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- PDB-6t6p: Crystal structure of Klebsiella pneumoniae FabG2(NADH-dependent) ... -

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Basic information

Entry
Database: PDB / ID: 6t6p
TitleCrystal structure of Klebsiella pneumoniae FabG2(NADH-dependent) at 1.57 A resolution
Components3-oxoacyl-[acyl-carrier protein] reductase
KeywordsBIOSYNTHETIC PROTEIN / Fatty acid biosynthesis / FabG / (3-oxoacyl-(Acyl-carrier-protein) reductase) / NADH / NADPH / complex / FAS-II
Function / homology
Function and homology information


monocarboxylic acid metabolic process / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / lipid metabolic process / nucleotide binding
Similarity search - Function
: / 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 domain superfamily
Similarity search - Domain/homology
PHOSPHATE ION / 3-oxoacyl-[acyl-carrier protein] reductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae 30684/NJST258_2 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.57 Å
AuthorsVella, P. / Schnell, R. / Lindqvist, Y. / Schneider, G.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Vinnova Sweden
CitationJournal: Bioorg.Med.Chem. / Year: 2021
Title: A FabG inhibitor targeting an allosteric binding site inhibits several orthologs from Gram-negative ESKAPE pathogens.
Authors: Vella, P. / Rudraraju, R.S. / Lundback, T. / Axelsson, H. / Almqvist, H. / Vallin, M. / Schneider, G. / Schnell, R.
History
DepositionOct 18, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_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
B: 3-oxoacyl-[acyl-carrier protein] reductase
C: 3-oxoacyl-[acyl-carrier protein] reductase
D: 3-oxoacyl-[acyl-carrier protein] reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)104,88729
Polymers102,5734
Non-polymers2,31425
Water11,854658
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration, The crystal asymetric unit contains a tetramer (chains A,B,C,D) this is identical to the biological tetramer
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area19030 Å2
ΔGint-86 kcal/mol
Surface area31930 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.639, 94.358, 151.068
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12A
22C
13A
23D
14B
24C
15B
25D
16C
26D

NCS domain segments:

Component-ID: _ / Beg auth comp-ID: SER / Beg label comp-ID: SER / End auth comp-ID: LEU / End label comp-ID: LEU / Refine code: _ / Auth seq-ID: 0 - 244 / Label seq-ID: 1 - 245

Dom-IDEns-IDAuth asym-IDLabel asym-ID
11AA
21BB
12AA
22CC
13AA
23DD
14BB
24CC
15BB
25DD
16CC
26DD

NCS ensembles :
ID
1
2
3
4
5
6

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Components

#1: Protein
3-oxoacyl-[acyl-carrier protein] reductase


Mass: 25643.330 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: This enzyme FabG2 is a homologue of the fatty acid biosynthesis enzyme FabG, however this variant is NADH-dependent, but catalyzes the reduction of the 3-oxo-acyl(C4)-CoA substrate.
Source: (gene. exp.) Klebsiella pneumoniae 30684/NJST258_2 (bacteria)
Gene: KPNJ2_02761 / Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: W8VGR4, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#3: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 21 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 658 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.49 Å3/Da / Density % sol: 50.58 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.2 M NH4H2PO4 0.1 M Tris-HCl pH 8.5 50 %v/v MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97626 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jul 27, 2016 / Details: Toroidal mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97626 Å / Relative weight: 1
ReflectionResolution: 1.57→80.03 Å / Num. obs: 137268 / % possible obs: 96 % / Redundancy: 3.9 % / Biso Wilson estimate: 12.6 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.053 / Rpim(I) all: 0.045 / Rrim(I) all: 0.07 / Net I/σ(I): 11.6
Reflection shellResolution: 1.57→1.6 Å / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 4795 / CC1/2: 0.845 / Rpim(I) all: 0.284 / Rrim(I) all: 0.418 / % possible all: 69.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4JRO

4jro


Resolution: 1.57→80.03 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.969 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.07 / ESU R Free: 0.069
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1702 6859 5 %RANDOM
Rwork0.1509 ---
obs0.1519 130321 95.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 67.36 Å2 / Biso mean: 17.321 Å2 / Biso min: 7.95 Å2
Baniso -1Baniso -2Baniso -3
1--0.48 Å2-0 Å20 Å2
2--0.64 Å2-0 Å2
3----0.16 Å2
Refinement stepCycle: final / Resolution: 1.57→80.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7168 0 146 658 7972
Biso mean--38.42 27.33 -
Num. residues----980
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0197468
X-RAY DIFFRACTIONr_bond_other_d00.027160
X-RAY DIFFRACTIONr_angle_refined_deg1.7041.96110080
X-RAY DIFFRACTIONr_angle_other_deg3.711316526
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.65951008
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.224.392296
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.521151246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.9171553
X-RAY DIFFRACTIONr_chiral_restr0.1050.21179
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.028447
X-RAY DIFFRACTIONr_gen_planes_other0.0120.021466
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A150260.07
12B150260.07
21A152560.05
22C152560.05
31A149420.07
32D149420.07
41B149980.07
42C149980.07
51B153720.05
52D153720.05
61C150360.06
62D150360.06
LS refinement shellResolution: 1.57→1.611 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.26 385 -
Rwork0.25 6979 -
all-7364 -
obs--70.41 %
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)
11.1004-0.07330.12940.4919-0.11641.04370.02970.128-0.108-0.0899-0.0335-0.00020.10140.10510.00380.02730.01860.00180.0269-0.0090.0122103.22690.352-14.958
20.94440.0703-0.13330.5385-0.05411.01780.0195-0.15890.05960.1037-0.0393-0.0309-0.06740.12710.01970.0287-0.0181-0.01160.045-0.00120.0111103.64196.75715.363
30.8847-0.0399-0.08880.56910.03930.98420.02440.11760.0755-0.085-0.03170.0074-0.0917-0.11780.00740.02540.0216-0.00390.03390.00460.008973.50798.611-14.884
40.86720.02510.07620.51560.04221.04490.0205-0.1358-0.0670.0968-0.03470.03550.0538-0.12860.01420.0247-0.01740.01030.04080.00230.012373.07391.73315.34
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 244
2X-RAY DIFFRACTION2B0 - 244
3X-RAY DIFFRACTION3C0 - 244
4X-RAY DIFFRACTION4D0 - 244

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