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

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Basic information

Entry
Database: PDB / ID: 4bnt
TitleCrystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with 2-(trifluoromethyl)-1H- benzimidazole at 2.3A 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
2-(trifluoromethyl)-1H-benzimidazole / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 17, 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)113,0446
Polymers112,6724
Non-polymers3722
Water2,144119
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10430 Å2
ΔGint-57.8 kcal/mol
Surface area36600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.180, 109.152, 145.194
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(-0.1265, 0.9911, -0.04054), (0.9918, 0.1255, -0.02501), (-0.0197, -0.04337, -0.9989)-13.71, 9.994, -78.25
2given(0.1226, -0.9899, -0.07057), (-0.9884, -0.1282, 0.08172), (0.08995, 0.05973, -0.9942)-26.08, -23.27, -78.5
3given(-0.995, 0.005393, 0.09974), (-0.01034, -0.9987, -0.04915), (0.09935, -0.04994, 0.9938)-31.28, -17.83, 0.8472

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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-36E / 2-(trifluoromethyl)-1H-benzimidazole


Mass: 186.134 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H5F3N2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer details36E: THE LIGAND 2-(TRIFLUOROMETHYL)-1H-BENZIMIDAZOLE IS BOUND AT THE INTERFACES BETWEEN PROTEIN ...36E: THE LIGAND 2-(TRIFLUOROMETHYL)-1H-BENZIMIDAZOLE 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: 1.91 Å3/Da / Density % sol: 35.65 % / Description: NONE
Crystal growDetails: 0.2 M SODIUM MALONATE, 20% (W/V) PEG3350, 10 MM 2-(TRIFLUOROMETHYL)-1H-BENZIMIDAZOLE, FINAL PROTEIN CONCENTRATION 5MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Mar 29, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→29.08 Å / Num. obs: 38863 / % possible obs: 99.5 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 33.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.5
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.48 / Mean I/σ(I) obs: 3.5 / % possible all: 99.8

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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 4AFN CHAIN A

4afn


Resolution: 2.3→29.1 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.922 / SU B: 13.49 / SU ML: 0.16 / Cross valid method: THROUGHOUT / ESU R: 0.405 / ESU R Free: 0.242 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23623 1947 5 %RANDOM
Rwork0.19136 ---
obs0.19359 36879 99.28 %-
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: 38.876 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---3.05 Å20 Å2
3---3.15 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.1 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6883 0 26 119 7028
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0197014
X-RAY DIFFRACTIONr_bond_other_d0.0080.026920
X-RAY DIFFRACTIONr_angle_refined_deg1.5321.9729504
X-RAY DIFFRACTIONr_angle_other_deg1.3853.00115789
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.275939
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.10424.461269
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.86151149
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.2421548
X-RAY DIFFRACTIONr_chiral_restr0.0830.21130
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028121
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021543
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_it2.8963.1893780
X-RAY DIFFRACTIONr_mcbond_other2.8963.1883779
X-RAY DIFFRACTIONr_mcangle_it4.4534.7594708
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.6383.8253234
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.291 147 -
Rwork0.264 2680 -
obs--99.79 %
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)
10.3672-0.03730.04980.43340.05090.343-0.00560.01140.04320.0005-0.0052-0.0124-0.05020.02520.01070.03030.0043-0.01220.0336-0.00870.0129-11.13644.8518-21.727
20.314-0.1989-0.06490.4663-0.01710.2185-0.0086-0.015500.0034-0.0026-0.0585-0.03540.05730.01130.0204-0.0111-0.00320.04440.00850.0161-6.729-0.215-56.7792
30.29030.06460.03360.5263-0.0790.1713-0.01020.00160.0285-0.01010.00970.02420.0119-0.04450.00040.0191-0.00370.00180.05240.00510.0045-30.8626-15.3182-56.1017
40.17430.12770.04260.3309-0.05830.24830.0154-0.0114-0.01170.0259-0.0007-0.03030.0594-0.0086-0.01470.0496-0.0029-0.00630.0406-0.00830.0067-22.7745-21.3252-21.1957
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-2 - 247
2X-RAY DIFFRACTION2B0 - 247
3X-RAY DIFFRACTION3C-4 - 247
4X-RAY DIFFRACTION4D-4 - 247

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