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

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Basic information

Entry
Database: PDB / ID: 4bnv
TitleCrystal structure of 3-oxoacyl-(acyl-carrier-protein) reductase (FabG) from Pseudomonas aeruginosa in complex with 1-(2-chlorophenyl)-3-(1- methylbenzimidazol-2-yl)urea at 2.5A 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-Q7U / 3-oxoacyl-[acyl-carrier-protein] reductase FabG
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 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 Resolution
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)113,2736
Polymers112,6724
Non-polymers6012
Water1,02757
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10110 Å2
ΔGint-60 kcal/mol
Surface area36650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)53.860, 108.070, 146.610
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(-0.1124, -0.9928, -0.0411), (-0.9933, 0.1112, 0.03089), (-0.0261, 0.0443, -0.9987)8.109, 9.571, -67.13
2given(0.1048, 0.9934, -0.04625), (0.9919, -0.1078, -0.06767), (-0.07221, -0.03878, -0.9966)23.84, -30.37, -67.05
3given(-0.9957, 0.001981, 0.09254), (-0.000212, -0.9998, 0.01913), (0.09257, 0.01903, 0.9955)37.89, -19.41, -1.344

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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-Q7U / 1-(2-chlorophenyl)-3-(1-methylbenzimidazol-2-yl)urea


Mass: 300.743 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13ClN4O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 57 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE LIGAND 1-(2-CHLOROPHENYL)-3-(1-METHYLBENZIMIDAZOL-2-YL)UREA IS BOUND AT THE INTERFACES BETWEEN ...THE LIGAND 1-(2-CHLOROPHENYL)-3-(1-METHYLBENZIMIDAZOL-2-YL)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: 1.9 Å3/Da / Density % sol: 35.25 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M BIS-TRIS PROPANE PH 7.5, 0.2 M SODIUM MALONATE, 20% (W/V) PEG3350, 1 MM 1-(2-CHLOROPHENYL)-3-(1-METHYLBENZIMIDAZOL-2-YL)UREA, FINAL PROTEIN CONCENTRATION 3.3 MG/ML

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9762
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: 0.9762 Å / Relative weight: 1
ReflectionResolution: 2.5→36.92 Å / Num. obs: 30064 / % possible obs: 98.9 % / Observed criterion σ(I): -3 / Redundancy: 4.3 % / Biso Wilson estimate: 35.8 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 9.4
Reflection shellResolution: 2.5→2.61 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2.6 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.7.0032refinement
iMOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4BNT CHAIN A

4bnt


Resolution: 2.5→36.94 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.927 / SU B: 22.238 / SU ML: 0.234 / Cross valid method: THROUGHOUT / ESU R: 1.854 / ESU R Free: 0.325 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25697 1502 5 %RANDOM
Rwork0.20421 ---
obs0.20685 28514 98.52 %-
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: 60.776 Å2
Baniso -1Baniso -2Baniso -3
1-0.65 Å20 Å20 Å2
2---1.11 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 2.5→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6862 0 42 57 6961
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0197015
X-RAY DIFFRACTIONr_bond_other_d0.0060.026924
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9719497
X-RAY DIFFRACTIONr_angle_other_deg1.2223.00215786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4145934
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.95324.259270
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.201151138
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.0521548
X-RAY DIFFRACTIONr_chiral_restr0.0680.21120
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.028127
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021566
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_it4.25.4433766
X-RAY DIFFRACTIONr_mcbond_other4.1995.4423765
X-RAY DIFFRACTIONr_mcangle_it6.3488.1384687
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it5.1096.2333249
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: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.342 117 -
Rwork0.284 2124 -
obs--99.25 %
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)
10.31720.0707-0.01990.32080.0850.1979-0.007-0.0024-0.01270.01040.00780.0347-0.0189-0.034-0.00090.00470.00490.00580.00980.00530.01556.1347-2.1688-16.0559
20.3505-0.0015-0.01380.3891-0.05330.15850.03670.00830.0052-0.0154-0.02490.01-0.023-0.0318-0.01170.01370.0073-0.00550.00980.00180.010510.24342.7074-51.4008
30.2536-0.1047-0.09670.2640.08050.0902-0.0245-0.03310.00910.0160.0452-0.00720.0020.0288-0.02070.00510.0028-0.00070.0116-0.00690.014930.2086-17.4048-16.8458
40.1734-0.17540.0270.28630.0390.20920.0332-0.00620-0.0377-0.01290.02450.05740.0017-0.02030.0290.006-0.00540.0056-0.00420.02422.5092-23.1146-51.644
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 246
2X-RAY DIFFRACTION2B0 - 246
3X-RAY DIFFRACTION3C-10 - 247
4X-RAY DIFFRACTION4D-3 - 247

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