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- PDB-4bo6: Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (... -

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Basic information

Entry
Database: PDB / ID: 4bo6
TitleCrystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with 2,3-dihydroindol-1-yl-(2- thiophen-3-yl-1,3-thiazol-4-yl)methanone at 2.8A resolution
Components3-OXOACYL-[ACYL-CARRIER-PROTEIN] REDUCTASE FABG
KeywordsOXIDOREDUCTASE / ROSSMANN FOLD / FATTY ACID BIOSYNTHESIS
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 3-oxoacyl-[acyl-carrier-protein] reductase / fatty acid elongation / oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor / NAD binding / NADP binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / : / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold ...3-oxoacyl-(acyl-carrier-protein) reductase / : / PKS_KR / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / 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-36P / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsCukier, C.D. / Schnell, R. / Lindqvist, Y. / Schneider, G.
CitationJournal: Acs Chem.Biol. / Year: 2013
Title: Discovery of an Allosteric Inhibitor Binding Site in 3-Oxo-Acyl-Acp Reductase from Pseudomonas Aeruginosa
Authors: Cukier, C.D. / Hope, A. / Elamin, A. / Moynie, L. / Schnell, R. / Schach, S. / Kneuper, H. / Singh, M. / Naismith, J. / Lindqvist, Y. / Gray, D. / Schneider, G.
History
DepositionMay 18, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2013Provider: repository / Type: Initial release
Revision 1.1Nov 27, 2013Group: Database references
Revision 1.2Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] REDUCTASE FABG
B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] REDUCTASE FABG
C: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] REDUCTASE FABG
D: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] REDUCTASE FABG
hetero molecules


Theoretical massNumber of molelcules
Total (without water)113,2976
Polymers112,6724
Non-polymers6252
Water45025
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11000 Å2
ΔGint-62.8 kcal/mol
Surface area37330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.490, 108.860, 147.400
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.1083, -0.9933, 0.04038), (-0.9939, 0.1074, -0.02351), (0.01901, -0.04268, -0.9989)-8.462, -9.8, -67.49
2given(0.102, 0.9936, 0.04929), (0.9918, -0.1054, 0.07188), (0.07662, 0.04155, -0.9962)-24.08, 30.77, -67.21
3given(-0.9954, 0.001316, -0.09597), (0.001076, -0.9997, -0.02488), (-0.09597, -0.02487, 0.9951)-38.79, 19.16, -1.361

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Components

#1: Protein
3-OXOACYL-[ACYL-CARRIER-PROTEIN] REDUCTASE FABG / 3-OXOACYL-ACYL-CARRIER-PROTEIN REDUCTASE / 3-KETOACYL-ACYL CARRIER PROTEIN REDUCTASE / BETA- ...3-OXOACYL-ACYL-CARRIER-PROTEIN REDUCTASE / 3-KETOACYL-ACYL CARRIER PROTEIN REDUCTASE / BETA-KETOACYL-ACYL CARRIER PROTEIN REDUCTASE / BETA-KETOACYL-ACP REDUCTASE / 3-OXOACYL-ACP REDUCTASE


Mass: 28167.961 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PNIC-PA2967 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: O54438, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-36P / 2,3-dihydroindol-1-yl-(2-thiophen-3-yl-1,3-thiazol-4-yl)methanone


Mass: 312.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H12N2OS2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 25 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details36P: THE LIGAND 2,3-DIHYDROINDOL-1-YL-(2-THIOPHEN-3-YL-1,3- THIAZOL-4-YL)METHANONE IS BOUND AT THE ...36P: THE LIGAND 2,3-DIHYDROINDOL-1-YL-(2-THIOPHEN-3-YL-1,3- THIAZOL-4-YL)METHANONE IS BOUND AT THE INTERFACES BETWEEN PROTEIN CHAINS A AND B, AND BETWEEN PROTEIN CHAINS C AND D.

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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: 1.95 Å3/Da / Density % sol: 36.81 % / Description: NONE
Crystal growpH: 7
Details: 0.24 M SODIUM MALONATE PH 7.0, 20% (W/V) PEG3350, 1 MM 2,3-DIHYDROINDOL-1-YL-(2-THIOPHEN- 3-YL-1,3-THIAZOL-4-YL)METHANONE, FINAL PROTEIN CONCENTRATION 5 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0409
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 6, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0409 Å / Relative weight: 1
ReflectionResolution: 2.8→15.93 Å / Num. obs: 19603 / % possible obs: 88.2 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 34.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.5
Reflection shellResolution: 2.8→2.97 Å / Redundancy: 4.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.7 / % possible all: 79.9

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BNW, LIGAND-FREE

4bnw


Resolution: 2.8→15.94 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.901 / SU B: 33.919 / SU ML: 0.313 / Cross valid method: THROUGHOUT / ESU R Free: 0.468 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25537 965 4.9 %RANDOM
Rwork0.19679 ---
obs0.19968 18605 87.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 38.305 Å2
Baniso -1Baniso -2Baniso -3
1--1.2 Å20 Å20 Å2
2---1.9 Å20 Å2
3---3.11 Å2
Refinement stepCycle: LAST / Resolution: 2.8→15.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6958 0 42 25 7025
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197128
X-RAY DIFFRACTIONr_bond_other_d0.0060.027018
X-RAY DIFFRACTIONr_angle_refined_deg1.3971.9669658
X-RAY DIFFRACTIONr_angle_other_deg1.2133.00116018
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7275958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.20624.357280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.327151160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.2721549
X-RAY DIFFRACTIONr_chiral_restr0.0650.21138
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028301
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021590
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.4453.393832
X-RAY DIFFRACTIONr_mcbond_other2.4453.393831
X-RAY DIFFRACTIONr_mcangle_it4.1095.064772
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.5593.823296
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.8→2.873 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 63 -
Rwork0.278 1230 -
obs--78.99 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°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)
10.30970.0699-0.02280.26920.08150.0890.00560.0133-0.0027-0.00380.0087-0.00710.00930.0087-0.01440.0235-0.00110.00370.0044-0.00540.0079-10.7274-2.6586-51.5666
20.20410.1693-0.00520.3184-0.08020.1692-0.01320.0074-0.00760.02140.014-0.03950.0080.0228-0.00080.01550.0088-0.01290.0084-0.00730.015-6.89252.3579-15.962
30.2849-0.1079-0.03250.21530.0290.0314-0.0148-0.028-0.00170.00590.04150.01650.0002-0.0067-0.02670.01430.008-0.00360.01880.01370.0268-30.777317.3545-16.9298
40.1533-0.04020.14190.37560.04760.22830.02110.01590.0006-0.0286-0.0162-0.0051-0.03070.0036-0.00490.02760.00840.00750.00510.00570.0117-23.242823.1162-51.6358
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 247
2X-RAY DIFFRACTION2B-4 - 247
3X-RAY DIFFRACTION3C-10 - 247
4X-RAY DIFFRACTION4D-3 - 247

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