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- PDB-4bo9: Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (... -

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Basic information

Entry
Database: PDB / ID: 4bo9
TitleCrystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with 5-(2-(furan-2-ylmethoxy) phenyl)-2-phenyltetrazole at 2.9A 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
5-[2-(FURAN-2-YLMETHOXY)PHENYL]-2-PHENYLTETRAZOLE / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 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 1.2Dec 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)113,3096
Polymers112,6724
Non-polymers6372
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10380 Å2
ΔGint-55.8 kcal/mol
Surface area37240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.707, 108.866, 149.950
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(-0.116, 0.9916, 0.05709), (0.9919, 0.1127, 0.05815), (0.05123, 0.06337, -0.9967)-96.67, 82.49, 60.3
2given(0.1032, -0.9907, 0.08885), (-0.987, -0.113, -0.114), (0.123, -0.07594, -0.9895)130.5, 153.4, 74.98
3given(-0.9868, -0.01041, -0.1616), (0.003597, -0.9991, 0.04237), (-0.1619, 0.04123, 0.9859)45.44, 232.6, -1.334

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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-3X3 / 5-[2-(FURAN-2-YLMETHOXY)PHENYL]-2-PHENYLTETRAZOLE


Mass: 318.329 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H14N4O2
Nonpolymer detailsTHE LIGAND 5-[2-(FURAN-2-YLMETHOXY)PHENYL]-2-PHENYLTETRAZOLE IS BOUND AT THE INTERFACES BETWEEN ...THE LIGAND 5-[2-(FURAN-2-YLMETHOXY)PHENYL]-2-PHENYLTETRAZOLE 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: 2.1 Å3/Da / Density % sol: 41.35 % / Description: LIGAND FREE PDB
Crystal growpH: 7
Details: 0.1 M HEPES PH 7.0, 1.1 M SODIUM MALONATE, 0.5% (V/V) JEFFAMINE ED-2001, 1MM 5-[2-(FURAN-2-YLMETHOXY)PHENYL]-2-PHENYLTETRAZOLE, FINAL PROTEIN CONCENTRATION 6.7 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 9, 2012 / Details: SAGITALLY FOCUSING GE(220) AND A MULTILAYER
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.9→39.6 Å / Num. obs: 21289 / % possible obs: 98.6 % / Observed criterion σ(I): -3 / Redundancy: 5.8 % / Biso Wilson estimate: 54.7 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.5
Reflection shellResolution: 2.9→3.08 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3 / % possible all: 99.5

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BNW

4bnw


Resolution: 2.9→39.63 Å / Cor.coef. Fo:Fc: 0.909 / Cor.coef. Fo:Fc free: 0.886 / SU B: 70.994 / SU ML: 0.579 / Cross valid method: THROUGHOUT / ESU R Free: 0.553 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.31806 1047 5 %RANDOM
Rwork0.27216 ---
obs0.27447 20050 97.31 %-
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: 77.562 Å2
Baniso -1Baniso -2Baniso -3
1-13.21 Å20 Å20 Å2
2---5.58 Å20 Å2
3----7.63 Å2
Refinement stepCycle: LAST / Resolution: 2.9→39.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6803 0 48 0 6851
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0196925
X-RAY DIFFRACTIONr_bond_other_d0.0060.026846
X-RAY DIFFRACTIONr_angle_refined_deg1.4051.9729374
X-RAY DIFFRACTIONr_angle_other_deg1.1733.00115616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1235929
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.80924.491265
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.664151130
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.9231548
X-RAY DIFFRACTIONr_chiral_restr0.0650.21113
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.028048
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021524
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_it2.3753.653746
X-RAY DIFFRACTIONr_mcbond_other2.3753.6493745
X-RAY DIFFRACTIONr_mcangle_it3.9575.4634665
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.1743.9463179
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: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.405 86 -
Rwork0.355 1459 -
obs--99.74 %
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)
12.11150.0966-0.24382.0385-0.65780.5065-0.02920.05970.0738-0.10970.06680.0130.2958-0.0877-0.03760.2521-0.0299-0.0110.57560.04360.595211.9871104.692651.7365
21.4374-0.1472-0.0752.3496-0.51981.0515-0.0797-0.0390.1075-0.22510.01880.35530.1376-0.3470.06090.1499-0.0652-0.05880.51740.02270.41838.9815109.618416.0334
31.40560.11460.03593.51410.47670.3239-0.08550.09020.0733-0.05530.1226-0.34460.13740.148-0.03710.1765-0.0115-0.02260.4760.02670.419633.1268124.940918.026
41.9758-0.2803-0.24861.5412-0.64380.55760.1175-0.0815-0.17120.3014-0.02050.1707-0.3787-0.0295-0.0970.3073-0.00990.00390.4718-0.03120.521724.0766130.400752.493
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 247
2X-RAY DIFFRACTION2B-1 - 247
3X-RAY DIFFRACTION3C1 - 247
4X-RAY DIFFRACTION4D-4 - 247

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