC	5.5.0109	refinement
XDS		data reduction
XSCALE		data scaling
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4FQ9

4fq9

Resolution: 2.03→54.15 Å / Cor.coef. F_o:F_c: 0.965 / Cor.coef. F_o:F_c free: 0.955 / SU B: 9.906 / SU ML: 0.117 / Cross valid method: THROUGHOUT / ESU R: 0.162 / ESU R Free: 0.144 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.20571	3280	5 %	RANDOM
R_work	0.17202	-	-	-
obs	0.17378	61487	98 %	-

Solvent computation

Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK

Displacement parameters

B_iso mean: 42.398 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	2.17 Å²	0 Å²	0 Å²
2-	-	1.92 Å²	0 Å²
3-	-	-	-4.09 Å²

Refinement step

Cycle: LAST / Resolution: 2.03→54.15 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	6490	0	95	355	6940

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.022	6728
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	4644
X-RAY DIFFRACTION	r_angle_refined_deg	1.275	1.969	9083
X-RAY DIFFRACTION	r_angle_other_deg	0.763	3.003	11119
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	8.499	5	839
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	36.84	23.525	295
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.551	15	1074
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.979	15	46
X-RAY DIFFRACTION	r_chiral_restr	0.077	0.2	974
X-RAY DIFFRACTION	r_gen_planes_refined	0.014	0.021	7547
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1418
X-RAY DIFFRACTION	r_nbd_refined
X-RAY DIFFRACTION	r_nbd_other
X-RAY DIFFRACTION	r_nbtor_refined
X-RAY DIFFRACTION	r_nbtor_other
X-RAY DIFFRACTION	r_xyhbond_nbd_refined
X-RAY DIFFRACTION	r_xyhbond_nbd_other
X-RAY DIFFRACTION	r_metal_ion_refined
X-RAY DIFFRACTION	r_metal_ion_other
X-RAY DIFFRACTION	r_symmetry_vdw_refined
X-RAY DIFFRACTION	r_symmetry_vdw_other
X-RAY DIFFRACTION	r_symmetry_hbond_refined
X-RAY DIFFRACTION	r_symmetry_hbond_other
X-RAY DIFFRACTION	r_symmetry_metal_ion_refined
X-RAY DIFFRACTION	r_symmetry_metal_ion_other
X-RAY DIFFRACTION	r_mcbond_it	1.37	1.5	4153
X-RAY DIFFRACTION	r_mcbond_other	0.546	1.5	1755
X-RAY DIFFRACTION	r_mcangle_it	2.096	2	6626
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	3.662	3	2575
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it	5.47	4.5	2457
X-RAY DIFFRACTION	r_scangle_other
X-RAY DIFFRACTION	r_long_range_B_refined
X-RAY DIFFRACTION	r_long_range_B_other
X-RAY DIFFRACTION	r_rigid_bond_restr
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-ID	Number	Type	Rms dev position (Å)	Weight position
A	797	tight positional	0.06	0.05
B	797	tight positional	0.06	0.05
A	983	medium positional	0.16	0.5
B	983	medium positional	0.16	0.5
A	13	loose positional	0.07	5
B	13	loose positional	0.07	5
A	797	tight thermal	0.45	0.5
B	797	tight thermal	0.45	0.5
A	983	medium thermal	0.42	2
B	983	medium thermal	0.42	2
A	13	loose thermal	0.37	10
B	13	loose thermal	0.37	10

LS refinement shell

Resolution: 2.03→2.083 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.29	247	-
R_work	0.255	4557	-
obs	-	-	99.48 %

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	6.155	-6.5031	1.9489	16.4141	1.2485	5.6613	-0.1742	-0.8251	0.019	0.9478	0.2192	-0.3686	-0.253	0.7802	-0.045	0.2205	-0.1601	-0.0929	0.3734	0.0153	0.2752	-12.056	35.175	-12.597
2	0.7494	-0.1205	-0.0982	1.448	-0.121	2.1891	0.066	-0.0285	0.0723	0.0394	-0.05	-0.1671	-0.0315	0.2803	-0.016	0.1338	-0.0652	-0.0078	0.187	0.0006	0.2384	-19.913	31.164	-23.238
3	2.1094	-0.0882	0.2321	3.471	-2.1712	5.2411	0.0807	-0.2353	-0.0296	0.2398	0.2001	0.2091	0.2124	-0.4109	-0.2807	0.1808	-0.0949	-0.0114	0.1734	-0.0326	0.2186	-29.075	29.259	-18.819
4	20.1283	7.0957	-1.6703	9.8898	0.9813	2.1626	-0.0914	0.9399	0.0332	-0.8594	-0.097	-0.1069	1.318	0.5948	0.1885	0.7542	0.2949	0.041	0.2506	-0.0469	0.214	-22.855	7.153	-46.501
5	0.8937	0.1247	-0.0187	0.8164	-0.019	1.9753	0.1183	0.0079	-0.1183	-0.0507	-0.0613	-0.0712	0.3215	0.2051	-0.057	0.2468	0.0256	-0.0288	0.1345	0.0088	0.2297	-25.798	14.576	-35.296
6	2.5237	0.4038	-0.6848	2.88	-1.6228	4.8278	0.2047	0.1983	0.1674	-0.203	0.0114	0.1377	-0.0338	-0.1776	-0.2161	0.2396	-0.0115	-0.0216	0.1137	-0.0418	0.2121	-32.709	21.573	-38.806
7	21.798	1.8652	-1.2007	5.027	1.2755	0.4311	-0.0154	-1.413	0.9443	0.8031	-0.2148	-0.087	-0.4376	-0.2914	0.2301	0.4044	0.141	-0.1529	0.3738	-0.166	0.277	-42.374	74.494	-10.701
8	1.0039	-0.3553	-0.0264	0.8812	-0.3363	1.7173	-0.0871	-0.0237	0.1134	0.0571	0.0678	-0.0351	-0.185	-0.2876	0.0193	0.1703	-0.0051	-0.0268	0.2391	-0.0045	0.2101	-41.698	66.546	-21.801
9	4.0799	-1.11	2.4004	2.4611	-1.0195	4.448	0.0442	-0.3129	-0.3255	0.1079	0.1125	-0.0089	0.3608	-0.3856	-0.1567	0.1556	-0.0499	0.0149	0.2793	-0.0143	0.1838	-42.78	56.992	-17.881
10	5.0985	-4.2019	-2.0832	6.9483	-2.5966	0.1976	0.1084	0.5378	0.0394	-0.8174	-0.2877	-0.295	0.0116	0.101	0.1793	0.2577	-0.053	0.0765	0.318	0.0553	0.2755	-21.645	57.639	-46.761
11	0.9478	-0.4334	0.4196	1.2169	-0.0156	1.6635	0.0164	0.0774	0.0717	-0.1415	-0.0588	-0.2019	0.0188	-0.0719	0.0424	0.1442	-0.0811	0.0243	0.1726	0.0137	0.2439	-28.721	56.269	-35.168
12	4.0255	-1.0433	2.55	3.652	-1.7586	4.9656	0.1884	0.2431	-0.1204	-0.4646	0.0903	0.4094	0.1319	-0.479	-0.2787	0.1938	-0.0861	0.0305	0.2769	-0.0144	0.2156	-37.747	52.225	-38.452
13	4.6161	1.1056	-1.4023	2.7796	0.938	1.6982	0.7967	-0.8218	-0.8712	0.5351	-0.666	-0.3146	-0.2382	0.2225	-0.1306	0.4326	-0.231	-0.2446	0.2066	0.1473	0.4558	-45.047	-4.225	-20.107
14	6.0316	0.2718	0.1909	3.6822	2.7767	-0.598	1.4016	-1.218	-0.0616	0.2206	-0.8161	-0.3068	-0.1633	-0.1255	-0.5855	0.9424	-0.4546	-0.0694	0.2674	0.0535	0.2449	-49.876	4.478	-17.64
15	5.1855	0.8684	-0.8231	2.9044	-0.2413	3.1706	1.2913	-0.773	0.0121	0.3184	-0.7684	0.0718	-0.9398	0.1233	-0.5229	0.6672	-0.2455	-0.0003	0.1078	0.0386	0.3322	-47.872	5.297	-20.119

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 14
2	X-RAY DIFFRACTION	2	A	15 - 131
3	X-RAY DIFFRACTION	3	A	132 - 171
4	X-RAY DIFFRACTION	4	B	2 - 14
5	X-RAY DIFFRACTION	5	B	15 - 131
6	X-RAY DIFFRACTION	6	B	132 - 171
7	X-RAY DIFFRACTION	7	C	2 - 14
8	X-RAY DIFFRACTION	8	C	15 - 131
9	X-RAY DIFFRACTION	9	C	132 - 171
10	X-RAY DIFFRACTION	10	D	2 - 15
11	X-RAY DIFFRACTION	11	D	16 - 131
12	X-RAY DIFFRACTION	12	D	132 - 171
13	X-RAY DIFFRACTION	13	E	3 - 90
14	X-RAY DIFFRACTION	14	E	91 - 116
15	X-RAY DIFFRACTION	15	E	117 - 171

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