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- PDB-6t77: Crystal structure of Klebsiella pneumoniae FabG(NADPH-dependent) ... -

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Basic information

Entry
Database: PDB / ID: 6t77
TitleCrystal structure of Klebsiella pneumoniae FabG(NADPH-dependent) NADP-complex at 1.75 A resolution
Components3-oxoacyl-ACP reductase
KeywordsBIOSYNTHETIC PROTEIN / Fatty acid biosynthesis / FabG / (3-oxoacyl-(Acyl-carrier-protein) reductase) / NADPH / complex / FAS-II
Function / homology
Function and homology information


: / : / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity / fatty acid biosynthetic process / NAD binding
Similarity search - Function
3-oxoacyl-(acyl-carrier-protein) reductase / Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding domain superfamily
Similarity search - Domain/homology
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 3-oxoacyl-[acyl-carrier-protein] reductase
Similarity search - Component
Biological speciesKlebsiella pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 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 21, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 2, 2021Group: Database references / Refinement description
Category: citation / citation_author / pdbx_refine_tls_group
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

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Assembly

Deposited unit
A: 3-oxoacyl-ACP reductase
B: 3-oxoacyl-ACP reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,7334
Polymers51,2462
Non-polymers1,4872
Water3,909217
1
A: 3-oxoacyl-ACP reductase
B: 3-oxoacyl-ACP reductase
hetero molecules

A: 3-oxoacyl-ACP reductase
B: 3-oxoacyl-ACP reductase
hetero molecules


  • defined by author&software
  • Evidence: gel filtration, The same tetrameric arrangement is observed as for many FabG enzymes from various bacteria. The asymmetric unit contains a dimer (chains A,B), the tetramer is formed by the ...Evidence: gel filtration, The same tetrameric arrangement is observed as for many FabG enzymes from various bacteria. The asymmetric unit contains a dimer (chains A,B), the tetramer is formed by the dimerization of this dimer.
  • 105 kDa, 4 polymers
  • Search similar-shape structures of this assembly by Omokage search (details)
Theoretical massNumber of molelcules
Total (without water)105,4678
Polymers102,4934
Non-polymers2,9744
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_554-x,y,-z-1/21
Buried area17020 Å2
ΔGint-83 kcal/mol
Surface area32990 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.723, 118.842, 119.759
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: MET / Beg label comp-ID: MET / End auth comp-ID: VAL / End label comp-ID: VAL / Refine code: _ / Auth seq-ID: 1 - 244 / Label seq-ID: 2 - 245

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein 3-oxoacyl-ACP reductase / 3-oxoacyl-ACP reductase FabG / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier- ...3-oxoacyl-ACP reductase FabG / 3-oxoacyl-[acyl-carrier-protein] reductase / 3-oxoacyl-[acyl-carrier-protein] reductase FabG / Beta-ketoacyl-ACP reductase / FabG protein


Mass: 25623.238 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: The protein was expressed in E.coli with N-terminal His6-tag (removable by TEV protease cleavage). The tag removal results in a protein with one extra Serine residue at the N-terminus.
Source: (gene. exp.) Klebsiella pneumoniae (bacteria)
Gene: fabG, fabG_1, fabG_10, fabG_11, fabG_13, fabG_17, fabG_2, fabG_20, fabG_29, fabG_3, fabG_5, fabG_6, fabG_7, fabG_9, B4U21_08660, B4U25_10170, B4U30_10945, BANRA_00187, BANRA_00827, BL124_ ...Gene: fabG, fabG_1, fabG_10, fabG_11, fabG_13, fabG_17, fabG_2, fabG_20, fabG_29, fabG_3, fabG_5, fabG_6, fabG_7, fabG_9, B4U21_08660, B4U25_10170, B4U30_10945, BANRA_00187, BANRA_00827, BL124_00014385, BN49_2178, BU230_37105, BVX91_09955, C1459_07275, C3483_16280, C3F39_04320, C4Y50_026525, C7V41_16750, C8P71_1985, CSC88_11955, CWN54_18865, DD581_15755, DD583_12070, DM059_09455, DN589_06290, DXF97_11560, E0760_18120, EAO17_24465, EXT45_09615, FAQ72_04165, FAQ97_22680, FAS39_22705, NCTC11679_03520, NCTC13465_02289, NCTC13635_06738, NCTC1936_03302, NCTC204_06212, NCTC5052_01093, NCTC8849_02353, NCTC9128_07518, NCTC9178_04075, NCTC9617_01456, NCTC9637_04333, NCTC9645_00460, PMK1_03430, SAMEA104305404_12205, SAMEA104567806_03967, SAMEA104567857_00497, SAMEA104567903_00037, SAMEA23986918_09908, SAMEA3531848_01000, SAMEA4364603_00036, SAMEA4394730_07307, SAMEA4873640_04565, SK89_00756, SM87_01800
Plasmid: pNIC28Bsa4
Details (production host): N-terminal His6-tag (removable by TEV protease cleavage)
Production host: Escherichia coli BL21(DE3) (bacteria)
References: UniProt: W9B6I8, 3-oxoacyl-[acyl-carrier-protein] reductase
#2: Chemical ChemComp-NAP / NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE / 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE


Mass: 743.405 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H28N7O17P3
Details: In chain A it is partialy disordered, and only the Pho-Adenine nucleotide segment is resolved in the electron density map.
Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 217 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.39 Å3/Da / Density % sol: 48.44 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 4.2
Details: 9.5 mg/ml protein solution mixed with NADP+ at 11.5 mM concentration Well solution: 0.1 M phosphate-citrate 4.2 pH 40 %v/v PEG 300

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.96862 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Jun 17, 2017 / Details: Toroidal mirrors
RadiationMonochromator: Si (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.96862 Å / Relative weight: 1
ReflectionResolution: 1.75→59.88 Å / Num. obs: 47966 / % possible obs: 96.8 % / Redundancy: 3.8 % / Biso Wilson estimate: 27.9 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.026 / Net I/σ(I): 15
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.38 / Mean I/σ(I) obs: 2 / Num. unique obs: 2647 / CC1/2: 0.861 / Rpim(I) all: 0.297 / % possible all: 99.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0158refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1Q7B

1q7b


Resolution: 1.75→59.88 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.963 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.103 / ESU R Free: 0.103
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.1938 2449 5.1 %RANDOM
Rwork0.1579 ---
obs0.1596 45483 96.4 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 108.71 Å2 / Biso mean: 38.978 Å2 / Biso min: 21.55 Å2
Baniso -1Baniso -2Baniso -3
1-2.4 Å20 Å2-0 Å2
2---1.82 Å20 Å2
3----0.58 Å2
Refinement stepCycle: final / Resolution: 1.75→59.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3568 0 75 217 3860
Biso mean--45.91 42.42 -
Num. residues----488
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0170.0193753
X-RAY DIFFRACTIONr_bond_other_d00.023586
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9885093
X-RAY DIFFRACTIONr_angle_other_deg3.73838270
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7035504
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.33123.688141
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76615640
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.6831530
X-RAY DIFFRACTIONr_chiral_restr0.1090.2602
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.024221
X-RAY DIFFRACTIONr_gen_planes_other0.0130.02753
Refine LS restraints NCS

Ens-ID: 1 / Number: 14464 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.07 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.75→1.795 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 176 -
Rwork0.236 3418 -
all-3594 -
obs--99.06 %
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)
10.38260.3472-0.3161.26970.19221.10450.04170.01020.05340.2015-0.00840.07310.1939-0.1817-0.03320.1164-0.0459-0.05970.08180.01240.1082-13.092-20.117-21.44
20.84610.60050.09261.5185-0.11871.03910.0955-0.11840.15780.3216-0.01510.1541-0.1331-0.077-0.08050.09410.02760.02830.0513-0.02620.0448-8.75810.155-16.89
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 244
2X-RAY DIFFRACTION1A301
3X-RAY DIFFRACTION2B1 - 244
4X-RAY DIFFRACTION2B301

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