PDB-5end: Crystal structure of beta-ketoacyl-acyl carrier protein reductase...

ID or keywords:

Entry

Database: PDB / ID: 5end

Title

Crystal structure of beta-ketoacyl-acyl carrier protein reductase (FabG)(Q152A) from Vibrio cholerae

Components

3-oxoacyl-[acyl-carrier-protein] reductase FabG

Keywords

OXIDOREDUCTASE /

STRUCTURAL GENOMICS / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / CSGID /

Vibrio cholerae / FabG / beta-ketoacyl-acyl carrier protein reductase

Function / homology

Function and homology information

3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding /

NADP binding
Similarity search - Function

Biological species

Vibrio cholerae serotype O1 (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.55 Å

Authors

Hou, J. / Cooper, D.R. / Zheng, H. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)

Citation

Journal: J.Bacteriol. / Year: 2015
Title: Dissecting the Structural Elements for the Activation of beta-Ketoacyl-(Acyl Carrier Protein) Reductase from Vibrio cholerae.
Authors: Hou, J. / Zheng, H. / Chruszcz, M. / Zimmerman, M.D. / Shumilin, I.A. / Osinski, T. / Demas, M. / Grimshaw, S. / Minor, W.

History

Deposition	Nov 9, 2015	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Dec 23, 2015	Provider: repository / Type: Initial release
Revision 1.1	Jan 27, 2016	Group: Database references
Revision 1.2	Feb 24, 2016	Group: Data collection
Revision 1.3	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

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	5end.cif.gz	173 KB	Display	PDBx/mmCIF format
PDB format	pdb5end.ent.gz	143.5 KB	Display	PDB format
PDBx/mmJSON format	5end.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/en/5end ftp://data.pdbj.org/pub/pdb/validation_reports/en/5end	HTTPS FTP

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Related structure data

Related structure data	3op4C 3rroC 3rshC 3tzcC 3tzkC 3u09C 4i08C 4wjzC 4wk6C C: citing same article (ref.)
Similar structure data	3grp-d 2bd0-d 4osp-d 4eso-d 1ahh-1 5h5x-2 6ihh-1 2pr2-1 2hq1-1 1kp5-3 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: CSGID-IDP90557

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (5) #77 - May 2006 Glucose Oxidase similarity (3) #188 - Aug 2015 Tetrahydrobiopterin Biosynthesis similarity (2) #216 - Dec 2017 Biodegradable Plastic similarity (2)

Deposited unit

A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG

B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG

hetero molecules

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

1

A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG

B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG

hetero molecules

A: 3-oxoacyl-[acyl-carrier-protein] reductase FabG

B: 3-oxoacyl-[acyl-carrier-protein] reductase FabG

hetero molecules

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

Unit cell

Length a, b, c (Å)	63.995, 63.995, 190.474
Angle α, β, γ (deg.)	90.000, 90.000, 120.000
Int Tables number	171
Space group name H-M	P6₂

Noncrystallographic symmetry (NCS)

NCS domain:

ID	Ens-ID	Details
1	1	A
2	1	B
1	2	A
2	2	B
1	3	A
2	3	B
1	4	A
2	4	B

NCS domain segments:

Dom-ID	Component-ID	Ens-ID	Refine code	Auth asym-ID	Auth seq-ID
1	1	1	1	A	5 - 86
2	1	1	1	B	5 - 86
1	1	2	1	A	107 - 142
2	1	2	1	B	107 - 142
1	1	3	1	A	154 - 187
2	1	3	1	B	154 - 187
1	1	4	1	A	212 - 242
2	1	4	1	B	212 - 242

NCS ensembles :

ID
1
2
3
4

#1: Protein	3-oxoacyl-[acyl-carrier-protein] reductase FabG / 3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta- ...3-ketoacyl-acyl carrier protein reductase / Beta-Ketoacyl-acyl carrier protein reductase / Beta-ketoacyl-ACP reductase Mass: 26028.805 Da / Num. of mol.: 2 / Mutation: Q152A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961) (bacteria) Strain: ATCC 39315 / El Tor Inaba N16961 / Gene: fabG, VC_2021 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIL References: UniProt: Q9KQH7, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C₃H₈O₃
#3: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 49 / 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: 2.16 Å³/Da / Density % sol: 43.13 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7 / Details: 0.1M Tris, 20% PEG1000

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 19-BM / Wavelength: 0.979 Å

Detector

Type: ADSC QUANTUM 210r / Detector: CCD / Date: Oct 16, 2015 / Details: Mirrors

Radiation

Monochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.979 Å / Relative weight: 1

Reflection

Redundancy: 5 % / Number: 72363 / R_merge(I) obs: 0.097 / Χ²: 0.86 / D res high: 2.55 Å / D res low: 50 Å / Num. obs: 14503 / % possible obs: 99.9

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	ID	R_merge(I) obs	Chi squared	Redundancy
6.92	50	1	0.035	1.098	4.6
5.49	6.92	1	0.049	0.768	5
4.8	5.49	1	0.05	0.803	5
4.36	4.8	1	0.054	1.139	5
4.05	4.36	1	0.063	1.085	5
3.81	4.05	1	0.074	0.952	5
3.62	3.81	1	0.097	1.369	5
3.46	3.62	1	0.086	0.845	5
3.33	3.46	1	0.108	0.843	5
3.21	3.33	1	0.151	0.769	5
3.11	3.21	1	0.179	0.736	5
3.02	3.11	1	0.21	0.757	5
2.94	3.02	1	0.254	0.741	5
2.87	2.94	1	0.287	0.734	5
2.81	2.87	1	0.381	0.769	5
2.75	2.81	1	0.376	0.765	5
2.69	2.75	1	0.479	0.728	5.1
2.64	2.69	1	0.617	0.786	5
2.59	2.64	1	0.63	0.789	5
2.55	2.59	1	0.755	0.779	5

Reflection twin

Crystal-ID	ID	Operator	Domain-ID	Fraction
1	1	H, K, L	1	0.892
1	1	K, H, -L	2	0.108

Reflection

Resolution: 2.55→50 Å / Num. obs: 14503 / % possible obs: 99.9 % / Redundancy: 5 % / R_merge(I) obs: 0.097 / R_pim(I) all: 0.047 / R_rim(I) all: 0.108 / Χ²: 0.862 / Net I/av σ(I): 15.355 / Net I/σ(I): 6.4 / Num. measured all: 72363

Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	CC_1/2	R_pim(I) all	R_rim(I) all	Χ²	% possible all
2.55-2.59	5	0.755	698	0.659	0.374	0.844	0.779	100
2.59-2.64	5	0.63	734	0.748	0.313	0.705	0.789	100
2.64-2.69	5	0.617	734	0.719	0.307	0.691	0.786	100
2.69-2.75	5.1	0.479	702	0.842	0.234	0.535	0.728	100
2.75-2.81	5	0.376	738	0.902	0.186	0.42	0.765	100
2.81-2.87	5	0.381	715	0.883	0.188	0.426	0.769	100
2.87-2.94	5	0.287	728	0.918	0.141	0.321	0.734	100
2.94-3.02	5	0.254	724	0.939	0.124	0.284	0.741	100
3.02-3.11	5	0.21	707	0.958	0.103	0.235	0.757	100
3.11-3.21	5	0.179	742	0.97	0.087	0.2	0.736	100
3.21-3.33	5	0.151	711	0.964	0.074	0.168	0.769	100
3.33-3.46	5	0.108	732	0.981	0.052	0.12	0.843	100
3.46-3.62	5	0.086	728	0.985	0.042	0.096	0.845	100
3.62-3.81	5	0.097	726	0.98	0.047	0.108	1.369	100
3.81-4.05	5	0.074	728	0.99	0.036	0.083	0.952	100
4.05-4.36	5	0.063	718	0.989	0.031	0.071	1.085	99.7
4.36-4.8	5	0.054	723	0.989	0.026	0.06	1.139	99.7
4.8-5.49	5	0.05	731	0.996	0.023	0.055	0.803	99.7
5.49-6.92	5	0.049	734	0.996	0.023	0.055	0.768	100
6.92-50	4.6	0.035	750	0.993	0.017	0.039	1.098	99.1

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

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

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT / Resolution: 2.55→47.9 Å / Cor.coef. F_o:F_c: 0.925 / Cor.coef. F_o:F_c free: 0.895 / SU B: 21.916 / SU ML: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.462 / ESU R Free: 0.07 / 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	0.2548	667	4.8 %	RANDOM
R_work	0.2061	-	-	-
obs	0.2084	13264	96.94 %	-

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: 99.77 Å² / B_iso mean: 44.008 Å² / B_iso min: 14.69 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-6.11 Å²	-0 Å²	-0 Å²
2-	-	-6.11 Å²	-0 Å²
3-	-	-	12.22 Å²

Refinement step

Cycle: final / Resolution: 2.55→47.9 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	3211	0	6	49	3266
B_iso mean	-	-	43.91	30.82	-
Num. residues	-	-	-	-	454

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.011	0.019	3244
X-RAY DIFFRACTION	r_bond_other_d	0.002	0.02	3150
X-RAY DIFFRACTION	r_angle_refined_deg	1.515	1.963	4389
X-RAY DIFFRACTION	r_angle_other_deg	1.069	3	7184
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.185	5	448
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	37.851	24.336	113
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	15.206	15	516
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	11.299	15	21
X-RAY DIFFRACTION	r_chiral_restr	0.072	0.2	536
X-RAY DIFFRACTION	r_gen_planes_refined	0.007	0.02	3750
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	679
X-RAY DIFFRACTION	r_mcbond_it	0.764	2.176	1810
X-RAY DIFFRACTION	r_mcbond_other	0.763	2.176	1809
X-RAY DIFFRACTION	r_mcangle_it	1.353	3.257	2252

Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION / Type: TIGHT THERMAL / Weight position: 0.5

Ens-ID	Number	Rms dev position (Å)
1	1135	3.89
2	555	4.07
3	462	2.36
4	452	2.2

LS refinement shell

Resolution: 2.55→2.616 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.343	39	-
R_work	0.249	711	-
all	-	750	-
obs	-	-	72.46 %

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	2.6205	0.4264	-0.3088	3.9578	-0.3387	2.8466	0.4662	-0.3286	0.1367	0.5496	-0.3876	0.2846	-0.1076	-0.1962	-0.0786	0.1977	-0.1942	0.0969	0.2581	-0.1042	0.0541	10.5687	-12.8447	20.2751
2	1.0902	0.8407	-0.3222	2.9074	0.6608	2	0.2623	-0.2445	0.01	0.4569	-0.2637	0.0359	-0.0466	-0.0352	0.0014	0.203	-0.1367	-0.0015	0.2929	-0.0036	0.0503	25.7852	-7.855	16.1707
3	2.962	-1.2702	0.4165	4.5909	-1.2524	1.4193	-0.0207	-0.1129	0.4443	0.5538	-0.0545	0.3341	-0.452	-0.1038	0.0753	0.1901	-0.0382	0.035	0.2331	-0.088	0.164	14.1864	1.7051	5.4935
4	4.3913	0.2696	-0.0863	2.5992	-0.7391	2.5026	0.138	0.1719	-0.2345	0.0777	-0.0851	0.3106	0.263	0.1662	-0.0529	0.1437	0.0566	-0.0755	0.2988	-0.1039	0.1303	9.6417	-15.787	-16.6934
5	2.5537	0.4242	0.3835	1.2139	1.0321	1.6094	0.1681	0.6787	0.0878	-0.2563	-0.1304	0.0532	-0.0641	0.2554	-0.0377	0.1422	0.1451	-0.0325	0.4491	-0.0123	0.0183	18.1239	-4.7735	-20.6963
6	3.5739	-0.9969	1.0213	3.241	-1.1347	2.0435	0.2297	0.3049	-0.1815	-0.2745	-0.277	-0.1781	0.3376	0.3594	0.0472	0.1528	0.0395	-0.0041	0.3122	-0.0573	0.0653	22.8493	-11.1698	-6.3699

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	3 - 102
2	X-RAY DIFFRACTION	2	A	103 - 181
3	X-RAY DIFFRACTION	3	A	182 - 246
4	X-RAY DIFFRACTION	4	B	2 - 54
5	X-RAY DIFFRACTION	5	B	55 - 164
6	X-RAY DIFFRACTION	6	B	165 - 246

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