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- PDB-1h4f: E. COLI BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I K328R -

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Basic information

Entry
Database: PDB / ID: 1h4f
TitleE. COLI BETA-KETOACYL [ACYL CARRIER PROTEIN] SYNTHASE I K328R
Components3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
KeywordsTRANSFERASE / FATTY ACID SYNTHASE / THIOLASE FOLD / CLAISEN CONDENSATION
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
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. / Mcguire, K.A. / 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: Structures of Beta-Ketoacyl-Acyl Carrier Protein Synthase I Complexed with Fatty Acids Elucidate its Catalytic Machinery
Authors: Olsen, J.G. / Kadziola, A. / von Wettstein-Knowles, P. / Siggaard-Andersen, M. / Larsen, S.
History
DepositionFeb 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 29, 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: 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.pdbx_database_id_DOI / _citation.title / _citation_author.name / _diffrn_source.pdbx_synchrotron_site
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

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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)170,8098
Polymers170,7374
Non-polymers724
Water16,718928
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)85,4054
Polymers85,3682
Non-polymers362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
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)85,4054
Polymers85,3682
Non-polymers362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)58.928, 139.040, 211.656
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 ACYL CARRIER PROTEIN SYNTHASE I


Mass: 42684.219 Da / Num. of mol.: 4 / Mutation: YES
Source method: isolated from a genetically manipulated source
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-NH4 / AMMONIUM ION


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


Mass: 18.015 Da / Num. of mol.: 928 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED MUTATION LYS 328 TO ARG CHAINS A-D

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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: 7.4
Details: 2% PEG 400, 1.9 M AMMONIUM SULPHATE, 0.1 M BIS-TRIS PROPANE PH 6.5
Crystal grow
*PLUS
Temperature: 294 K / pH: 8 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
114.0 mg/mlprotein1drop
225 mMTrizma1drop
32 mMEDTA1drop
41 mMdithiothreitol1droppH8.0
52 %(w/v)PEG4001reservoir
6100 %bis-tris propane1reservoirpH6.5
71.9 Mammonium sulfate1reservoirpH7.4

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.03
DetectorType: MARRESEARCH / Detector: CCD / Date: Sep 15, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.03 Å / Relative weight: 1
ReflectionResolution: 2→29.9 Å / Num. obs: 67310 / % possible obs: 90.8 % / Redundancy: 3.5 % / Biso Wilson estimate: 7.9 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 11.2
Reflection shellResolution: 2→2.2 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.146 / Mean I/σ(I) obs: 5.1 / % possible all: 90.1
Reflection
*PLUS
Highest resolution: 2 Å / Lowest resolution: 29.9 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.061
Reflection shell
*PLUS
% possible obs: 90.1 % / Rmerge(I) obs: 0.143

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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→29.94 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3608355.48 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.227 5318 5 %RANDOM
Rwork0.178 ---
obs0.178 106579 90.1 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 46.8278 Å2 / ksol: 0.378499 e/Å3
Displacement parametersBiso mean: 19.6 Å2
Baniso -1Baniso -2Baniso -3
1--2.29 Å20 Å20 Å2
2--5.55 Å20 Å2
3----3.25 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.26 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.23 Å0.16 Å
Refinement stepCycle: LAST / Resolution: 2→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11916 0 4 928 12848
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.015
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_deg1.7
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.03
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it2.921.5
X-RAY DIFFRACTIONc_mcangle_it3.642
X-RAY DIFFRACTIONc_scbond_it4.392
X-RAY DIFFRACTIONc_scangle_it5.362.5
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.267 893 5.1 %
Rwork0.213 16538 -
obs--89.4 %
Refinement
*PLUS
Lowest resolution: 29.9 Å / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.4
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.03

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