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- PDB-1e5m: Beta ketoacyl acyl carrier protein synthase II (KASII) from Synec... -

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Basic information

Entry
Database: PDB / ID: 1e5m
TitleBeta ketoacyl acyl carrier protein synthase II (KASII) from Synechocystis sp.
ComponentsBETA KETOACYL ACYL CARRIER PROTEIN SYNTHASE II
KeywordsCONDENSING ENZYME / BIOSYNTHETIC ROLE / CARBON-CARBON BOND FORMATION
Function / homology
Function and homology information


3-oxoacyl-[acyl-carrier-protein] synthase activity => GO:0004315 / beta-ketoacyl-[acyl-carrier-protein] synthase II / fatty acid biosynthetic process
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Beta-ketoacyl synthase / Beta-ketoacyl synthase, active site / Ketosynthase family 3 (KS3) active site signature. / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
3-oxoacyl-[acyl-carrier-protein] synthase 2
Similarity search - Component
Biological speciesSYNECHOCYSTIS SP. (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsMoche, M. / Edwards, P. / Dehesh, K. / Lindqvist, Y.
CitationJournal: J.Mol.Biol. / Year: 2001
Title: The Crystal Structure of Beta-Ketoacyl-Acyl Carrier Protein Synthase II from Synechocystis Sp. At 1.54 A Resolution and its Relationship to Other Condensing Enzymes
Authors: Moche, M. / Dehesh, K. / Edwards, P. / Lindqvist, Y.
History
DepositionJul 27, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 16, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 17, 2018Group: Advisory / Data collection / Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Dec 13, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: BETA KETOACYL ACYL CARRIER PROTEIN SYNTHASE II


Theoretical massNumber of molelcules
Total (without water)44,0481
Polymers44,0481
Non-polymers00
Water6,287349
1
A: BETA KETOACYL ACYL CARRIER PROTEIN SYNTHASE II

A: BETA KETOACYL ACYL CARRIER PROTEIN SYNTHASE II


Theoretical massNumber of molelcules
Total (without water)88,0962
Polymers88,0962
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_674x-y+1,-y+2,-z-1/31
MethodPQS
Unit cell
Length a, b, c (Å)100.800, 100.800, 74.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein BETA KETOACYL ACYL CARRIER PROTEIN SYNTHASE II / KAS II


Mass: 44047.961 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) SYNECHOCYSTIS SP. (bacteria) / Strain: PCC6803 / Description: SYNECHOCYSTIS SP. PCC6803 / Plasmid: PQE-30 (PCGN 8386) / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15[PREP4]
References: UniProt: P73283, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 349 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.49 Å3/Da / Density % sol: 50.54 %
Crystal growpH: 5.5 / Details: pH 5.50
Crystal grow
*PLUS
pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
114 mg/mlprotein1drop
275 mMimidazole1drop
325 mMTris1drop
4300 mM1dropNaCl
522 %(w/v)PEG40001reservoir
60.085 Mtri-sodium citrate1reservoir
70.170 Mammonium acetate1reservoir
815 %(v/v)glycerol1reservoir
915 %(w/v)1,2,3 heptanetriol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.995
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 15, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.995 Å / Relative weight: 1
ReflectionResolution: 1.54→20 Å / Num. obs: 63411 / % possible obs: 97.5 % / Redundancy: 5.3 % / Biso Wilson estimate: 14.7 Å2 / Rsym value: 0.058 / Net I/σ(I): 17.9
Reflection shellResolution: 1.54→1.6 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.3 / Rsym value: 0.187 / % possible all: 90.9
Reflection
*PLUS
Rmerge(I) obs: 0.058
Reflection shell
*PLUS
% possible obs: 90.9 % / Rmerge(I) obs: 0.187

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Processing

Software
NameVersionClassification
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
CNS0.5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1KAS

1kas


Resolution: 1.54→20 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE SIDE CHAIN OF THE RESIDUES GLU98 AND GLN416 WERE DISORDERED AND NOT VISIBLE IN THE ELECTRON DENSITY. THE ATOMS OF THE SIDE CHAINS WERE THEREFORE MODELLED WITH THEIR OCCUPANCY SET TO ZERO
RfactorNum. reflection% reflectionSelection details
Rfree0.199 1916 3 %RANDOM
Rwork0.175 ---
obs0.175 63411 97.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46 Å2 / ksol: 0.386 e/Å3
Displacement parametersBiso mean: 14.6 Å2
Baniso -1Baniso -2Baniso -3
1-1.09 Å20.68 Å20 Å2
2--1.09 Å20 Å2
3----2.18 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.18 Å0.15 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.1 Å
Refinement stepCycle: LAST / Resolution: 1.54→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3043 0 0 349 3392
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.76
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 1.54→1.64 Å / Rfactor Rfree error: 0.014 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.231 289 3 %
Rwork0.212 9457 -
obs--90.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Software
*PLUS
Name: CNS / Version: 0.5, 0.9, 1.0 / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.76

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