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- PDB-4bo4: Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (... -

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Basic information

Entry
Database: PDB / ID: 4bo4
TitleCrystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with N-(2-methoxyphenyl)-3,4- dihydro-2H-quinoline-1-carboxamide at 2.7A 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-36G / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 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)113,2376
Polymers112,6724
Non-polymers5652
Water54030
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11080 Å2
ΔGint-59.5 kcal/mol
Surface area38310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.420, 108.610, 148.310
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(-0.1034, 0.9937, -0.0424), (0.9946, 0.1031, -0.01097), (-0.006528, -0.04331, -0.999)-9.352, 10.43, 68.3
2given(0.1076, -0.9932, -0.04394), (-0.9921, -0.1102, 0.06045), (-0.06488, 0.03708, -0.9972)-24.14, -30.69, 68.11
3given(-0.9966, -0.01186, 0.08125), (0.009482, -0.9995, -0.02965), (0.08156, -0.02878, 0.9963)-39.42, -17.6, 1.076

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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-36G / N-(2-methoxyphenyl)-3,4-dihydro-2H-quinoline-1-carboxamide


Mass: 282.337 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H18N2O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details36G: THE LIGAND N-(2-METHOXYPHENYL)-3,4-DIHYDRO-2H-QUINOLINE- 1-CARBOXAMIDE IS BOUND AT THE ...36G: THE LIGAND N-(2-METHOXYPHENYL)-3,4-DIHYDRO-2H-QUINOLINE- 1-CARBOXAMIDE 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: 1.99 Å3/Da / Density % sol: 38.11 % / Description: NONE
Crystal growpH: 7
Details: 0.1M HEPES PH 7.0, 1M SUCCINIC ACID, 1% (W/V) PEG MME 2000, 1MM N-(2-METHOXYPHENYL)-3,4- DIHYDRO-2H-QUINOLINE-1-CARBOXAMIDE, 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: 2.7→30.82 Å / Num. obs: 25271 / % possible obs: 99.7 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 39.2 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 9.1
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 100

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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-FRE

4bnw


Resolution: 2.7→22.95 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.891 / SU B: 29.66 / SU ML: 0.286 / Cross valid method: THROUGHOUT / ESU R Free: 0.392 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25963 1246 4.9 %RANDOM
Rwork0.20621 ---
obs0.20884 23947 99.18 %-
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: 49.247 Å2
Baniso -1Baniso -2Baniso -3
1-2.73 Å20 Å20 Å2
2---1.05 Å20 Å2
3----1.69 Å2
Refinement stepCycle: LAST / Resolution: 2.7→22.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7113 0 42 30 7185
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0197254
X-RAY DIFFRACTIONr_bond_other_d0.0060.027169
X-RAY DIFFRACTIONr_angle_refined_deg1.3811.9669822
X-RAY DIFFRACTIONr_angle_other_deg1.2093.00216353
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6275973
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.39724.331284
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.581151189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.3031551
X-RAY DIFFRACTIONr_chiral_restr0.0680.21161
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028439
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021618
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_it3.1284.3533904
X-RAY DIFFRACTIONr_mcbond_other3.1284.3523903
X-RAY DIFFRACTIONr_mcangle_it5.1036.5084864
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.3754.8973350
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: 2.7→2.77 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.322 90 -
Rwork0.295 1782 -
obs--99.84 %
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)
10.24850.01960.04340.32430.14530.11370.01080.0048-0.01690.00820.0131-0.0051-0.00940.031-0.02390.0192-0-0.01070.0177-0.01870.0265-11.42633.182351.7827
20.2604-0.2235-0.02670.3523-0.0630.3263-0.01020.0187-0.0075-0.01650.022-0.0431-0.03550.0573-0.01180.0138-0.02170.01450.0343-0.0220.0228-7.3854-2.312216.293
30.33660.104-0.00760.2639-0.0270.1513-0.03520.04950.0172-0.02110.0680.02460.0073-0.0166-0.03280.0112-0.0081-0.01220.01970.00920.0193-31.7614-17.586717.8031
40.12980.19710.05770.36470.03850.14650.02780.0002-0.00910.05130.0155-0.02190.0604-0.001-0.04330.03650.0086-0.0270.0073-0.00870.0224-23.3814-22.839651.9688
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 247
2X-RAY DIFFRACTION2B-5 - 247
3X-RAY DIFFRACTION3C-10 - 247
4X-RAY DIFFRACTION4D-4 - 247

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