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- PDB-6tbc: Crystal structure of S. aureus FabI in complex with NADPH and kal... -

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Basic information

Entry
Database: PDB / ID: 6tbc
TitleCrystal structure of S. aureus FabI in complex with NADPH and kalimantacin B
ComponentsEnoyl-[acyl-carrier-protein] reductase [NADPH]
KeywordsBIOSYNTHETIC PROTEIN / enoyl-[acyl carrier protein] reductase / fatty acid biosynthesis / Rossmann fold / short-chain dehydrogenase/reductase
Function / homology
Function and homology information


enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific) / : / fatty acid elongation / enoyl-[acyl-carrier-protein] reductase (NADH) activity / fatty acid biosynthetic process / NADP binding / nucleotide binding / identical protein binding
Similarity search - Function
Enoyl-[acyl-carrier-protein] reductase (NADH) / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-N5H / Chem-NDP / Enoyl-[acyl-carrier-protein] reductase [NADPH] / Enoyl-[acyl-carrier-protein] reductase [NADPH] FabI
Similarity search - Component
Biological speciesStaphylococcus aureus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.55 Å
AuthorsFage, C.D. / Masschelein, J.
Funding support Belgium, United Kingdom, 2items
OrganizationGrant numberCountry
Research Foundation - Flanders12H1716N Belgium
Engineering and Physical Sciences Research CouncilEP/M027503/1 United Kingdom
CitationJournal: Angew.Chem.Int.Ed.Engl. / Year: 2020
Title: The Kalimantacin Polyketide Antibiotics Inhibit Fatty Acid Biosynthesis in Staphylococcus aureus by Targeting the Enoyl-Acyl Carrier Protein Binding Site of FabI.
Authors: Fage, C.D. / Lathouwers, T. / Vanmeert, M. / Gao, L.J. / Vrancken, K. / Lammens, E.M. / Weir, A.N.M. / Degroote, R. / Cuppens, H. / Kosol, S. / Simpson, T.J. / Crump, M.P. / Willis, C.L. / ...Authors: Fage, C.D. / Lathouwers, T. / Vanmeert, M. / Gao, L.J. / Vrancken, K. / Lammens, E.M. / Weir, A.N.M. / Degroote, R. / Cuppens, H. / Kosol, S. / Simpson, T.J. / Crump, M.P. / Willis, C.L. / Herdewijn, P. / Lescrinier, E. / Lavigne, R. / Anne, J. / Masschelein, J.
History
DepositionNov 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation / citation_author / Item: _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Jul 1, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title / _citation_author.name
Revision 1.3Oct 21, 2020Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Jan 24, 2024Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Enoyl-[acyl-carrier-protein] reductase [NADPH]
B: Enoyl-[acyl-carrier-protein] reductase [NADPH]
C: Enoyl-[acyl-carrier-protein] reductase [NADPH]
D: Enoyl-[acyl-carrier-protein] reductase [NADPH]
E: Enoyl-[acyl-carrier-protein] reductase [NADPH]
F: Enoyl-[acyl-carrier-protein] reductase [NADPH]
G: Enoyl-[acyl-carrier-protein] reductase [NADPH]
H: Enoyl-[acyl-carrier-protein] reductase [NADPH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)238,07524
Polymers227,7228
Non-polymers10,35316
Water41423
1
A: Enoyl-[acyl-carrier-protein] reductase [NADPH]
B: Enoyl-[acyl-carrier-protein] reductase [NADPH]
C: Enoyl-[acyl-carrier-protein] reductase [NADPH]
D: Enoyl-[acyl-carrier-protein] reductase [NADPH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,03812
Polymers113,8614
Non-polymers5,1778
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20970 Å2
ΔGint-87 kcal/mol
Surface area34450 Å2
MethodPISA
2
E: Enoyl-[acyl-carrier-protein] reductase [NADPH]
F: Enoyl-[acyl-carrier-protein] reductase [NADPH]
G: Enoyl-[acyl-carrier-protein] reductase [NADPH]
H: Enoyl-[acyl-carrier-protein] reductase [NADPH]
hetero molecules


Theoretical massNumber of molelcules
Total (without water)119,03812
Polymers113,8614
Non-polymers5,1778
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area20860 Å2
ΔGint-84 kcal/mol
Surface area33780 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.316, 108.564, 296.183
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14A
24E
15A
25F
16A
26G
17A
27H
18B
28C
19B
29D
110B
210E
111B
211F
112B
212G
113B
213H
114C
214D
115C
215E
116C
216F
117C
217G
118C
218H
119D
219E
120D
220F
121D
221G
122D
222H
123E
223F
124E
224G
125E
225H
126F
226G
127F
227H
128G
228H

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11SERSERLYSLYSAA-3 - 2562 - 261
21SERSERLYSLYSBB-3 - 2562 - 261
12HISHISILEILEAA-2 - 2553 - 260
22HISHISILEILECC-2 - 2553 - 260
13METMETILEILEAA-1 - 2554 - 260
23METMETILEILEDD-1 - 2554 - 260
14METMETILEILEAA-1 - 2554 - 260
24METMETILEILEEE-1 - 2554 - 260
15METMETILEILEAA-1 - 2554 - 260
25METMETILEILEFF-1 - 2554 - 260
16HISHISILEILEAA-2 - 2553 - 260
26HISHISILEILEGG-2 - 2553 - 260
17METMETILEILEAA-1 - 2554 - 260
27METMETILEILEHH-1 - 2554 - 260
18HISHISILEILEBB-2 - 2553 - 260
28HISHISILEILECC-2 - 2553 - 260
19METMETILEILEBB-1 - 2554 - 260
29METMETILEILEDD-1 - 2554 - 260
110METMETILEILEBB-1 - 2554 - 260
210METMETILEILEEE-1 - 2554 - 260
111METMETILEILEBB-1 - 2554 - 260
211METMETILEILEFF-1 - 2554 - 260
112HISHISILEILEBB-2 - 2553 - 260
212HISHISILEILEGG-2 - 2553 - 260
113METMETILEILEBB-1 - 2554 - 260
213METMETILEILEHH-1 - 2554 - 260
114METMETILEILECC-1 - 2554 - 260
214METMETILEILEDD-1 - 2554 - 260
115METMETILEILECC-1 - 2554 - 260
215METMETILEILEEE-1 - 2554 - 260
116METMETILEILECC-1 - 2554 - 260
216METMETILEILEFF-1 - 2554 - 260
117HISHISLYSLYSCC-2 - 2563 - 261
217HISHISLYSLYSGG-2 - 2563 - 261
118METMETILEILECC-1 - 2554 - 260
218METMETILEILEHH-1 - 2554 - 260
119METMETLYSLYSDD-1 - 2564 - 261
219METMETLYSLYSEE-1 - 2564 - 261
120METMETLYSLYSDD-1 - 2564 - 261
220METMETLYSLYSFF-1 - 2564 - 261
121METMETILEILEDD-1 - 2554 - 260
221METMETILEILEGG-1 - 2554 - 260
122METMETLYSLYSDD-1 - 2564 - 261
222METMETLYSLYSHH-1 - 2564 - 261
123METMETLYSLYSEE-1 - 2564 - 261
223METMETLYSLYSFF-1 - 2564 - 261
124METMETILEILEEE-1 - 2554 - 260
224METMETILEILEGG-1 - 2554 - 260
125METMETLYSLYSEE-1 - 2564 - 261
225METMETLYSLYSHH-1 - 2564 - 261
126METMETILEILEFF-1 - 2554 - 260
226METMETILEILEGG-1 - 2554 - 260
127METMETLYSLYSFF-1 - 2564 - 261
227METMETLYSLYSHH-1 - 2564 - 261
128METMETILEILEGG-1 - 2554 - 260
228METMETILEILEHH-1 - 2554 - 260

NCS ensembles :
ID
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28

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Components

#1: Protein
Enoyl-[acyl-carrier-protein] reductase [NADPH] / ENR


Mass: 28465.264 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Plasmid: pET28a / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: A0A0J9X1X7, UniProt: Q6GI75*PLUS, enoyl-[acyl-carrier-protein] reductase (NADPH, Re-specific)
#2: Chemical
ChemComp-NDP / NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE


Mass: 745.421 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C21H30N7O17P3
#3: Chemical
ChemComp-N5H / (2~{E},5~{R},10~{E},12~{E},15~{S},19~{R})-20-[[(2~{R},3~{R})-3-aminocarbonyloxy-2-methyl-butanoyl]amino]-3,5,15-trimethyl-7-methylidene-19-oxidanyl-17-oxidanylidene-icosa-2,10,12-trienoic acid


Mass: 548.711 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C30H48N2O7 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 23 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.27 Å3/Da / Density % sol: 45.82 % / Description: Box-like
Crystal growTemperature: 295.15 K / Method: vapor diffusion, hanging drop
Details: 0.2 M NaCl, 0.1 M Na/K phosphate pH 6.2, 20% (w/v) PEG 1000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jul 10, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.55→29.64 Å / Num. obs: 68812 / % possible obs: 99.9 % / Redundancy: 13.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.091 / Rpim(I) all: 0.026 / Rrim(I) all: 0.094 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Rpim(I) allRrim(I) allNet I/σ(I) obs% possible all
2.55-2.6113.54.8066171745640.3271.3514.9940.6100
11.96-29.6210.90.04680207370.9990.0140.04845.793.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation7.81 Å29.65 Å
Translation7.81 Å29.65 Å

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Processing

Software
NameVersionClassification
XDSJan 26, 2018data reduction
Aimless0.7.4data scaling
PHASER2.8.2phasing
REFMAC5.8.0253refinement
PDB_EXTRACT3.25data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6TBB

6tbb


Resolution: 2.55→29.64 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.954 / SU B: 16.338 / SU ML: 0.32 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.31
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.237 3451 5 %RANDOM
Rwork0.1903 ---
obs0.1927 65272 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 218.17 Å2 / Biso mean: 92.288 Å2 / Biso min: 55.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å2-0 Å2-0 Å2
2---4.02 Å20 Å2
3---4.28 Å2
Refinement stepCycle: final / Resolution: 2.55→29.64 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15908 0 696 23 16627
Biso mean--95.14 83.23 -
Num. residues----2070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.01316845
X-RAY DIFFRACTIONr_bond_other_d0.0010.01715846
X-RAY DIFFRACTIONr_angle_refined_deg1.5551.69222766
X-RAY DIFFRACTIONr_angle_other_deg1.2051.62336733
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.20752062
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85223.407819
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.397152908
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.7581588
X-RAY DIFFRACTIONr_chiral_restr0.0550.22214
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218714
X-RAY DIFFRACTIONr_gen_planes_other0.0010.023374
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A76850.1
12B76850.1
21A75500.11
22C75500.11
31A76280.09
32D76280.09
41A77130.09
42E77130.09
51A76470.1
52F76470.1
61A76550.09
62G76550.09
71A76570.09
72H76570.09
81B76060.1
82C76060.1
91B75970.09
92D75970.09
101B76510.09
102E76510.09
111B76470.1
112F76470.1
121B76500.1
122G76500.1
131B76340.1
132H76340.1
141C75600.1
142D75600.1
151C75590.1
152E75590.1
161C75860.1
162F75860.1
171C76780.1
172G76780.1
181C75910.09
182H75910.09
191D76500.09
192E76500.09
201D75770.1
202F75770.1
211D76260.09
212G76260.09
221D76300.09
222H76300.09
231E76240.09
232F76240.09
241E75810.1
242G75810.1
251E76860.09
252H76860.09
261F76290.1
262G76290.1
271F76340.09
272H76340.09
281G76180.1
282H76180.1
LS refinement shellResolution: 2.55→2.616 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.404 280 -
Rwork0.384 4724 -
all-5004 -
obs--100 %

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