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- PDB-4bo8: Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (... -

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Basic information

Entry
Database: PDB / ID: 4bo8
TitleCrystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with 1-(2-amino-4- phenylimidazol-1-yl)-3-(2-fluorophenyl)urea 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-34X / 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 1.2Dec 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)113,3917
Polymers112,6724
Non-polymers7193
Water93752
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10780 Å2
ΔGint-71 kcal/mol
Surface area37060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.060, 108.570, 147.780
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(-0.1075, -0.9937, 0.03015), (-0.994, 0.1068, -0.02344), (0.02007, -0.03249, -0.9993)-8.547, -9.639, -68.2
2given(0.1063, 0.9931, 0.04977), (0.9915, -0.1097, 0.0701), (0.07507, 0.04189, -0.9963)-23.9, 30.64, -67.86
3given(-0.9968, -9.8E-5, -0.08012), (0.003033, -0.9993, -0.03651), (-0.08006, -0.03664, 0.9961)-37.83, 18.65, -0.9506

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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-34X / 1-(2-AMINO-4-PHENYLIMIDAZOL-1-YL)-3-(2-FLUOROPHENYL)UREA


Mass: 311.314 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H14FN5O
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 52 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details34X: THE LIGAND 1-(2-AMINO-4-PHENYLIMIDAZOL-1-YL)-3-(2- FLUOROPHENYL)UREA IS BOUND AT THE ...34X: THE LIGAND 1-(2-AMINO-4-PHENYLIMIDAZOL-1-YL)-3-(2- FLUOROPHENYL)UREA 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: 1.93 Å3/Da / Density % sol: 36.3 % / Description: LIGAND FREE PDB
Crystal growpH: 6.5
Details: 0.1 M SODIUM CACODYLATE PH 6.5, 0.2 M SODIUM CHLORIDE, 2 M AMMONIUM SULPHATE, 1MM 1-(2-AMINO- 4-PHENYLIMIDAZOL-1-YL)-3-(2-FLUOROPHENYL)UREA, FINAL PROTEIN CONCENTRATION 5 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: 2.7→37.08 Å / Num. obs: 23723 / % possible obs: 96.2 % / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Biso Wilson estimate: 21.8 Å2 / Rmerge(I) obs: 0.18 / Net I/σ(I): 6.2
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.9 / % possible all: 99.7

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Processing

Software
NameVersionClassification
REFMAC5.7.0029refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BNW

4bnw


Resolution: 2.7→37.11 Å / Cor.coef. Fo:Fc: 0.814 / Cor.coef. Fo:Fc free: 0.793 / SU B: 34.653 / SU ML: 0.335 / Cross valid method: THROUGHOUT / ESU R Free: 0.47 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.30093 1186 5 %RANDOM
Rwork0.2521 ---
obs0.25454 22484 95.96 %-
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: 29.599 Å2
Baniso -1Baniso -2Baniso -3
1-1.58 Å20 Å20 Å2
2---1.17 Å20 Å2
3----0.41 Å2
Refinement stepCycle: LAST / Resolution: 2.7→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6906 0 51 52 7009
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197096
X-RAY DIFFRACTIONr_bond_other_d0.0060.026999
X-RAY DIFFRACTIONr_angle_refined_deg1.4571.9719619
X-RAY DIFFRACTIONr_angle_other_deg1.2483.00215974
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3825959
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.85724.44277
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.754151160
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.5641549
X-RAY DIFFRACTIONr_chiral_restr0.0650.21137
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028273
X-RAY DIFFRACTIONr_gen_planes_other0.0040.021582
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
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
Rfree0.313 95 -
Rwork0.267 1657 -
obs--99.6 %
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)
10.3509-0.0407-0.1650.40170.13490.44050.00340.0261-0.0292-0.01640.00250.00010.03330.0361-0.00590.02180.00360.00310.0091-0.00690.0154-10.8851-2.651-51.77
20.3717-0.00430.12560.5615-0.13330.4916-0.01850.0178-0.0250.01060.0071-0.0520.01820.06340.01150.00650.00610.0010.01280.00150.0112-6.3422.2385-16.5674
30.4221-0.1519-0.0810.4471-0.03830.1867-0.0082-0.0159-0.00660.02160.02090.0445-0.0046-0.0296-0.01270.00970.00440.00110.01590.00280.0128-30.336617.3175-16.927
40.1834-0.2053-0.07170.3759-0.09540.35020.03070.01830.0078-0.0326-0.0327-0.0236-0.0773-0.02980.0020.03760.0204-0.00060.01220.00230.0183-22.785723.3173-51.9201
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 247
2X-RAY DIFFRACTION2B0 - 247
3X-RAY DIFFRACTION3C-10 - 247
4X-RAY DIFFRACTION4D-4 - 247

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