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- PDB-2byx: KAS I LYS328ALA Mutant in complex with fatty acid -

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Basic information

Entry
Database: PDB / ID: 2byx
TitleKAS I LYS328ALA Mutant in complex with fatty acid
Components3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
KeywordsTRANSFERASE / CONDENSING ENZYME / FATTY ACID BIOSYNTHESIS / KAS I / ACYLTRANSFERASE / LIPID SYNTHESIS
Function / homology
Function and homology information


monounsaturated fatty acid biosynthetic process / beta-ketoacyl-[acyl-carrier-protein] synthase I / 3-oxoacyl-[acyl-carrier-protein] synthase activity / fatty acid biosynthetic process / cytosol
Similarity search - Function
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. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain ...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. / Ketosynthase family 3 (KS3) domain profile. / Beta-ketoacyl synthase, N-terminal / Beta-ketoacyl synthase, C-terminal / Polyketide synthase, beta-ketoacyl synthase domain / Beta-ketoacyl synthase, N-terminal domain / Beta-ketoacyl synthase, C-terminal domain / Thiolase-like / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
LAURIC ACID / AMMONIUM ION / 3-oxoacyl-[acyl-carrier-protein] synthase 1 / 3-oxoacyl-[acyl-carrier-protein] synthase 1
Similarity search - Component
Biological speciesESCHERICHIA COLI (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsOlsen, J.G. / von Wettstein-Knowles, P. / Henriksen, A.
Citation
Journal: FEBS J. / Year: 2006
Title: Fatty acid synthesis. Role of active site histidines and lysine in Cys-His-His-type beta-ketoacyl-acyl carrier protein synthases.
Authors: von Wettstein-Knowles, P. / Olsen, J.G. / McGuire, K.A. / Henriksen, A.
#1: Journal: Structure / Year: 2001
Title: Structure of B-Ketoacyl-Acyl Carrier Protein Complexed with Fatty Acids Elucidate its Catalytic Machinery
Authors: Olsen, J.G. / Kadziola, A. / von Wettstein-Knowles, P. / Siggaard-Andersen, M. / Larsen, S.
History
DepositionAug 9, 2005Deposition site: PDBE / Processing site: PDBE
SupersessionFeb 1, 2006ID: 1OER
Revision 1.0Feb 1, 2006Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2014Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Jan 17, 2018Group: Data collection / Database references / Category: citation / citation_author / diffrn_source
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
Revision 1.3Dec 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 / struct_conn / struct_site
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 / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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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 I
B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
C: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
D: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)177,00012
Polymers176,1274
Non-polymers8738
Water19,7981099
1
A: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
B: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5006
Polymers88,0632
Non-polymers4374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6680 Å2
ΔGint-48.2 kcal/mol
Surface area30870 Å2
MethodPQS
2
C: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
D: 3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
hetero molecules


Theoretical massNumber of molelcules
Total (without water)88,5006
Polymers88,0632
Non-polymers4374
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6540 Å2
ΔGint-44 kcal/mol
Surface area31310 Å2
MethodPQS
Unit cell
Length a, b, c (Å)59.110, 139.460, 211.660
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 I / BETA-KETOACYL-ACP SYNTHASE I / KAS I


Mass: 44031.672 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: FATTY ACID THIOESTER AT C163 / Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Production host: ESCHERICHIA COLI (E. coli)
References: UniProt: P14926, UniProt: P0A953*PLUS, beta-ketoacyl-[acyl-carrier-protein] synthase I
#2: Chemical
ChemComp-DAO / LAURIC ACID


Mass: 200.318 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H24O2
#3: Chemical
ChemComp-NH4 / AMMONIUM ION


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


Mass: 18.015 Da / Num. of mol.: 1099 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsN-TERMINAL HIS-TAG MRGSHHHHHHGS

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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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growpH: 7.2
Details: 1.9 M (NH4)2SO4, 2 % PEG400, 0.1 M BIS-TRIS PROPANE. 1 MICRO LITRE OF A 65 MILLI-MOLAR DODECANOYL-ACP WAS ADDED TO THE MOTHER LIQUOR OVER NIGHT OR LONGER RESULTING IN ENZYME-FATTY ACID COMPLEX FORMATION, pH 7.20

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: May 15, 2001 / Details: MIRRORS
RadiationMonochromator: SI(111) CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2→30 Å / Num. obs: 117565 / % possible obs: 98.1 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 8.8 Å2 / Rmerge(I) obs: 0.09
Reflection shellResolution: 2→2.13 Å / Rmerge(I) obs: 0.19 / % possible all: 92.5

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1DD8

1dd8


Resolution: 2→30 Å / Rfactor Rfree error: 0.002 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.206 10874 5 %RANDOM
Rwork0.171 ---
obs0.171 117565 98.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 53.5863 Å2 / ksol: 0.406555 e/Å3
Displacement parametersBiso mean: 17.2 Å2
Baniso -1Baniso -2Baniso -3
1-0.89 Å20 Å20 Å2
2--1.26 Å20 Å2
3----2.15 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.23 Å0.18 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.12 Å
Refinement stepCycle: LAST / Resolution: 2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11916 0 56 1099 13071
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.005
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_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.006 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.236 1827 5.2 %
Rwork0.197 33417 -
obs--92.5 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION2ION.PARAMION.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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