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- PDB-5bqs: S. Pneumoniae Fabh with small molecule inhibitor 4 -

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Basic information

Entry
Database: PDB / ID: 5bqs
TitleS. Pneumoniae Fabh with small molecule inhibitor 4
Components3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTransferase/Transferase Inhibitor / Fabh / Fatty acid synthesis / anti-bacterials / Transferase-Transferase Inhibitor complex
Function / homology
Function and homology information


beta-ketoacyl-[acyl-carrier-protein] synthase III / beta-ketoacyl-acyl-carrier-protein synthase III activity / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytoplasm
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III, C-terminal / 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-4VN / 3-oxoacyl-[acyl-carrier-protein] synthase 3
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / Resolution: 1.9 Å
AuthorsKazmirski, S.L. / McKinney, D.C.
CitationJournal: Acs Infect Dis. / Year: 2016
Title: Antibacterial FabH Inhibitors with Mode of Action Validated in Haemophilus influenzae by in Vitro Resistance Mutation Mapping.
Authors: McKinney, D.C. / Eyermann, C.J. / Gu, R.F. / Hu, J. / Kazmirski, S.L. / Lahiri, S.D. / McKenzie, A.R. / Shapiro, A.B. / Breault, G.
History
DepositionMay 29, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 18, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 28, 2016Group: Database references
Revision 1.2Mar 6, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_oper_list / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_symmetry

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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] synthase 3
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)70,3526
Polymers69,6132
Non-polymers7404
Water4,936274
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-63 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.191, 77.734, 64.633
Angle α, β, γ (deg.)90.000, 108.970, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-oxoacyl-[acyl-carrier-protein] synthase 3 / 3-oxoacyl-[acyl-carrier-protein] synthase III / Beta-ketoacyl-ACP synthase III / KAS III


Mass: 34806.270 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: P1031 / Gene: fabH, SPP_0448 / Production host: Escherichia coli (E. coli)
References: UniProt: C1CIR8, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-4VN / 1-{5-[2-chloro-5-(hydroxymethyl)phenyl]pyridin-2-yl}piperidine-4-carboxylic acid


Mass: 346.808 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H19ClN2O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 274 / Source method: isolated from a natural source / Formula: H2O

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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: 1.85 Å3/Da / Density % sol: 33.49 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 2M Na Malonate, 0.1 PCPT Buffer

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Apr 5, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 1.9→61.12 Å / Num. obs: 36472 / % possible obs: 91.1 % / Redundancy: 3.14 % / Rsym value: 0.062 / Net I/σ(I): 9.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 3.11 % / Rmerge(I) obs: 0.375 / Mean I/σ(I) obs: 2.2 / % possible all: 89.7

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
SCALEPACKdata scaling
PDB_EXTRACT3.15data extraction
AMoREphasing
RefinementResolution: 1.9→26.54 Å / Cor.coef. Fo:Fc: 0.9487 / Cor.coef. Fo:Fc free: 0.9337 / SU R Cruickshank DPI: 0.239 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.238 / SU Rfree Blow DPI: 0.182 / SU Rfree Cruickshank DPI: 0.184
RfactorNum. reflection% reflectionSelection details
Rfree0.2488 1836 5.04 %RANDOM
Rwork0.2106 ---
obs0.2125 36406 91 %-
Displacement parametersBiso max: 115.9 Å2 / Biso mean: 44.4 Å2 / Biso min: 23.43 Å2
Baniso -1Baniso -2Baniso -3
1-6.615 Å20 Å20.6715 Å2
2---9.4891 Å20 Å2
3---2.8741 Å2
Refine analyzeLuzzati coordinate error obs: 0.272 Å
Refinement stepCycle: final / Resolution: 1.9→26.54 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4884 0 50 274 5208
Biso mean--51.3 49.26 -
Num. residues----646
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1759SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes124HARMONIC2
X-RAY DIFFRACTIONt_gen_planes767HARMONIC5
X-RAY DIFFRACTIONt_it5023HARMONIC20
X-RAY DIFFRACTIONt_nbd0SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion689SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact6424SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d5023HARMONIC20.009
X-RAY DIFFRACTIONt_angle_deg6799HARMONIC21.09
X-RAY DIFFRACTIONt_omega_torsion3.31
X-RAY DIFFRACTIONt_other_torsion18.04
LS refinement shellResolution: 1.9→1.96 Å / Total num. of bins used: 18
RfactorNum. reflection% reflection
Rfree0.2477 157 5.41 %
Rwork0.2144 2747 -
all0.2162 2904 -
obs--89.32 %
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)
12.263-0.0551-0.10680.6896-0.28451.8955-0.0024-0.5048-0.12040.05330.05610.0463-0.0192-0.1567-0.0537-0.12620.00550.0105-0.06540.0289-0.12959.7186-8.8769-0.1486
21.28330.1499-0.13670.5893-0.45481.9305-0.00010.20980.0352-0.1321-0.00590.0124-0.02910.09930.006-0.0518-0.00210.0055-0.109-0.0007-0.096420.7497-4.385-25.9233
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|324 A|401 - A|402 A|501 - A|636 }A2 - 324
2X-RAY DIFFRACTION1{ A|2 - A|324 A|401 - A|402 A|501 - A|636 }A401 - 402
3X-RAY DIFFRACTION1{ A|2 - A|324 A|401 - A|402 A|501 - A|636 }A501 - 636
4X-RAY DIFFRACTION2{ B|2 - B|324 B|401 - B|402 B|501 - B|638 }B2 - 324
5X-RAY DIFFRACTION2{ B|2 - B|324 B|401 - B|402 B|501 - B|638 }B401 - 402
6X-RAY DIFFRACTION2{ B|2 - B|324 B|401 - B|402 B|501 - B|638 }B501 - 638

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