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

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Basic information

Entry
Database: PDB / ID: 4bnx
TitleCrystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with 6-(4-(2-chloroanilino)- 1H-quinazolin-2-ylidene)cyclohexa-2, 4-dien-1-one 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 / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / 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-O74 / 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 1.2Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
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)113,3676
Polymers112,6724
Non-polymers6962
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11170 Å2
ΔGint-67.5 kcal/mol
Surface area36490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.430, 140.920, 143.210
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.000511, -0.5237, 0.8519), (-0.5362, -0.7189, -0.4423), (0.8441, -0.457, -0.2804)64.75, 317.1, 121.8
2given(0.000482, 0.6011, -0.7991), (0.5694, -0.6571, -0.4939), (-0.822, -0.4548, -0.3426)-54.28, 294.6, 145.3
3given(-0.996, -0.07976, -0.03917), (-0.06762, 0.3944, 0.9164), (-0.05764, 0.9155, -0.3983)41, 63.68, -94.18

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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-O74 / 6-[4-(2-chloroanilino)-1H-quinazolin-2-ylidene]cyclohexa-2,4-dien-1-one


Mass: 347.798 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H14ClN3O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsO74: THE LIGAND 6-(4-(2-CHLOROANILINO)-1H-QUINAZOLIN-2-YLIDENE) CYCLOHEXA-2, 4-DIEN-1-ONE IS BOUND ...O74: THE LIGAND 6-(4-(2-CHLOROANILINO)-1H-QUINAZOLIN-2-YLIDENE) CYCLOHEXA-2, 4-DIEN-1-ONE 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: 2.46 Å3/Da / Density % sol: 49.96 % / Description: NONE
Crystal growpH: 8
Details: 0.1 M MIB BUFFER PH 8.0, 25% (W/V) PEG1500, 1 MM 6-(4-(2-CHLOROANILINO)-1H-QUINAZOLIN-2-YLIDENE)CYCLOHEXA-2, 4-DIEN-1-ONE, FINAL PROTEIN CONCENTRATION 6.7 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9763
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 25, 2012 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 2.3→50.22 Å / Num. obs: 49007 / % possible obs: 99.2 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 34.6 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 7.8
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 4 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 2.4 / % possible all: 97.7

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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: 2.3→50.27 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.926 / SU B: 17.577 / SU ML: 0.196 / Cross valid method: THROUGHOUT / ESU R: 0.318 / ESU R Free: 0.235 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25452 2482 5.1 %RANDOM
Rwork0.21278 ---
obs0.21483 46523 99.07 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 52.293 Å2
Baniso -1Baniso -2Baniso -3
1--3.04 Å2-0 Å2-0 Å2
2---1.61 Å20 Å2
3---4.65 Å2
Refinement stepCycle: LAST / Resolution: 2.3→50.27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6987 0 50 89 7126
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0197193
X-RAY DIFFRACTIONr_bond_other_d0.0070.027123
X-RAY DIFFRACTIONr_angle_refined_deg1.5311.9739753
X-RAY DIFFRACTIONr_angle_other_deg1.3363.00116269
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3485978
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.43124.61282
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.925151197
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.8961550
X-RAY DIFFRACTIONr_chiral_restr0.0770.21151
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028394
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021592
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 206 -
Rwork0.328 3302 -
obs--96.99 %
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)
10.3115-0.016-0.19980.2434-0.05520.1992-0.0013-0.03340.04840.06670.0274-0.05810.01310.0364-0.0260.0705-0.0116-0.03430.0969-0.04450.05325.1419180.486358.1595
20.24050.16130.04430.43210.16930.0849-0.00780.0307-0.03910.07230.0664-0.11870.02310.0039-0.05860.077-0.0016-0.01810.079-0.02790.056319.6067147.861543.9006
30.2744-0.0177-0.02260.3282-0.00910.0038-0.05350.0520.0122-0.09450.0555-0.02130.00060.0051-0.0020.116-0.04930.01230.11550.0050.00366.8064161.447722.8527
40.1450.0250.00580.02650.06290.2696-0.0195-0.02510.08060.0166-0.00590.0247-0.0064-0.0240.02550.07210.0094-0.00590.0758-0.01160.0578-0.9727186.507847.0302
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 246
2X-RAY DIFFRACTION2B-4 - 246
3X-RAY DIFFRACTION3C-6 - 246
4X-RAY DIFFRACTION4D0 - 247

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