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- PDB-4ryb: Crystal structure of beta-ketoacyl-ACP synthase III (FabH) from N... -

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Basic information

Entry
Database: PDB / ID: 4ryb
TitleCrystal structure of beta-ketoacyl-ACP synthase III (FabH) from Neisseria meningitidis
Components3-oxoacyl-[acyl-carrier-protein] synthase 3
KeywordsTRANSFERASE / KASIII / FabH / Thiolase fold / CONDENSING ENZYME
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
3-oxoacyl-[acyl-carrier-protein] synthase 3
Similarity search - Component
Biological speciesNeisseria meningitidis FAM18 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.45 Å
AuthorsNanson, J.D. / Forwood, J.K.
CitationJournal: to be published
Title: Crystal structure of beta-ketoacyl-ACP synthase III (FabH) from Neisseria meningitidis
Authors: Nanson, J.D. / Forwood, J.K.
History
DepositionDec 14, 2014Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 31, 2014Provider: repository / Type: Initial release
Revision 1.1Nov 8, 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_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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] synthase 3
B: 3-oxoacyl-[acyl-carrier-protein] synthase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9534
Polymers67,7692
Non-polymers1842
Water1,53185
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5680 Å2
ΔGint-40 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.290, 96.360, 193.020
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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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: 33884.531 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis FAM18 (bacteria)
Gene: fabH / Plasmid: pMCSG21 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) pLysS
References: UniProt: A1KRY9, beta-ketoacyl-[acyl-carrier-protein] synthase III
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 85 / 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: 2.27 Å3/Da / Density % sol: 45.91 %
Crystal growTemperature: 296.15 K / Method: vapor diffusion, hanging drop / pH: 7.3
Details: 200M sodium fluoride, 20% PEG 3350, 5mM TCEP, pH 7.3, VAPOR DIFFUSION, HANGING DROP, temperature 296.15K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX2 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: May 2, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.45→43.11 Å / Num. obs: 21912 / % possible obs: 95.6 %
Reflection shell
Resolution (Å)Mean I/σ(I) obsDiffraction-ID% possible all
2.45-2.554.3196.3
8.83-43.1118.7191.9

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Processing

Software
NameVersionClassification
Blu-Icedata collection
PHASERphasing
PHENIX(phenix.refine: dev_1834)refinement
XDSdata reduction
Aimlessdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4DFE

4dfe


Resolution: 2.45→43.107 Å / SU ML: 0.34 / σ(F): 1.33 / Phase error: 24.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2324 1063 4.86 %
Rwork0.2015 --
obs0.203 21883 94.47 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 226.21 Å2 / Biso mean: 49.3933 Å2 / Biso min: 23.43 Å2
Refinement stepCycle: LAST / Resolution: 2.45→43.107 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4738 0 12 85 4835
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0054826
X-RAY DIFFRACTIONf_angle_d0.8316544
X-RAY DIFFRACTIONf_chiral_restr0.039762
X-RAY DIFFRACTIONf_plane_restr0.002844
X-RAY DIFFRACTIONf_dihedral_angle_d12.3331722
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4502-2.56170.32731710.3032555272696
2.5617-2.69670.30021280.27762592272095
2.6967-2.86570.32621270.26222597272496
2.8657-3.08690.25931290.23942631276095
3.0869-3.39740.25081290.2192584271395
3.3974-3.88870.22521190.18572652277195
3.8887-4.89830.16691380.14642596273494
4.8983-43.11350.20071220.16982613273590
Refinement TLS params.Method: refined / Origin x: -10.5394 Å / Origin y: -21.2714 Å / Origin z: -24.423 Å
111213212223313233
T0.2316 Å2-0.0377 Å20.052 Å2-0.2254 Å2-0.0214 Å2--0.2207 Å2
L1.492 °20.287 °2-0.3273 °2-1.327 °20.1754 °2--1.7536 °2
S-0.0235 Å °0.0291 Å °-0.058 Å °0.0141 Å °-0.0041 Å °-0.0121 Å °0.0682 Å °0.037 Å °0.0276 Å °
Refinement TLS groupSelection details: ALL

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