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- PDB-2z6j: Crystal Structure of S. pneumoniae Enoyl-Acyl Carrier Protein Red... -

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Basic information

Entry
Database: PDB / ID: 2z6j
TitleCrystal Structure of S. pneumoniae Enoyl-Acyl Carrier Protein Reductase (FabK) in Complex with an Inhibitor
ComponentsTrans-2-enoyl-ACP reductase II
KeywordsOXIDOREDUCTASE / FATTY ACID SYNTHESIS / ANTIBIOTICS / FLAVOPROTEIN
Function / homology
Function and homology information


nitronate monooxygenase activity / enoyl-[acyl-carrier-protein] reductase (NADH) activity / nucleotide binding / metal ion binding
Similarity search - Function
Enoyl-(acyl-carrier-protein) reductase II, putative / Nitronate monooxygenase / Nitronate monooxygenase / Aldolase class I / Aldolase-type TIM barrel / TIM Barrel / Alpha-Beta Barrel / Alpha Beta
Similarity search - Domain/homology
FLAVIN MONONUCLEOTIDE / Chem-TUI / Probable nitronate monooxygenase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsSaito, J. / Yamada, M. / Watanabe, T. / Takeuchi, Y.
CitationJournal: Protein Sci. / Year: 2008
Title: Crystal structure of enoyl-acyl carrier protein reductase (FabK) from Streptococcus pneumoniae reveals the binding mode of an inhibitor.
Authors: Saito, J. / Yamada, M. / Watanabe, T. / Iida, M. / Kitagawa, H. / Takahata, S. / Ozawa, T. / Takeuchi, Y. / Ohsawa, F.
History
DepositionAug 1, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Apr 1, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: Trans-2-enoyl-ACP reductase II
B: Trans-2-enoyl-ACP reductase II
hetero molecules


Theoretical massNumber of molelcules
Total (without water)72,73511
Polymers70,5792
Non-polymers2,1569
Water1,29772
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6740 Å2
ΔGint-87.6 kcal/mol
Surface area22770 Å2
MethodPISA
Unit cell
Length a, b, c (Å)50.630, 126.485, 53.522
Angle α, β, γ (deg.)90.00, 112.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Trans-2-enoyl-ACP reductase II / Enoyl-Acyl-carrier-protein / reductase


Mass: 35289.422 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Plasmid: pET-21b(+) / Production host: Escherichia coli (E. coli)
References: UniProt: Q9FBC5, enoyl-[acyl-carrier-protein] reductase (NADH)

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Non-polymers , 5 types, 81 molecules

#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-FMN / FLAVIN MONONUCLEOTIDE / RIBOFLAVIN MONOPHOSPHATE


Mass: 456.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H21N4O9P
#4: Chemical ChemComp-TUI / 2-(4-(2-((3-(5-(PYRIDIN-2-YLTHIO)THIAZOL-2-YL)UREIDO)METHYL)-1H-IMIDAZOL-4-YL)PHENOXY)ACETIC ACID


Mass: 482.535 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H18N6O4S2
#5: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 72 / 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: 2.25 Å3/Da / Density % sol: 45.35 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 8-15% PEG 1000, 8-15% MPD, 0.1M MES pH 5.5-7.0, 0.1M ammonium chloride, 0.2M calcium chloride, 5mM dithiothreitol , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL32B2 / Wavelength: 1 Å
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Apr 16, 2005
Details: A fixed exit Si double crystal monochromator followed byStandard double crystal monochromator and Rh-coated downward-deflection mirror with a typical glancing angle of 3.7 mrad.
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→29.08 Å / Num. obs: 25448 / % possible obs: 91.9 % / Redundancy: 3 % / Biso Wilson estimate: 27.024 Å2 / Rmerge(I) obs: 0.083 / Net I/σ(I): 9.2
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.163 / Mean I/σ(I) obs: 4.5 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
BSSdata collection
CrystalCleardata reduction
CrystalCleardata scaling
RefinementStarting model: 2Z6I

2z6i


Resolution: 2.3→29.08 Å / Cor.coef. Fo:Fc: 0.905 / Cor.coef. Fo:Fc free: 0.859 / SU B: 9.273 / SU ML: 0.229 / Cross valid method: THROUGHOUT / ESU R: 0.568 / ESU R Free: 0.326 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: AUTHOR skipped the molecular replacement and directly proceeded to rigid body refinement using the model. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.30638 1288 5.1 %RANDOM
Rwork0.24946 ---
obs0.25226 24154 91.86 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.443 Å2
Baniso -1Baniso -2Baniso -3
1--0.52 Å20 Å2-2.62 Å2
2---2.73 Å20 Å2
3---1.28 Å2
Refinement stepCycle: LAST / Resolution: 2.3→29.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4507 0 132 80 4719
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0224707
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2162.0046357
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4865608
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.86525.455165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.87315812
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.0841518
X-RAY DIFFRACTIONr_chiral_restr0.0770.2732
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.023428
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1880.22056
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2940.23193
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2147
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1320.24
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2450.235
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.320.22
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4331.53109
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.75624791
X-RAY DIFFRACTIONr_scbond_it1.09231843
X-RAY DIFFRACTIONr_scangle_it1.744.51566
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.378 98 -
Rwork0.257 1666 -
obs--87.54 %

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