PDB-4one: Crystal Structure of a 3-oxoacyl-[acyl-carrier protein] reductase...

ID or keywords:

Entry

Database: PDB / ID: 4one

Title

Crystal Structure of a 3-oxoacyl-[acyl-carrier protein] reductase from Brucella melitensis

Components

3-oxoacyl-(Acyl-carrier protein) reductase

Keywords

OXIDOREDUCTASE / Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID / short chain dehydrogenase / KR domain / reductase

Function / homology

Function and homology information

3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / quinone binding / fatty acid biosynthetic process / nucleotide binding
Similarity search - Function

Biological species

Brucella melitensis (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.65 Å

Authors

Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: To be Published
Title: Crystal Structure of a 3-oxoacyl-[acyl-carrier protein] reductase from Brucella melitensis
Authors: Dranow, D.M. / Vogan, E. / Edwards, T.E. / Lorimer, D.

History

Deposition	Jan 28, 2014	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Feb 12, 2014	Provider: repository / Type: Initial release
Revision 1.1	Nov 22, 2017	Group: Refinement description / Category: software
Revision 1.2	Sep 20, 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_ref_seq_dif / struct_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4one.cif.gz	387.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4one.ent.gz	317.8 KB	Display	PDB format
PDBx/mmJSON format	4one.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

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Validation report

Summary document	4one_validation.pdf.gz	455.8 KB	Display	wwPDB validaton report
Full document	4one_full_validation.pdf.gz	458.8 KB	Display
Data in XML	4one_validation.xml.gz	45.3 KB	Display
Data in CIF	4one_validation.cif.gz	69 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/on/4one ftp://data.pdbj.org/pub/pdb/validation_reports/on/4one	HTTPS FTP

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Related structure data

Related structure data	4da9S S: Starting model for refinement
Similar structure data	3aut-1 3u5t-3 6ixm-d 2zat-d 1h5q-2 5x8h-d 6xex-1 3ppi-d 3gk3-d 3ay7-1 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: SSGCID-BrmeA.00010.a

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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) #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

B: 3-oxoacyl-(Acyl-carrier protein) reductase

C: 3-oxoacyl-(Acyl-carrier protein) reductase

D: 3-oxoacyl-(Acyl-carrier protein) reductase

hetero molecules

111 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

Unit cell

Length a, b, c (Å)	63.400, 125.520, 65.320
Angle α, β, γ (deg.)	90.00, 104.69, 90.00
Int Tables number	4
Space group name H-M	P12₁1

#1: Protein	3-oxoacyl-(Acyl-carrier protein) reductase Mass: 27733.045 Da / Num. of mol.: 4 / Fragment: UNP residues 47-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Brucella melitensis (bacteria) / Strain: 16M / ATCC 23456 / NCTC 10094 / Gene: BMEI0026 / Production host: Escherichia coli (E. coli) References: UniProt: Q8YJQ6, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical	ChemComp-CL / CHLORIDE ION Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 1005 / 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: 2.27 Å³/Da / Density % sol: 45.73 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: JCSG+(d5): 70% MPD, 100mM HEPES free acid/ Sodium Hydroxide, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 21-ID-F / Wavelength: 0.97857 Å

Detector

Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 19, 2013 / Details: Beryllium Lenses

Radiation

Monochromator: Diamond [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97857 Å / Relative weight: 1

Reflection

Resolution: 1.65→63.18 Å / Num. all: 118442 / Num. obs: 116611 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.6 % / R_merge(I) obs: 0.045 / Net I/σ(I): 18.33

Reflection shell

Resolution (Å)	Highest resolution (Å)	R_merge(I) obs	Mean I/σ(I) obs	Diffraction-ID	% possible all
1.65-1.69		0.253	3.93	1	87.4
1.69-1.74		0.229	4.86	1	95.7
1.74-1.79		0.205	6.47	1	99.8
1.79-1.84		0.164	7.95	1	99.8
1.84-1.91		0.131	9.75	1	99.8
1.91-1.97		0.105	11.72	1	99.9
1.97-2.05		0.088	13.78	1	99.6
2.05-2.13		0.07	16.6	1	99.7
2.13-2.22		0.06	18.94	1	99.9
2.22-2.33		0.054	20.65	1	99.6
2.33-2.46		0.048	23.03	1	99.8
2.46-2.61		0.044	24.99	1	99.6
2.61-2.79		0.041	27.41	1	99.7
2.79-3.01		0.037	29.93	1	99.2
3.01-3.3		0.034	33.78	1	99.5
3.3-3.69		0.031	36.33	1	99.5
3.69-4.26		0.031	38.23	1	99.4
4.26-5.22		0.03	39.99	1	99.7
5.22-7.38		0.029	38.87	1	99.6
	7.38	0.027	40.56	1	96.9

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Phasing

Phasing	Method: molecular replacement

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Processing

Software

Name	Version	Classification
XSCALE		data scaling
MOLREP		phasing
REFMAC	5.8.0049	refinement
PDB_EXTRACT	3.14	data extraction

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4DA9

4da9

Resolution: 1.65→63.18 Å / Cor.coef. F_o:F_c: 0.976 / Cor.coef. F_o:F_c free: 0.968 / SU B: 2.755 / SU ML: 0.047 / SU R Cruickshank DPI: 0.0734 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.072 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.15495	5737	4.9 %	RANDOM
R_work	0.13225	-	-	-
obs	0.13335	110874	98.51 %	-
all	-	122348	-	-

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 mean: 17.75 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.25 Å²	0 Å²	-1.04 Å²
2-	-	0.09 Å²	0 Å²
3-	-	-	0.18 Å²

Refinement step

Cycle: LAST / Resolution: 1.65→63.18 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	7210	0	28	1005	8243

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.012	0.019	7485
X-RAY DIFFRACTION	r_bond_other_d	0.001	0.02	7405
X-RAY DIFFRACTION	r_angle_refined_deg	1.484	1.966	10159
X-RAY DIFFRACTION	r_angle_other_deg	0.822	3	16895
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	5.662	5	1030
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	31.037	22.482	274
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.463	15	1187
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	15.946	15	62
X-RAY DIFFRACTION	r_chiral_restr	0.095	0.2	1212
X-RAY DIFFRACTION	r_gen_planes_refined	0.008	0.02	8638
X-RAY DIFFRACTION	r_gen_planes_other	0.002	0.02	1688
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	0.757	0.922	4051
X-RAY DIFFRACTION	r_mcbond_other	0.756	0.922	4050
X-RAY DIFFRACTION	r_mcangle_it	1.235	1.378	5074
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	1.364	1.113	3434
X-RAY DIFFRACTION	r_scbond_other
X-RAY DIFFRACTION	r_scangle_it
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

LS refinement shell

Resolution: 1.65→1.693 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.209	404	-
R_work	0.182	7191	-
obs	-	-	87.28 %

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	2.5208	0.2431	-0.3396	2.068	-0.0178	2.9965	-0.0393	-0.1726	0.0077	0.1201	0.0452	-0.1867	0.098	0.1248	-0.006	0.0783	0.0196	-0.0513	0.0488	0.0069	0.0528	27.9597	-94.0606	13.2949
2	0.5873	-0.0907	0.6549	0.3004	0.2129	1.4239	0.1049	-0.0088	-0.12	0.093	0.0245	-0.0488	0.2043	0.0354	-0.1294	0.104	0.0115	-0.0408	0.0217	0.0018	0.0627	22.9528	-101.9207	5.5834
3	4.8885	-1.4847	-2.4706	6.862	2.7862	12.7216	0.0357	-0.311	0.0981	0.4371	-0.0683	0.1422	-0.0181	-0.0687	0.0326	0.0958	-0.0268	0.0185	0.0885	0.0418	0.0639	11.4033	-96.8151	18.4375
4	0.4978	0.1323	0.123	0.5994	-0.0536	0.2082	-0.0174	0.0158	-0.0178	-0.0028	0.0028	-0.0755	0.0436	-0.0014	0.0147	0.0547	0.0069	-0.0069	0.0336	0.0004	0.0556	22.9808	-87.072	-1.7323
5	0.712	0.113	0.4018	0.5595	0.0434	1.6159	0.0717	0.0103	-0.0915	-0.0373	-0.0081	0.1149	0.15	-0.1113	-0.0636	0.0645	-0.0185	-0.0379	0.0189	-0.0025	0.0693	-4.8368	-103.0171	-25.9329
6	0.4284	0.0235	-0.6718	0.3978	0.3311	5.4247	0.0934	-0.0277	-0.1158	0.0089	-0.0441	0.0116	0.1078	-0.0178	-0.0493	0.0647	-0.013	-0.0185	0.0278	0.0105	0.067	6.2454	-102.8658	-11.133
7	0.436	-0.0632	0.2301	0.5636	-0.1763	0.1606	0.022	-0.0129	-0.0319	0.0065	0.0064	0.0761	0.0109	0.0012	-0.0285	0.0663	-0.0054	-0.0061	0.0467	0.0037	0.0686	1.9191	-92.2378	-15.785
8	0.6596	0.2317	0.0448	0.5621	0.351	0.5936	-0.0192	-0.0368	-0.0177	0.0128	-0.0465	0.1074	0.0334	-0.0999	0.0658	0.0485	0.0076	-0.0024	0.0291	0.0106	0.0751	-5.7647	-83.2484	-14.7513
9	1.3014	-0.0379	0.6462	0.2908	0.049	1.3058	-0.1429	-0.0961	0.1411	0.071	-0.0046	0.0053	-0.283	0.0106	0.1474	0.1295	0.0076	-0.0637	0.0167	-0.0234	0.0779	23.8379	-57.3294	9.6499
10	0.6712	-0.1655	0.4673	0.3803	-0.0503	0.6601	-0.0735	-0.0142	0.0736	0.0497	-0.0109	-0.0088	-0.1556	0.0131	0.0844	0.0783	0.0046	-0.0316	0.0195	-0.0101	0.0643	16.1607	-64.1373	-3.0121
11	1.13	0.8944	0.3098	0.8941	-0.0891	0.9762	0.1032	-0.186	0.2053	0.1501	-0.0749	0.1651	-0.0694	-0.1229	-0.0283	0.0856	0.0169	0.0141	0.0736	-0.0311	0.0971	12.4036	-74.4463	9.7996
12	3.169	3.8337	4.2206	4.8388	5.1572	5.6344	-0.0067	-0.0777	0.0387	-0.0973	-0.0677	0.1381	-0.029	-0.0937	0.0744	0.0969	0.0112	0.0104	0.0917	-0.0009	0.104	5.4945	-79.995	3.5039
13	2.6809	0.3479	-0.3706	1.9468	-0.0523	2.5485	-0.0551	0.1497	0.1048	-0.2453	0.0527	0.0913	0.0223	-0.1519	0.0025	0.104	-0.0107	-0.056	0.0338	0.0248	0.0535	-4.1281	-66.2465	-32.8366
14	0.7136	0.1188	0.4683	0.439	-0.2424	0.9062	-0.1199	0.0159	0.0996	-0.0523	0.0404	0.0635	-0.1749	-0.0252	0.0794	0.0865	-0.0013	-0.0435	0.0051	0.0053	0.0684	1.1357	-58.805	-25.5028
15	0.7352	0.3532	0.206	0.7276	0.0587	0.7321	-0.0459	-0.0057	0.0337	-0.03	0.0228	0.0085	-0.0649	0.0028	0.0231	0.0581	0.0026	-0.0192	0.0193	0.0065	0.061	4.6631	-70.6549	-19.4993
16	0.8169	-0.2254	0.1562	0.7945	-0.0832	0.5577	0.0613	0.0657	0.0457	-0.1198	-0.0126	-0.0136	-0.0064	0.0195	-0.0487	0.0763	-0.0046	-0.0022	0.0126	-0.0005	0.0471	6.5569	-79.3516	-25.4898

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	2 - 25
2	X-RAY DIFFRACTION	2	A	26 - 122
3	X-RAY DIFFRACTION	3	A	123 - 133
4	X-RAY DIFFRACTION	4	A	134 - 254
5	X-RAY DIFFRACTION	5	B	2 - 94
6	X-RAY DIFFRACTION	6	B	95 - 131
7	X-RAY DIFFRACTION	7	B	132 - 202
8	X-RAY DIFFRACTION	8	B	203 - 254
9	X-RAY DIFFRACTION	9	C	2 - 95
10	X-RAY DIFFRACTION	10	C	96 - 192
11	X-RAY DIFFRACTION	11	C	200 - 243
12	X-RAY DIFFRACTION	12	C	244 - 254
13	X-RAY DIFFRACTION	13	D	2 - 25
14	X-RAY DIFFRACTION	14	D	26 - 131
15	X-RAY DIFFRACTION	15	D	132 - 211
16	X-RAY DIFFRACTION	16	D	212 - 254

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