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- PDB-2iwz: Human mitochondrial beta-ketoacyl ACP synthase complexed with hex... -

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Basic information

Entry
Database: PDB / ID: 2iwz
TitleHuman mitochondrial beta-ketoacyl ACP synthase complexed with hexanoic acid
Components3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE
KeywordsTRANSFERASE / MITOCHONDRIA / MITOCHONDRION / LIPID SYNTHESIS / FATTY ACID SYNTHESIS / FATTY ACID BIOSYNTHESIS / BETA-KETOACYL ACP SYNTHASE / TRANSIT PEPTIDE / ACYLTRANSFERASE / CLAISEN CONDENSATION / KAS / CERULENIN / HOMO SAPIENS
Function / homology
Function and homology information


short-chain fatty acid biosynthetic process / medium-chain fatty acid biosynthetic process / acyl-CoA metabolic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / Mitochondrial protein degradation / fatty acid biosynthetic process / mitochondrial matrix / mitochondrion / cytosol
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
HEXANOIC ACID / AMMONIUM ION / 3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.65 Å
AuthorsChristensen, C.E. / Kragelund, B.B. / von Wettstein-Knowles, P. / Henriksen, A.
Citation
Journal: Protein Sci. / Year: 2007
Title: Structure of the Human Beta-Ketoacyl [Acp] Synthase from the Mitochondrial Type II Fatty Acid Synthase.
Authors: Christensen, C.E. / Kragelund, B.B. / von Wettstein-Knowles, P. / Henriksen, A.
#1: Journal: J.Biol.Chem. / Year: 2005
Title: Cloning, Expression, and Characterization of the Human Mitochondrial Beta-Ketoacyl Synthase
Authors: Zhang, L. / Joshi, A.K. / Hofmann, J. / Schweizer, E. / Smith, S.
History
DepositionJul 5, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 6, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jan 17, 2018Group: Database references / Structure summary / Category: audit_author / citation / citation_author
Item: _audit_author.name / _citation.page_last / _citation_author.name
Revision 1.3Jan 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 1.4Jul 24, 2019Group: Data collection / Derived calculations / Category: diffrn_source / struct_conn
Item: _diffrn_source.pdbx_synchrotron_site / _struct_conn.pdbx_leaving_atom_flag
Revision 1.5Dec 13, 2023Group: Data collection / Database references ...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
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf
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-[ACYL-CARRIER-PROTEIN] SYNTHASE
B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)93,1486
Polymers92,8792
Non-polymers2684
Water12,358686
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)71.912, 95.920, 114.637
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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


Mass: 46439.566 Da / Num. of mol.: 2 / Fragment: RESIDUES 38-459
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Description: SUMIO SUGANO, UNIVERSITY OF TOKYO SUPPLIED DNA / Plasmid: PQE30 / Production host: Escherichia coli M15 (bacteria) / Variant (production host): PREP4
References: UniProt: Q9NWU1, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical ChemComp-6NA / HEXANOIC ACID


Mass: 116.158 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H12O2
#3: Chemical ChemComp-NH4 / AMMONIUM ION


Mass: 18.038 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: H4N
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 686 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsGENETICALLY MODIFIED N-TERMINAL

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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: 2.19 Å3/Da / Density % sol: 43.8 %
Crystal growpH: 7.8 / Details: 24% PEG3350, 0.2M NH4CL, pH 7.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.8157
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 31, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8157 Å / Relative weight: 1
ReflectionResolution: 1.5→32.3 Å / Num. obs: 132820 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 5.4 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 5.4
Reflection shellResolution: 1.48→1.55 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1 / % possible all: 79.7

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1W0I

1w0i


Resolution: 1.65→32.31 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.311 / SU ML: 0.057 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.089 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.188 4831 5 %RANDOM
Rwork0.155 ---
obs0.156 90951 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 24.98 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.21 Å20 Å2
3----0.1 Å2
Refinement stepCycle: LAST / Resolution: 1.65→32.31 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6299 0 16 686 7001
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0226737
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2771.969200
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.385930
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.75223.919273
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.476151080
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.041538
X-RAY DIFFRACTIONr_chiral_restr0.0910.21031
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025204
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2020.23408
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3060.24710
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1230.2625
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2240.269
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1050.225
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.63634464
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.6467006
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.45732529
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.03462163
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.65→1.69 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.251 350
Rwork0.19 6639
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)
10.37210.0386-0.01210.2478-0.22130.8121-0.0133-0.01860.07760.0161-0.0329-0.0288-0.20520.19490.04610.0125-0.052-0.0061-0.00150.00040.007724.5645.94524.676
20.61650.0524-0.11050.2577-0.01170.7591-0.0490.0813-0.0391-0.045-0.0072-0.0377-0.02240.19870.0562-0.0071-0.0050.0250.03180.0050.000824.04334.3711.854
30.39660.275-0.03160.6890.13980.91280.0297-0.0674-0.10910.068-0.0411-0.08010.20110.04990.01140.0308-0.00220.0033-0.04520.01090.02149.6921.18536.82
40.43210.1464-0.08520.3344-0.13740.77880.0176-0.06070.00660.049-0.04430.0565-0.0152-0.01520.02670.0073-0.01130.0142-0.0303-0.02020.01713.43432.81935.597
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 180
2X-RAY DIFFRACTION2A181 - 459
3X-RAY DIFFRACTION3B34 - 158
4X-RAY DIFFRACTION4B159 - 459

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