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- PDB-1w0i: Arabidopsis thaliana Mitochondrial KAS -

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Basic information

Entry
Database: PDB / ID: 1w0i
TitleArabidopsis thaliana Mitochondrial KAS
Components3-OXOACYL CARRIER PROTEIN SYNTHASE
KeywordsSYNTHASE / BETA-KETOACYL-(ACYL CARRIER PROTEIN) SYNTHASE / CONDENSING ENZYME / FATTY ACID ELONGATION / LIPID METABOLISM
Function / homology
Function and homology information


thylakoid membrane organization / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / mitochondrion
Similarity search - Function
3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / 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 ...3-oxoacyl-[acyl-carrier-protein] synthase 2 / Beta-ketoacyl synthase / Thiolase/Chalcone synthase / Peroxisomal Thiolase; Chain A, domain 1 / Ketosynthase family 3 (KS3) domain profile. / 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, mitochondrial
Similarity search - Component
Biological speciesARABIDOPSIS THALIANA (thale cress)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsOlsen, J.G. / Rasmussen, A.V. / von Wettstein-Knowles, P. / Henriksen, A.
Citation
Journal: FEBS Lett. / Year: 2004
Title: Structure of the mitochondrial beta-ketoacyl-[acyl carrier protein] synthase from Arabidopsis and its role in fatty acid synthesis.
Authors: Olsen, J.G. / Rasmussen, A.V. / von Wettstein-Knowles, P. / Henriksen, A.
#1: Journal: J.Biol.Chem. / Year: 2003
Title: Identification and Molecular Characterization of the Beta-Ketoacyl-(Acyl Carrier Protein) Synthase Component of the Arabidopsis Mitochondrial Fatty Acid Synthase
Authors: Yasuno, R. / von Wettstein-Knowles, P. / Wada, H.
History
DepositionJun 4, 2004Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 10, 2004Provider: 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: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.page_last ..._audit_author.name / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.4Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / 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_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_label_seq_id
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-OXOACYL CARRIER PROTEIN SYNTHASE
B: 3-OXOACYL CARRIER PROTEIN SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,2937
Polymers91,9262
Non-polymers3665
Water10,178565
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.218, 93.246, 74.007
Angle α, β, γ (deg.)90.00, 106.43, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein 3-OXOACYL CARRIER PROTEIN SYNTHASE / 3-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE / MITOCHONDRIAL BETA-KETOACYL-ACYL CARRIER PROTEIN SYNTHASE


Mass: 45963.086 Da / Num. of mol.: 2 / Fragment: RESIDUES 31-461
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ARABIDOPSIS THALIANA (thale cress) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C41
References: UniProt: Q8L3X9, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: K
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 565 / 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: 4

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Sample preparation

CrystalDensity Matthews: 2.38 Å3/Da / Density % sol: 48.4 %
Crystal growpH: 6 / Details: 1.6 M (NH4)2SO4, 0.1 M MES-BUFFER PH 6.0

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Data collection

DiffractionMean temperature: 200 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.802
DetectorType: MARRESEARCH / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.802 Å / Relative weight: 1
ReflectionResolution: 2.1→23.6 Å / Num. obs: 54180 / % possible obs: 95.4 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 4.9 Å2 / Rmerge(I) obs: 0.14 / Net I/σ(I): 4.4
Reflection shellResolution: 2.1→2.19 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.26 / Mean I/σ(I) obs: 1.8 / % possible all: 95.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EK4

1ek4


Resolution: 2.1→23.66 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 1951801.29 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.221 2627 5 %RANDOM
Rwork0.178 ---
obs0.178 52211 94.9 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 60.3903 Å2 / ksol: 0.434122 e/Å3
Displacement parametersBiso mean: 14.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.43 Å20 Å22.57 Å2
2---1.16 Å20 Å2
3---1.6 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.19 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2.1→23.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6444 0 17 565 7026
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.692
X-RAY DIFFRACTIONc_scbond_it2.162
X-RAY DIFFRACTIONc_scangle_it3.052.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.262 82 4.6 %
Rwork0.212 1718 -
obs--17.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP

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