PDB-7scl: The X-ray crystal structure of Staphylococcus aureus Fatty Acid K...

ID or keywords:

Entry

Database: PDB / ID: 7scl

Title

The X-ray crystal structure of Staphylococcus aureus Fatty Acid Kinase B1 (FakB1) mutant R173A in complex with Palmitate to 1.60 Angstrom resolution

Components

Fatty Acid Kinase B1

Keywords

TRANSFERASE/SUBSTRATE / Fatty acid kinase B1 / Fatty acid transporter / TRANSFERASE / TRANSFERASE-SUBSTRATE complex

Function / homology

DegV / DegV, C-terminal domain / Uncharacterised protein, DegV family COG1307 / DegV domain profile. / lipid binding / PALMITIC ACID / DegV domain-containing protein MW0711

Function and homology information

Biological species

Staphylococcus aureus (bacteria)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT / Resolution: 1.6 Å

Authors

Cuypers, M.G. / Gullett, J.M. / Subramanian, C. / Rock, C.O. / White, S.W.

Funding support

United States, 1items

Citation

Journal: J.Biol.Chem. / Year: 2022
Title: Identification of structural transitions in bacterial fatty acid binding proteins that permit ligand entry and exit at membranes.
Authors: Gullett, J.M. / Cuypers, M.G. / Grace, C.R. / Pant, S. / Subramanian, C. / Tajkhorshid, E. / Rock, C.O. / White, S.W.

History

Deposition	Sep 28, 2021	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Oct 27, 2021	Provider: repository / Type: Initial release
Revision 1.1	May 11, 2022	Group: Database references / Category: citation / citation_author Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2	Oct 18, 2023	Group: Data collection / Refinement description Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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PDBx/mmCIF format	7scl.cif.gz	296.7 KB	Display	PDBx/mmCIF format
PDB format	pdb7scl.ent.gz	197.8 KB	Display	PDB format
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Validation report

Summary document	7scl_validation.pdf.gz	718.5 KB	Display	wwPDB validaton report
Full document	7scl_full_validation.pdf.gz	724 KB	Display
Data in XML	7scl_validation.xml.gz	26.4 KB	Display
Data in CIF	7scl_validation.cif.gz	38 KB	Display
Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/sc/7scl ftp://data.pdbj.org/pub/pdb/validation_reports/sc/7scl	HTTPS FTP

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Related structure data

Related structure data	6mh9C 6nm1C 7sg3C 5utoS S: Starting model for refinement C: citing same article (ref.)
Similar structure data	4nmy-2 6nyu-1 4nmy-1 3kmg-2 6nm1-2 6mn4-3 3elw-d 6mn5-2 1af2-d 5vb7-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) 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	#147 - Mar 2012 Rhodopsin similarity (1) #100 - Apr 2008 Adrenergic Receptors similarity (1) #164 - Aug 2013 Serotonin Receptor similarity (1) #171 - Mar 2014 Neurotransmitter Transporters similarity (1) #27 - Mar 2002 Bacteriorhodopsin similarity (1)

Deposited unit

A: Fatty Acid Kinase B1

B: Fatty Acid Kinase B1

hetero molecules

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

1

A: Fatty Acid Kinase B1

hetero molecules

defined by author
Evidence: gel filtration
34.6 kDa, 1 polymers
Search similar-shape structures of this assembly by Omokage search (details)

2

B: Fatty Acid Kinase B1

hetero molecules

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

Unit cell

Length a, b, c (Å)	33.189, 53.900, 84.414
Angle α, β, γ (deg.)	104.332, 90.657, 107.493
Int Tables number	1
Space group name H-M	P1
Space group name Hall	P1
Symmetry operation	#1: x,y,z

#1: Protein	Fatty Acid Kinase B1 / DegV domain-containing protein MW0711 Mass: 34186.738 Da / Num. of mol.: 2 / Mutation: R173A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: MW0711 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8NXM4
#2: Chemical	ChemComp-PLM / PALMITIC ACID Mass: 256.424 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₁₆H₃₂O₂ / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₃H₈O₃
#4: Water	ChemComp-HOH / water Mass: 18.015 Da / Num. of mol.: 359 / Source method: isolated from a natural source / Formula: H₂O
Has ligand of interest	Y

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Experiment

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

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Sample preparation

Crystal	Density Matthews: 2.03 Å³/Da / Density % sol: 39.47 % Description: Crystal Seeded from crunched and diluted WT crystals from the same crystallization condition, large flattened and elongated rhomboedron.
Crystal grow	Temperature: 291 K / Method: vapor diffusion, hanging drop Details: pH 6.5 0.1M MES/IMIDAZOLE, 12.5% PEG1000, 12.5% PEG3350, 12.5% MPD, 0.03M NaNO3, 0.03M Na2HPO4, 0.03M (NH4)2SO4

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Data collection

Diffraction	Mean temperature: 100 K / Serial crystal experiment: N
Diffraction source	Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
Detector	Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Sep 21, 2021
Radiation	Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength	Wavelength: 1 Å / Relative weight: 1
Reflection	Resolution: 1.6→49.6 Å / Num. obs: 63745 / % possible obs: 89.7 % / Redundancy: 3.8 % / B_iso Wilson estimate: 24 Å² / CC_1/2: 0.998 / R_merge(I) obs: 0.056 / R_pim(I) all: 0.033 / Χ²: 0.42 / Net I/σ(I): 7
Reflection shell	Resolution: 1.6→1.63 Å / R_merge(I) obs: 0.596 / Mean I/σ(I) obs: 2 / Num. unique obs: 2951 / CC_1/2: 0.841 / R_pim(I) all: 0.351 / Χ²: 0.42 / % possible all: 83.5

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Processing

Software

Name	Version	Classification
PHENIX	dev_4302	refinement
XDS		data reduction
Aimless		data scaling
MOLREP		phasing

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: 5UTO

5uto

Resolution: 1.6→40.72 Å / SU ML: 0.1825 / Cross valid method: FREE R-VALUE / σ(F): 2.01 / Phase error: 20.9376
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2

	R_factor	Num. reflection	% reflection
R_free	0.1931	3146	5.06 %
R_work	0.1619	59026	-
obs	0.1634	62172	87.49 %

Solvent computation

Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL

Displacement parameters

B_iso mean: 40.49 Å²

Refinement step

Cycle: LAST / Resolution: 1.6→40.72 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4408	0	48	359	4815

Refine LS restraints

Refine-ID	Type	Dev ideal	Number
X-RAY DIFFRACTION	f_bond_d	0.008	4548
X-RAY DIFFRACTION	f_angle_d	1.0222	6143
X-RAY DIFFRACTION	f_chiral_restr	0.0659	695
X-RAY DIFFRACTION	f_plane_restr	0.0069	790
X-RAY DIFFRACTION	f_dihedral_angle_d	6.5793	652

LS refinement shell

Resolution (Å)	R_factor R_free	Num. reflection R_free	R_factor R_work	Num. reflection R_work	Refine-ID	% reflection obs (%)
1.6-1.62	0.3189	113	0.2485	2271	X-RAY DIFFRACTION	73.95
1.63-1.65	0.2794	137	0.2393	2564	X-RAY DIFFRACTION	83.21
1.65-1.68	0.2712	132	0.219	2636	X-RAY DIFFRACTION	85.83
1.68-1.71	0.2567	147	0.2075	2660	X-RAY DIFFRACTION	87.39
1.71-1.74	0.2736	158	0.1992	2686	X-RAY DIFFRACTION	86.31
1.74-1.78	0.2287	132	0.1922	2671	X-RAY DIFFRACTION	88.28
1.78-1.82	0.2216	161	0.1874	2709	X-RAY DIFFRACTION	89.46
1.82-1.86	0.2378	155	0.1881	2781	X-RAY DIFFRACTION	89.43
1.86-1.91	0.224	168	0.1882	2729	X-RAY DIFFRACTION	91.13
1.91-1.96	0.2468	132	0.1925	2793	X-RAY DIFFRACTION	89.64
1.96-2.02	0.2206	134	0.1828	2781	X-RAY DIFFRACTION	90.89
2.02-2.08	0.2521	138	0.1778	2736	X-RAY DIFFRACTION	87.68
2.08-2.16	0.1865	154	0.1708	2616	X-RAY DIFFRACTION	86.54
2.16-2.24	0.2045	101	0.1686	2365	X-RAY DIFFRACTION	76.37
2.24-2.34	0.2144	151	0.1775	2871	X-RAY DIFFRACTION	93.16
2.34-2.47	0.2121	127	0.1709	2885	X-RAY DIFFRACTION	93.98
2.47-2.62	0.2233	176	0.1756	2774	X-RAY DIFFRACTION	91.87
2.62-2.82	0.208	173	0.1589	2794	X-RAY DIFFRACTION	91.1
2.82-3.11	0.1849	136	0.1555	2771	X-RAY DIFFRACTION	90.34
3.11-3.56	0.1503	133	0.1404	2667	X-RAY DIFFRACTION	86.66
3.56-4.48	0.138	120	0.1306	2478	X-RAY DIFFRACTION	80.38
4.48-40.72	0.1797	168	0.1556	2788	X-RAY DIFFRACTION	91.52

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	4.3599554911	-1.72548883561	-0.258707393523	1.57149311712	0.674858923055	0.465567643565	-0.507687168731	-0.578657828196	1.87337546055	0.0770733641419	0.373046436702	-0.626727756288	-0.216599085746	0.349069274535	0.374915076511	0.281143429667	0.0250634049342	-0.140829044788	0.222916452811	-0.0677270694603	0.687100614021	10.2295836898	-0.489009483684	-18.306630624
2	0.455326025923	-1.22133800016	-1.46046190359	4.33614616247	2.68883027353	6.91097872622	-0.425973496379	-1.70165219695	0.352673545963	0.937532931448	0.298046112567	-0.726240946035	-1.0179801839	-0.256109632894	-0.110302699706	0.805663447907	0.336356441219	-0.188114213749	1.11606052217	-0.202169575942	0.565804286202	11.8229605734	-6.98720926831	-2.54288598548
3	3.36346506543	-0.452698622418	-1.2134927695	4.73733611859	-0.650242769421	0.697296279443	-0.259570664207	-1.29859311387	-0.143309691738	0.802212310462	-0.44346453637	-0.0727112618649	-0.527631479978	-0.25510865915	-0.26033431684	0.549707467236	0.329456234143	-0.111651162175	0.84179294672	-0.205566278307	0.174874061164	8.55367666234	-13.3910287297	-1.80318082595
4	3.74669096185	-1.76119213505	0.562434681966	3.55884521303	-0.959870760957	2.77378378941	-0.382543687972	-0.0788188296305	1.20964347709	0.228795782569	0.120725652822	-0.542532090425	-0.592736305095	-0.317458423266	-0.0285758776818	0.280810018822	0.0651792771183	-0.120660800018	0.140027455506	-0.0133194090276	0.560369438648	0.53161214423	0.649174218122	-22.7177914115
5	6.0180718006	-2.51984107733	4.396078081	2.92661285291	-1.31737977351	3.43040093707	-0.374815202348	-1.61820221555	-0.349181652414	0.402926501852	0.324957777834	0.599661347082	0.254621198194	-0.501861428408	-0.0767475448897	0.579765603644	0.139535445322	0.216209269559	0.756090471978	0.235634634559	0.532955927371	-4.12820321708	-22.3570945639	-7.04854985311
6	0.585554959832	0.809286665197	0.14645058309	1.23968778795	0.382829204266	0.176365364409	-0.354391089142	-0.243027924751	-1.07806798056	0.39704170254	-0.0480285060777	1.25168964218	0.648727024831	-0.289917587138	-0.667916730628	0.532952915429	0.00981355552205	0.275796749221	0.268094939386	0.15137275967	0.646237549943	-4.44543927043	-26.1318974275	-14.8160860347
7	3.46323882099	-2.67923828377	1.82589752183	5.62928693023	-4.72777789144	4.09978632407	0.0281679384802	0.172472645964	-0.835625845568	-0.28385085583	0.0629472129045	0.565536571118	0.764203184143	-0.0251381819829	-0.309490047434	0.314147142034	-0.0332358337146	0.0794130301141	0.184973295259	-0.0128280422493	0.381546471572	2.78606996427	-28.5822092139	-26.034051096
8	5.42324266972	-0.688658011743	2.06582547913	2.8841813623	0.336262178726	2.64997605411	0.0160546641731	0.0773055755037	-0.280664611763	0.0239015589462	0.0453405562082	-0.0817302809631	0.329906406534	0.376322941846	-0.0594563780928	0.233882213332	0.0325703176054	0.0472285473847	0.202144613435	0.0272896280181	0.201566909235	11.7060879768	-22.7787871438	-24.2895136888
9	3.05716767939	-1.39175676037	-0.216016294937	1.84828027716	0.590948842548	3.95307488162	-0.196678902028	-0.118809545689	0.247141573387	0.021182820305	0.113708490333	-0.109200827929	0.0504922483513	0.177796433356	0.0763690012202	0.219965825977	-0.00241520342408	0.0081618081053	0.179429669653	0.0204340171646	0.203174971824	8.69344071904	-15.9657294772	-23.0199155539
10	6.1136574674	0.808100432244	0.346865557131	2.85170172035	-0.859506072017	4.26224517238	-0.0545255431045	-0.425246844454	0.595858373051	0.503146590205	0.0230596556909	-0.197985166834	-0.67524678329	-0.0889982347033	0.0746416310216	0.349657769227	0.00763095307943	-0.033222498649	0.261029339957	0.00116358659855	0.208451086095	-2.14505350042	26.2018698274	21.3011014513
11	3.79577290112	-0.890880336977	-1.78884441088	6.70000008675	2.88439406219	6.08458947829	-0.00294511786337	0.324432980666	0.134038000013	-0.217773484555	-0.259772434437	0.351103517917	-0.34579515607	-0.513358002244	0.314948622266	0.17233432978	0.0200428069155	-0.07158406456	0.318169487353	-0.0137048476741	0.211842773345	-10.4805701999	19.2008231395	14.1648253673
12	0.866137024975	1.54844425147	-0.865489039189	3.9489963138	1.13207982884	7.69084914733	0.0847491521336	1.51819046253	-0.0840751979965	-0.871581056259	-0.0744635486743	0.729326047827	0.170425754093	-0.574942452563	0.16553961969	0.515698470656	0.00054016406688	-0.096163274573	0.877572689282	-0.112796723206	0.321270219116	-11.8806757822	9.57604818236	2.05545357797
13	4.5829810355	1.98209824814	0.660337768024	5.15491400778	1.48431669717	2.45049626099	0.000159367235504	0.836286941243	-0.528775632143	-0.469978834287	0.0247457003175	-0.0208870104855	0.171222291563	-0.261939592628	0.0234343349761	0.411216754601	-0.0541365971098	-0.0127025698985	0.53677643682	-0.144853914065	0.227923410722	-9.72787157652	2.96674224106	3.5717165843
14	1.10567186606	-0.841144986666	-0.339000515757	5.90142680332	-0.393244947584	2.36990351469	0.0301087618903	0.288345665589	0.16262328992	-0.378030147663	-0.107536614034	-0.621172384302	-0.312648010363	0.0242959349524	0.0828931588468	0.228944224189	-0.040401350478	0.0197191286523	0.258279723359	0.0428097678731	0.237645937071	3.52126870769	23.3640832252	12.7031401514
15	1.34297155469	-0.198595348128	0.272369578005	6.54128612371	0.43456005847	2.57598465188	-0.12845970032	-0.126862529847	0.113013817892	0.348868766535	0.0179198264883	-0.106776931923	-0.297609842076	0.0230846573926	0.0851077113683	0.182821750969	-0.0337549158875	-0.0149668989343	0.2072360294	-0.00821214356785	0.146940580925	-0.0894812677563	18.0136271843	27.0397704006
16	3.68208340922	0.97386906502	0.724557220395	6.2168855204	-0.308417928875	5.67618203643	0.0547897532686	0.540366204147	-0.740929917901	-0.286379135283	-0.143485583262	-0.230014771803	0.69548770358	0.0803755919449	0.0660859679628	0.325213168171	0.0107390015325	0.0728219038819	0.306226967792	-0.115415518828	0.434937848239	0.650759347946	-5.73092283346	15.4741856841
17	3.06757125009	0.1708344874	0.181155886749	3.79828009916	2.63408142007	2.66690217441	0.0513549074773	-0.101151769093	-0.54974696479	0.455526727098	-0.118359223681	-0.0237390441537	0.62508702062	-0.175252323514	0.0467459436152	0.26398280338	-0.0112387821392	0.00649465322755	0.161966493122	0.0468758052239	0.275303270852	-3.06663654343	-5.75566152176	28.7273380214
18	4.80807158488	0.632693379596	2.13514773879	2.368233828	0.769697776391	5.64089902816	0.0607440561852	-0.166052167116	-0.259732782159	0.125733337305	-0.137272955774	0.234559563689	0.297433506524	-0.550016984548	0.0899015390317	0.191688168163	-0.0353993013407	0.0579017028126	0.224231472345	-0.0129573988517	0.188858231225	-13.2168107324	2.38969049207	28.0831577887
19	1.67394571177	0.377373686546	-0.285069871358	0.915532207379	-0.0961939985922	2.37181758088	-0.0349010922472	0.0648297892494	-0.00366415818115	-0.00898962906601	-0.0364886822124	0.0613416981273	-0.0889978162945	-0.248479513735	0.0854066189423	0.195659971246	-0.0257764580184	0.0133775865048	0.235939326794	-0.00756199352492	0.198709154235	-9.2084833884	7.0437872412	24.2665709718

Refinement TLS group

Refine-ID: X-RAY DIFFRACTION

ID	Refine TLS-ID	Selection details	Auth asym-ID	Label asym-ID	Auth seq-ID	Label seq-ID
1	1	chain 'A' and (resid 1 through 31 )	A	A	1 - 31	1 - 31
2	2	chain 'A' and (resid 32 through 45 )	A	A	32 - 45	32 - 45
3	3	chain 'A' and (resid 46 through 66 )	A	A	46 - 66	46 - 66
4	4	chain 'A' and (resid 67 through 161 )	A	A	67 - 161	67 - 161
5	5	chain 'A' and (resid 162 through 180 )	A	A	162 - 180	162 - 180
6	6	chain 'A' and (resid 181 through 206 )	A	A	181 - 206	181 - 206
7	7	chain 'A' and (resid 207 through 224 )	A	A	207 - 224	207 - 224
8	8	chain 'A' and (resid 225 through 251 )	A	A	225 - 251	225 - 251
9	9	chain 'A' and (resid 252 through 288 )	A	A	252 - 288	252 - 288
10	10	chain 'B' and (resid -4 through 11 )	B	E	-4 - 11	1 - 16
11	11	chain 'B' and (resid 12 through 31 )	B	E	12 - 31	17 - 36
12	12	chain 'B' and (resid 32 through 45 )	B	E	32 - 45	37 - 50
13	13	chain 'B' and (resid 46 through 66 )	B	E	46 - 66	51 - 71
14	14	chain 'B' and (resid 67 through 121 )	B	E	67 - 121	72 - 126
15	15	chain 'B' and (resid 122 through 161 )	B	E	122 - 161	127 - 166
16	16	chain 'B' and (resid 162 through 196 )	B	E	162 - 196	167 - 194
17	17	chain 'B' and (resid 197 through 224 )	B	E	197 - 224	195 - 222
18	18	chain 'B' and (resid 225 through 251 )	B	E	225 - 251	223 - 249
19	19	chain 'B' and (resid 252 through 288 )	B	E	252 - 288	250 - 286

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