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- PDB-4bo1: Crystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (... -

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Basic information

Entry
Database: PDB / ID: 4bo1
TitleCrystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with N-(4-chloro-2,5- dimethoxyphenyl)quinoline-8-carboxamide at 2.2A 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-NKH / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 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)113,3576
Polymers112,6724
Non-polymers6862
Water2,324129
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10420 Å2
ΔGint-57.7 kcal/mol
Surface area37100 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.110, 109.020, 145.490
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(-0.1262, -0.9914, 0.03427), (-0.9919, 0.1255, -0.02181), (0.01732, -0.03674, -0.9992)-10.9, -11.62, -67.14
2given(0.1241, 0.9901, 0.06578), (0.9887, -0.129, 0.07668), (0.0844, 0.05552, -0.9949)-21, 28.94, -66.59
3given(-0.9953, -0.005221, -0.09687), (0.009638, -0.9989, -0.04518), (-0.09653, -0.0459, 0.9943)-38.34, 14.38, -1.239

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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-NKH / N-(4-CHLORO-2,5-DIMETHOXYPHENYL)QUINOLINE-8-CARBOXAMIDE


Mass: 342.776 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H15ClN2O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsNKH: THE LIGAND N-(4-CHLORO-2,5-DIMETHOXYPHENYL)QUINOLINE-8- CARBOXAMIDE IS BOUND AT THE INTERFACES ...NKH: THE LIGAND N-(4-CHLORO-2,5-DIMETHOXYPHENYL)QUINOLINE-8- 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: 1.91 Å3/Da / Density % sol: 35.62 % / Description: NONE
Crystal growpH: 5.5
Details: 0.1 M BIS-TRIS PH 5.5, 0.2 M LITHIUM SULFATE, 25% (W/V) PEG3350, 1MM N-(4-CHLORO-2,5- DIMETHOXYPHENYL)QUINOLINE-8-CARBOXAMIDE, FINAL PROTEIN CONCENTRATION 6.7 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.9762
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 29, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.2→38.4 Å / Num. obs: 43748 / % possible obs: 98.5 % / Observed criterion σ(I): -3 / Redundancy: 3.6 % / Biso Wilson estimate: 25.9 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 6.7
Reflection shellResolution: 2.2→2.27 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.3 / % possible all: 97.2

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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: 2.2→37.16 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.934 / SU B: 13.263 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.329 / ESU R Free: 0.221 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.23667 2191 5 %RANDOM
Rwork0.19693 ---
obs0.19892 41480 97.85 %-
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: 41.293 Å2
Baniso -1Baniso -2Baniso -3
1--1.37 Å20 Å20 Å2
2---1.97 Å20 Å2
3---3.34 Å2
Refinement stepCycle: LAST / Resolution: 2.2→37.16 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6903 0 48 129 7080
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0197084
X-RAY DIFFRACTIONr_bond_other_d0.0080.026985
X-RAY DIFFRACTIONr_angle_refined_deg1.5131.9769601
X-RAY DIFFRACTIONr_angle_other_deg1.3473.00215931
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4645947
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.57924.42276
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.683151152
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0231550
X-RAY DIFFRACTIONr_chiral_restr0.080.21135
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.028223
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021564
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: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.32 167 -
Rwork0.258 3004 -
obs--96.3 %
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)
10.19390.0393-0.05930.2411-0.00810.2674-0.01650.0086-0.0118-0.01520.0063-0.01280.03360.02390.01020.0267-0.00890.01410.0176-0.01310.0135-10.8137-4.4309-51.6893
20.19580.16840.00320.2479-0.06590.1574-0.0083-0.0016-0.0085-0.0002-0.01-0.00410.01960.030.01830.01790.0058-0.00660.02360.01030.0186-6.43160.0744-15.9868
30.1659-0.104-0.00020.2477-0.03510.1335-0.0192-0.0087-0.0340.01660.01940.0117-0.0143-0.0266-0.00020.0190.0030.00020.02980.0050.0089-30.97115.3508-16.7233
40.0949-0.0883-0.10160.170.00830.20550.01450.00740.0048-0.0191-0.0069-0.0059-0.0404-0.0188-0.00760.04380.0068-0.00110.0165-0.00230.0022-22.898821.2264-51.9608
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-4 - 247
2X-RAY DIFFRACTION2B2 - 247
3X-RAY DIFFRACTION3C-4 - 247
4X-RAY DIFFRACTION4D-6 - 247

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