PDB-4v2p: Ketosynthase MxnB

ID or keywords:

Entry

Database: PDB / ID: 4v2p

Title

Ketosynthase MxnB

Components

KETOSYNTHASE

Ketoacyl synthase

Keywords

TRANSFERASE /

KETOSYNTHASE / MYXOPYRONIN

Function / homology

Function and homology information

3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process
Similarity search - Function

Biological species

MYXOCOCCUS FULVUS (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.67 Å

Authors

Koehnke, J.

Citation

Journal: Chem Sci / Year: 2015
Title: In vitro reconstitution of alpha-pyrone ring formation in myxopyronin biosynthesis.
Authors: Sucipto, H. / Sahner, J.H. / Prusov, E. / Wenzel, S.C. / Hartmann, R.W. / Koehnke, J. / Muller, R.

History

Deposition	Oct 13, 2014	Deposition site: PDBE / Processing site: PDBE
Revision 1.0	Aug 26, 2015	Provider: repository / Type: Initial release
Revision 1.1	Sep 27, 2017	Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.2	Apr 18, 2018	Group: Data collection / Database references / Category: citation Item: _citation.journal_abbrev / _citation.page_last ..._citation.journal_abbrev / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	4v2p.cif.gz	289.9 KB	Display	PDBx/mmCIF format
PDB format	pdb4v2p.ent.gz	246.4 KB	Display	PDB format
PDBx/mmJSON format	4v2p.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/v2/4v2p ftp://data.pdbj.org/pub/pdb/validation_reports/v2/4v2p	HTTPS FTP

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Related structure data

Similar structure data	4yuf-1 6o9n-1 6fm1-d 5ama-3 4ufb-2 2aj9-d 2qf1-d 3czk-d 2qo0-d 4wpv-d Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: KETOSYNTHASE

B: KETOSYNTHASE

hetero molecules

78.9 kDa, 2 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)	50.190, 58.790, 62.820
Angle α, β, γ (deg.)	104.75, 105.48, 93.90
Int Tables number	1
Space group name H-M	P1

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Protein , 1 types, 2 molecules AB

#1: Protein	KETOSYNTHASE / Ketoacyl synthase / MXNB Mass: 38846.312 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MYXOCOCCUS FULVUS (bacteria) / Strain: MX F50 / Plasmid: PCOLD / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: T1SF45

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Non-polymers , 5 types, 698 molecules

#2: Chemical	ChemComp-PO4 / PHOSPHATE ION / Phosphate Mass: 94.971 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: PO₄
#3: Chemical	ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol Mass: 118.174 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C₆H₁₄O₂ / Comment: precipitant*YM
#4: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#5: Chemical	ChemComp-NA / SODIUM ION Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#6: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 684 / 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: 2.2 Å³/Da / Density % sol: 44.08 % / Description: NONE

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Data collection

Diffraction	Mean temperature: 100 K
Diffraction source	Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.97625
Detector	Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 6, 2014
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 0.97625 Å / Relative weight: 1
Reflection	Resolution: 1.67→58.05 Å / Num. obs: 71183 / % possible obs: 92.6 % / Observed criterion σ(I): 2 / Redundancy: 2.2 % / R_merge(I) obs: 0.08 / Net I/σ(I): 9.1
Reflection shell	Resolution: 1.67→1.71 Å / Redundancy: 2.3 % / R_merge(I) obs: 0.41 / Mean I/σ(I) obs: 2 / % possible all: 92.2

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Processing

Software

Name	Version	Classification
REFMAC	5.8.0049	refinement
PHASER		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: NONE

Resolution: 1.67→58.05 Å / Cor.coef. F_o:F_c: 0.972 / Cor.coef. F_o:F_c free: 0.959 / SU B: 4.407 / SU ML: 0.063 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.091 / 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	0.17693	3598	5.1 %	RANDOM
R_work	0.14568	-	-	-
obs	0.14726	67585	92.62 %	-

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: 20.464 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.47 Å²	0.3 Å²	0.18 Å²
2-	-	0.24 Å²	0.32 Å²
3-	-	-	-0.78 Å²

Refinement step

Cycle: LAST / Resolution: 1.67→58.05 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	5083	0	70	684	5837

Refine LS restraints

Refine-ID	Type	Dev ideal	Dev ideal target	Number
X-RAY DIFFRACTION	r_bond_refined_d	0.008	0.019	5304
X-RAY DIFFRACTION	r_bond_other_d	0	0.02	5107
X-RAY DIFFRACTION	r_angle_refined_deg	1.479	1.994	7193
X-RAY DIFFRACTION	r_angle_other_deg	2.842	3	11766
X-RAY DIFFRACTION	r_dihedral_angle_1_deg	6.081	5	671
X-RAY DIFFRACTION	r_dihedral_angle_2_deg	33.197	22.96	223
X-RAY DIFFRACTION	r_dihedral_angle_3_deg	11.197	15	892
X-RAY DIFFRACTION	r_dihedral_angle_4_deg	16.057	15	44
X-RAY DIFFRACTION	r_chiral_restr	0.263	0.2	790
X-RAY DIFFRACTION	r_gen_planes_refined	0.005	0.021	5933
X-RAY DIFFRACTION	r_gen_planes_other	0.005	0.02	1187
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	0.535	1.404	2648
X-RAY DIFFRACTION	r_mcbond_other	0.534	1.405	2646
X-RAY DIFFRACTION	r_mcangle_it	0.504	2.097	3310
X-RAY DIFFRACTION	r_mcangle_other
X-RAY DIFFRACTION	r_scbond_it	0.871	2.097	2656
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	8.204		10411
X-RAY DIFFRACTION	r_sphericity_free
X-RAY DIFFRACTION	r_sphericity_bonded

LS refinement shell

Resolution: 1.67→1.713 Å / Total num. of bins used: 20

	R_factor	Num. reflection	% reflection
R_free	0.309	290	-
R_work	0.26	4936	-
obs	-	-	92.25 %

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	0.1708	0.2228	-0.0176	0.4312	-0.0136	0.1144	-0.0118	0.0121	0.0266	-0.012	0.022	0.0238	-0.0268	-0.0083	-0.0103	0.012	0.0055	-0.0015	0.0086	0.0022	0.0073	25.4416	12.4302	33.6401
2	0.0221	-0.0129	0.0047	0.0501	-0.0674	0.1016	-0.0059	0.0013	0.0016	0.0041	0.0035	0.0014	-0.0003	-0.0038	0.0023	0.0094	0.0001	0.0015	0.0147	-0.0016	0.0124	18.9653	-3.9086	47.5235
3	0.5452	-0.95	-0.2183	2.1792	-0.1038	0.5352	-0.0387	0.0038	-0.0379	0.0511	0.0213	0.0639	0.0322	-0.025	0.0173	0.0065	-0.0009	-0.0012	0.022	0.0004	0.0077	14.9534	-17.4858	45.5306
4	0.016	0.0238	-0.0414	0.043	-0.0484	0.1304	0.0057	-0.0002	-0.0007	0.0094	-0.0034	-0.0038	-0.0058	-0.0056	-0.0022	0.0056	0.0034	-0.0026	0.0099	-0.0008	0.0163	26.1036	-0.6248	37.48
5	0.0063	-0.0121	-0.0313	0.3649	0.3612	0.5344	0.0015	0.0031	0.0049	-0.0228	0.0144	-0.0138	-0.0448	0.0339	-0.0158	0.0104	-0.0017	0.0025	0.0166	0.0028	0.0122	44.7186	4.0023	44.4337
6	0.0629	0.0444	0.0069	0.0838	-0.1206	0.301	-0.0091	0.0168	-0.0188	-0.0167	0.0063	-0.0168	0.0294	0.0078	0.0028	0.0139	0.0021	0.0039	0.0107	-0.0046	0.0161	34.219	-13.5577	22.8362
7	0.1012	0.0704	-0.0211	0.0815	-0.0124	0.144	-0.0018	0.0094	0.0131	-0.013	0.0051	0.0048	-0.0027	-0.0009	-0.0033	0.0113	0.0022	0.0006	0.0126	0.0006	0.0108	24.6797	-1.1293	27.0878
8	0.1988	0.2478	0.1987	0.3824	0.2593	0.4307	-0.0109	-0.043	-0.0336	-0.0143	-0.0054	-0.0412	0.002	-0.0224	0.0163	0.0068	0.0073	0.0016	0.0382	0.0093	0.0185	40.3002	-19.9903	60.2511
9	0.0746	0.0957	-0.1302	0.2779	-0.012	0.3886	0.0283	-0.0155	-0.0001	0.0461	-0.0137	-0.018	-0.0361	0.0416	-0.0146	0.0164	0.0001	-0.005	0.0161	0.0018	0.0115	45.2393	-8.0662	70.0807
10	0.8187	-0.8816	0.2234	0.9493	-0.2404	0.0614	0.0076	-0.023	0.0024	-0.0249	0.008	-0.003	0.0101	-0.0072	-0.0155	0.0298	-0.004	0.0063	0.0103	-0.0005	0.0167	47.1234	-26.699	48.4932
11	0.0045	0.012	0.005	0.0579	-0.0308	0.1153	0.0004	0.0007	0.0024	0.0034	-0.0017	-0.0014	-0.003	-0.0005	0.0013	0.009	0.0019	0.001	0.0144	-0.0002	0.0125	37.4086	-11.9469	51.7068
12	0.0241	0.0101	-0.0431	0.1275	-0.0138	0.0784	0.0027	0.0013	0.0023	0.0207	0.0034	-0.0037	-0.0025	-0.0052	-0.0061	0.0093	0.0001	-0.0053	0.0123	-0.0008	0.01	27.538	-5.6017	59.3125
13	0.0337	-0.0559	-0.0447	0.3437	-0.1223	0.2199	-0.0037	0.0083	-0.0086	0.0092	-0.0068	0.0191	0.0081	-0.0252	0.0105	0.0069	-0.002	0.0013	0.0182	-0.0018	0.0134	16.4219	-21.3364	65.9944
14	0.016	-0.0077	-0.0324	0.0773	-0.0159	0.1362	0.0007	-0.0076	-0.0014	0.0086	-0.0015	-0.0022	0.0062	0.0007	0.0007	0.013	0.0005	-0.0001	0.0119	0	0.0113	32.3766	-21.657	67.113

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	A	8 - 53
2	X-RAY DIFFRACTION	2	A	54 - 136
3	X-RAY DIFFRACTION	3	A	137 - 144
4	X-RAY DIFFRACTION	4	A	145 - 192
5	X-RAY DIFFRACTION	5	A	193 - 235
6	X-RAY DIFFRACTION	6	A	236 - 256
7	X-RAY DIFFRACTION	7	A	257 - 335
8	X-RAY DIFFRACTION	8	B	7 - 28
9	X-RAY DIFFRACTION	9	B	29 - 70
10	X-RAY DIFFRACTION	10	B	71 - 76
11	X-RAY DIFFRACTION	11	B	77 - 174
12	X-RAY DIFFRACTION	12	B	175 - 232
13	X-RAY DIFFRACTION	13	B	233 - 256
14	X-RAY DIFFRACTION	14	B	257 - 335

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