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- PDB-2iwy: Human mitochondrial beta-ketoacyl ACP synthase -

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Basic information

Entry
Database: PDB / ID: 2iwy
TitleHuman mitochondrial beta-ketoacyl ACP synthase
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
AMMONIUM ION / 3-oxoacyl-[acyl-carrier-protein] synthase, mitochondrial
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.06 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: Data collection / Database references / Structure summary
Category: audit_author / citation ...audit_author / citation / citation_author / diffrn_source
Item: _audit_author.name / _citation.page_last ..._audit_author.name / _citation.page_last / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
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 1.4Dec 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)92,9154
Polymers92,8792
Non-polymers362
Water7,386410
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)72.626, 96.061, 115.468
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 / 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-NH4 / AMMONIUM ION


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


Mass: 18.015 Da / Num. of mol.: 410 / 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% PEG-3350, 0.2 M NH4CL, pH 7.80

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.063
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 4, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.063 Å / Relative weight: 1
ReflectionResolution: 2→36.9 Å / Num. obs: 51373 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 22.73 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 6.8
Reflection shellResolution: 2→2.15 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.27 / Mean I/σ(I) obs: 2.7 / % possible all: 96.4

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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: 2.06→36.94 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 7.59 / SU ML: 0.106 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.191 / ESU R Free: 0.161 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: DISORDERED SIDE CHAINS ARE NOT INCLUDE IN THE THE MODEL.
RfactorNum. reflection% reflectionSelection details
Rfree0.205 2496 5 %RANDOM
Rwork0.161 ---
obs0.163 47479 100 %-
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: 28.73 Å2
Baniso -1Baniso -2Baniso -3
1--0.08 Å20 Å20 Å2
2--0 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 2.06→36.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6242 0 2 410 6654
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0226409
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1031.9598700
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3725848
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.60423.865251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.249151012
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.3531533
X-RAY DIFFRACTIONr_chiral_restr0.0780.2980
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.024873
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1910.22845
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.24384
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1080.2423
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2160.249
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0780.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.89934314
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it4.1166672
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.4332376
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it5.06162025
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: 2.06→2.11 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.231 138
Rwork0.173 2834
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)
11.2317-0.56750.10360.4274-0.16181.3251-0.0049-0.04960.12210.0358-0.0035-0.0107-0.2230.2420.00840.0242-0.082-0.0126-0.0033-0.0011-0.019625.85947.39920.281
20.2691-0.01010.0460.03610.0580.64260.00580.00720.0595-0.0131-0.01560.0148-0.08190.21820.00990.01-0.02980.00520.0469-0.00910.005925.49738.81326.396
30.2630.0956-0.45551.0796-0.37820.8323-0.04070.0655-0.0301-0.0494-0.0668-0.1255-0.02430.09390.10750.01760.01-0.0113-0.00470.01340.032414.81437.7959.966
40.8345-0.1728-0.14010.40750.01461.5699-0.05210.1287-0.0399-0.0269-0.0190.02150.06360.28820.0711-0.03330.01170.03530.0829-0.0121-0.032327.77230.3314.693
50.97070.19960.18671.2005-0.86551.8855-0.02120.164-0.078-0.11970.0839-0.08720.08290.3111-0.06270.0240.01020.0350.052-0.0147-0.01520.8733.5414.535
60.69110.41440.3390.88170.17061.18970.1428-0.1211-0.12550.1676-0.1253-0.05040.3073-0.0062-0.01750.033-0.0166-0.002-0.02230.0155-0.01219.25121.82641.15
70.65550.360.01150.2037-0.06320.79510.0067-0.0915-0.10640.0069-0.1006-0.02280.13730.0820.0940.04290.03040.0157-0.00670.03650.042617.43624.11428.982
80.82590.43470.46280.60670.36091.04880.0849-0.176-0.00160.0553-0.09770.04910.0702-0.11180.01280.0108-0.02980.0288-0.0012-0.04-0.01924.00131.76138.827
91.51230.64490.12470.3520.17161.24370.0942-0.24680.23950.0451-0.17950.1555-0.0717-0.14790.08530.021-0.00960.046-0.0061-0.0880.031-5.3938.81538.774
101.32070.190.44580.1378-0.31891.47920.0744-0.08710.0290.13830.01520.0845-0.1451-0.2278-0.08960.01150.0040.03110.0015-0.03530.0704-7.00933.61332.47
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A34 - 158
2X-RAY DIFFRACTION2A159 - 284
3X-RAY DIFFRACTION3A285 - 320
4X-RAY DIFFRACTION4A321 - 431
5X-RAY DIFFRACTION5A432 - 459
6X-RAY DIFFRACTION6B37 - 130
7X-RAY DIFFRACTION7B131 - 239
8X-RAY DIFFRACTION8B240 - 312
9X-RAY DIFFRACTION9B313 - 430
10X-RAY DIFFRACTION10B431 - 459

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