PDB-4efi: Crystal Structure of 3-oxoacyl-(Acyl-carrier protein) Synthase fr...

ID or keywords:

Entry

Database: PDB / ID: 4efi

Title

Crystal Structure of 3-oxoacyl-(Acyl-carrier protein) Synthase from Burkholderia Xenovorans LB400

Components

3-oxoacyl-(Acyl-carrier protein) synthase

Keywords

TRANSFERASE /

Structural Genomics / Seattle Structural Genomics Center for Infectious Disease / SSGCID /

Acyltransferase

Function / homology

Function and homology information

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

Biological species

Burkholderia xenovorans (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 1.35 Å

Authors

Seattle Structural Genomics Center for Infectious Disease / Craig, T.K. / Abendroth, J. / Staker, B. / Stewart, L. / Seattle Structural Genomics Center for Infectious Disease (SSGCID)

Citation

Journal: Plos One / Year: 2013
Title: Combining functional and structural genomics to sample the essential Burkholderia structome.
Authors: Baugh, L. / Gallagher, L.A. / Patrapuvich, R. / Clifton, M.C. / Gardberg, A.S. / Edwards, T.E. / Armour, B. / Begley, D.W. / Dieterich, S.H. / Dranow, D.M. / Abendroth, J. / Fairman, J.W. / ...

History

Deposition	Mar 29, 2012	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Apr 11, 2012	Provider: repository / Type: Initial release
Revision 1.1	Oct 9, 2013	Group: Database references
Revision 1.2	Nov 15, 2017	Group: Refinement description / Category: software / Item: _software.name
Revision 1.3	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_site Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

Structure viewer	Molecule: MolmilJmol/JSmol

-
Download

PDBx/mmCIF format	4efi.cif.gz	206.1 KB	Display	PDBx/mmCIF format
PDB format	pdb4efi.ent.gz	165.7 KB	Display	PDB format
PDBx/mmJSON format	4efi.json.gz		Tree view	PDBx/mmJSON format
Others	Other downloads

-
Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/ef/4efi ftp://data.pdbj.org/pub/pdb/validation_reports/ef/4efi	HTTPS FTP

-
Related structure data

Related structure data	3d63C 3dahC 3eizC 3ej2C 3ek2C 3ezoC 3f0fC 3ftpC 3gk0C 3gk3C 3gvfC 3gwaC 3gweC 3imlC 3sz8C 3t4cC 3tmlC 3tmqC 3txyC 3u7jC 3ue9C 3uk1C 3uk2C 3undC 3uptC 3urrC 3uw1C 3uw2C 3uw3C 3v2iC 3v7nC 3v8hC 3v9oC 3v9pC 3vavC 4ddoC 4dfeSC 4dheC 4dhkC 4dutC 4dz4C 4e4tC 4eg0C 4egjC 4ek2C 4eqyC 4ewgC 4exqC 4f2gC 4f32C 4f3nC 4f3yC 4f4hC 4f7dC 4fk8C 4fryC 4g1kC 4g67C 4ghkC 4h3yC 4h3zC 4h4gC S: Starting model for refinement C: citing same article (ref.)
Similar structure data	3bih-d 6b97-1 5yw0-d 6jav-d 3jwr-1 3snl-1 6b96-1 6m7k-d 3d1r-d 5k71-2 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: BuxeA.00171.a

-
Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#90 - Jun 2007 Fatty Acid Synthase similarity (2) #137 - May 2011 Cytochrome bc1 similarity (1) #191 - Nov 2015 Glutamate-gated Chloride Receptors similarity (1) #216 - Dec 2017 Biodegradable Plastic similarity (1)

Deposited unit

A: 3-oxoacyl-(Acyl-carrier protein) synthase

hetero molecules

37.9 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author

2

A: 3-oxoacyl-(Acyl-carrier protein) synthase

hetero molecules

A: 3-oxoacyl-(Acyl-carrier protein) synthase

hetero molecules

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

Unit cell

Length a, b, c (Å)	101.377, 54.408, 60.836
Angle α, β, γ (deg.)	90.000, 103.770, 90.000
Int Tables number	5
Space group name H-M	C121

Components on special symmetry positions

ID	Model	Components
1	1	A-840- HOH

#1: Protein	3-oxoacyl-(Acyl-carrier protein) synthase Mass: 37857.117 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Burkholderia xenovorans (bacteria) / Strain: LB400 / Gene: Bxeno_A4297, Bxe_A0096 / Plasmid: AVA0421 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) References: UniProt: Q13SV4, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical	ChemComp-UNL / UNKNOWN LIGAND Num. of mol.: 1 / Source method: obtained synthetically
#3: Chemical	ChemComp-CL / CHLORIDE ION / Chloride Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Chemical	ChemComp-FMT / FORMIC ACID / Formic acid Mass: 46.025 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CH₂O₂
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 346 / Source method: isolated from a natural source / Formula: H₂O

-
Experiment

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

-
Sample preparation

Crystal	Density Matthews: 2.15 Å³/Da / Density % sol: 42.85 %
Crystal grow	Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: Protein was from BuxeA.00171.a.A1.PW33644 set up at 26.35mg/ml, .4/.4 uL drops at 16c. Crystals were found in condition: 20% PEG 2000MME, 100mM Tris pH 8.5, 200mM Trimethylamine n-oxide ...Details: Protein was from BuxeA.00171.a.A1.PW33644 set up at 26.35mg/ml, .4/.4 uL drops at 16c. Crystals were found in condition: 20% PEG 2000MME, 100mM Tris pH 8.5, 200mM Trimethylamine n-oxide cryoprotected with well solution +20% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal

Density Matthews: 2.15 Å³/Da / Density % sol: 42.85 %

Crystal grow

Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: Protein was from BuxeA.00171.a.A1.PW33644 set up at 26.35mg/ml, .4/.4 uL drops at 16c. Crystals were found in condition: 20% PEG 2000MME, 100mM Tris pH 8.5, 200mM Trimethylamine n-oxide ...

-
Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

ALS

/ Beamline: 5.0.1 / Wavelength: 0.9774 Å

Detector

Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 14, 2011

Radiation

Monochromator: Si(220) Asymmetric cut single crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.9774 Å / Relative weight: 1

Reflection

Redundancy: 7.2 % / Av σ(I) over netI: 18.68 / Number: 563565 / R_merge(I) obs: 0.082 / Χ²: 0.97 / D res high: 1.3 Å / D res low: 50 Å / Num. obs: 78305 / % possible obs: 99.1

Diffraction reflection shell

Highest resolution (Å)	Lowest resolution (Å)	% possible obs (%)	ID	R_merge(I) obs	Chi squared	Redundancy
3.21	50	89.7	1	0.035	0.336	6.6
2.54	3.21	98.9	1	0.059	0.689	7.1
2.22	2.54	99.3	1	0.09	1.297	6.8
2.02	2.22	100	1	0.103	1.44	7.3
1.87	2.02	100	1	0.109	1.374	7.4
1.76	1.87	100	1	0.118	1.085	7.4
1.68	1.76	100	1	0.142	1.043	7.4
1.6	1.68	100	1	0.168	1.001	7.4
1.54	1.6	100	1	0.202	0.975	7.4
1.49	1.54	100	1	0.247	0.942	7.3
1.44	1.49	99.9	1	0.309	0.914	7.3
1.4	1.44	99.8	1	0.382	0.869	7.3
1.36	1.4	99.6	1	0.474	0.823	7.3
1.33	1.36	99.6	1	0.551	0.802	7.2
1.3	1.33	99.4	1	0.61	0.78	6.7

Reflection

Resolution: 1.3→50 Å / Num. all: 79016 / Num. obs: 78305 / % possible obs: 99.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Χ²: 0.967 / Net I/σ(I): 9.8

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
1.3-1.33	6.7	0.61	5240	0.78	1	99.4
1.33-1.36	7.2	0.551	5174	0.802	1	99.6
1.36-1.4	7.3	0.474	5248	0.823	1	99.6
1.4-1.44	7.3	0.382	5233	0.869	1	99.8
1.44-1.49	7.3	0.309	5231	0.914	1	99.9
1.49-1.54	7.3	0.247	5243	0.942	1	100
1.54-1.6	7.4	0.202	5279	0.975	1	100
1.6-1.68	7.4	0.168	5206	1.001	1	100
1.68-1.76	7.4	0.142	5271	1.043	1	100
1.76-1.87	7.4	0.118	5286	1.085	1	100
1.87-2.02	7.4	0.109	5250	1.374	1	100
2.02-2.22	7.3	0.103	5270	1.44	1	100
2.22-2.54	6.8	0.09	5262	1.297	1	99.3
2.54-3.21	7.1	0.059	5267	0.689	1	98.9
3.21-50	6.6	0.035	4845	0.336	1	89.7

-
Phasing

Phasing

Method:

molecular replacement

Phasing MR

	Highest resolution	Lowest resolution
Rotation	2.5 Å	35.15 Å
Translation	2.5 Å	35.15 Å

-
Processing

Software

Name	Version	Classification
SCALEPACK		data scaling
PHASER	2.4.0	phasing
PHENIX	1.7.3_928	refinement
PDB_EXTRACT	3.1	data extraction
ADSC	Quantum	data collection
DENZO		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: PDB entry 4DFE

4dfe

Resolution: 1.35→35.154 Å / Occupancy max: 2 / Occupancy min: 0.21 / FOM work R set: 0.9102 / SU ML: 0.14 / σ(F): 1.34 / Phase error: 15.9 / Stereochemistry target values: ML

	R_factor	Num. reflection	% reflection	Selection details
R_free	0.1736	3473	4.99 %	RANDOM
R_work	0.1591	-	-	-
obs	0.1598	69575	98.46 %	-

Solvent computation

Shrinkage radii: 0.98 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / B_sol: 48.759 Å² / k_sol: 0.331 e/Å³

Displacement parameters

B_iso max: 61.64 Å² / B_iso mean: 20.806 Å² / B_iso min: 10.06 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	0.3686 Å²	-0 Å²	-0.4528 Å²
2-	-	-0.7192 Å²	0 Å²
3-	-	-	0.3506 Å²

Refinement step

Cycle: LAST / Resolution: 1.35→35.154 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	2557	0	5	346	2908

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.009	2757
X-RAY DIFFRACTION	f_angle_d	1.311	3775
X-RAY DIFFRACTION	f_chiral_restr	0.077	435
X-RAY DIFFRACTION	f_plane_restr	0.007	505
X-RAY DIFFRACTION	f_dihedral_angle_d	11.396	988

LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 25

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Num. reflection all	% reflection obs (%)
1.35-1.3685	0.2841	128	0.2342	2454	2582	91
1.3685-1.388	0.2344	134	0.2205	2523	2657	96
1.388-1.4088	0.2325	141	0.2051	2687	2828	99
1.4088-1.4308	0.1965	140	0.1944	2652	2792	100
1.4308-1.4542	0.2161	140	0.185	2659	2799	100
1.4542-1.4793	0.2162	142	0.1729	2684	2826	100
1.4793-1.5062	0.2101	138	0.1699	2632	2770	100
1.5062-1.5352	0.1636	140	0.1562	2656	2796	100
1.5352-1.5665	0.1824	142	0.1506	2687	2829	100
1.5665-1.6006	0.1656	143	0.1537	2727	2870	100
1.6006-1.6378	0.1684	139	0.1491	2631	2770	100
1.6378-1.6788	0.1634	140	0.1497	2676	2816	100
1.6788-1.7242	0.1777	141	0.1474	2676	2817	100
1.7242-1.7749	0.1869	141	0.1505	2691	2832	100
1.7749-1.8322	0.1947	141	0.1454	2670	2811	100
1.8322-1.8977	0.1596	141	0.156	2676	2817	100
1.8977-1.9736	0.1919	141	0.1595	2668	2809	100
1.9736-2.0634	0.1538	142	0.1483	2697	2839	100
2.0634-2.1722	0.1628	142	0.1468	2677	2819	100
2.1722-2.3083	0.173	140	0.15	2663	2803	98
2.3083-2.4865	0.1648	141	0.1465	2686	2827	100
2.4865-2.7366	0.1549	143	0.15	2688	2831	100
2.7366-3.1324	0.1672	138	0.1523	2661	2799	99
3.1324-3.9456	0.1662	123	0.1661	2393	2516	88
3.9456-35.154	0.1764	132	0.1726	2588	2720	93

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	2.3957	-0.9325	-0.1714	1.5248	0.1282	0.5428	0.0418	0.0369	-0.2887	-0.0436	-0.0062	0.0727	0.0779	0.0512	-0.0361	0.1386	-0.0038	-0.0117	0.1215	-0.0145	0.1066	-16.5963	-11.522	20.7344
2	1.0354	0.1577	-1.6678	0.8003	-0.8323	4.549	0.0707	0.1358	0.1566	-0.1431	-0.0878	0.0383	-0.4541	0.0637	0.0337	0.221	0.0082	-0.031	0.1885	0.0275	0.1833	-23.4173	19.2983	5.8525
3	0.527	-0.1775	0.2182	0.6472	-0.1413	0.8169	0.0198	0.0086	0.0105	-0.0128	-0.0248	0.0017	-0.0344	0.0282	0.008	0.0889	-0.007	0.0072	0.1246	0.0001	0.1198	-18.3271	2.6668	26.4127
4	1.0912	-0.1707	0.0073	0.6188	-0.0268	0.9816	-0.0136	0.1159	0.0892	-0.0979	-0.0149	-0.0825	-0.0869	0.099	0.0218	0.1217	0.0088	0.0054	0.1394	0.0113	0.1031	-6.5462	5.5553	18.8806
5	0.9582	0.4517	0.2603	7.8604	-0.337	1.4488	0.0159	0.2555	-0.1047	-0.8178	-0.0419	-0.3627	0.0518	0.126	0.0122	0.2335	0.0398	0.0259	0.2257	-0.0273	0.1576	-6.1803	-4.788	5.6282
6	1.5061	-0.4224	0.1384	2.5369	0.634	1.6663	0.0818	0.3225	-0.1421	-0.41	-0.076	-0.0082	0.1006	0.0067	0.0032	0.193	0.0324	-0.0154	0.2037	-0.0409	0.119	-17.2578	-5.2677	3.0983
7	0.7015	-0.3625	-0.1714	0.8979	-0.038	0.6635	0.066	0.0765	-0.0589	-0.076	-0.0328	0.1057	0.0504	-0.0672	-0.0326	0.1359	0.0038	-0.0206	0.1394	-0.0089	0.1208	-22.2328	-3.5459	14.3721

Refinement TLS group

ID	Refine-ID	Refine TLS-ID	Selection details	Auth asym-ID	Auth seq-ID
1	X-RAY DIFFRACTION	1	( CHAIN A AND RESID 8:26 )	A	8 - 26
2	X-RAY DIFFRACTION	2	( CHAIN A AND RESID 27:55 )	A	27 - 55
3	X-RAY DIFFRACTION	3	( CHAIN A AND RESID 56:178 )	A	56 - 178
4	X-RAY DIFFRACTION	4	( CHAIN A AND RESID 179:237 )	A	179 - 237
5	X-RAY DIFFRACTION	5	( CHAIN A AND RESID 238:260 )	A	238 - 260
6	X-RAY DIFFRACTION	6	( CHAIN A AND RESID 261:297 )	A	261 - 297
7	X-RAY DIFFRACTION	7	( CHAIN A AND RESID 298:358 )	A	298 - 358

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

Thousand views of thousand structures

Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi

-Movie

-Structure viewers

+Viewer log

-This page

-This web site

-Options

+Open data

-Basic information

-Structure visualization

-Downloads & links

-Download

-Validation report

-Related structure data

-Links

-Assembly

-Components

-Experimental details

-Experiment

-Sample preparation

-Data collection

-Phasing

-Processing

+About Yorodumi

-News

-Feb 9, 2022. New format data for meta-information of EMDB entries

-Aug 12, 2020. Covid-19 info

+Mar 5, 2020. Novel coronavirus structure data

+Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+Jul 12, 2017. Major update of PDB

-Yorodumi

-
Movie

-
Structure viewers

+
Viewer log

-
This page

-
This web site

-
Options

+
Open data

-
Basic information

-
Structure visualization

-
Downloads & links

-
Download

-
Validation report

-
Related structure data

-
Links

-
Assembly

-
Components

-
Experimental details

-
Experiment

-
Sample preparation

-
Data collection

-
Phasing

-
Processing

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

-
Aug 12, 2020. Covid-19 info

+
Mar 5, 2020. Novel coronavirus structure data

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

+
Jul 12, 2017. Major update of PDB

-
Yorodumi