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- PDB-2bz4: structure of E.coli KAS I H298Q mutant -

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Basic information

Entry
Database: PDB / ID: 2bz4
Titlestructure of E.coli KAS I H298Q mutant
Components3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
KeywordsTRANSFERASE / ACYLTRANSFERASE / CLAISEN CONDENSATION / FATTY ACID BIOSYNTHESIS / FATTY ACID SYNTHASE / THIOLASE FOLD
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: 1.86 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: 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.
#2: Journal: Biochemistry / Year: 2001
Title: Beta-Ketoacyl-(Acyl Carrier Protein) Synthase I of Escherichia Coli: Aspects of the Condensation Mechanism Revealed by Analyses of Mutations in the Active Site Pocket
Authors: Mcguire, K.A. / Siggaard-Andersen, M. / Bangera, M.G. / Olsen, J.G. / von Wettstein-Knowles, P.
#3: Journal: FEBS Lett. / Year: 1999
Title: The X-Ray Crystal Structure of Beta-Ketoacyl (Acyl Carrier Protein) Synthase I
Authors: Olsen, J.G. / Kadziola, A. / von Wettstein-Knowles, P. / Siggaard-Andersen, M. / Lindquist, Y. / Larsen, S.
History
DepositionAug 10, 2005Deposition site: PDBE / Processing site: PDBE
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_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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)176,47110
Polymers176,2074
Non-polymers2646
Water20,3391129
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)88,1394
Polymers88,1032
Non-polymers362
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7040 Å2
ΔGint-45.9 kcal/mol
Surface area30610 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)88,3326
Polymers88,1032
Non-polymers2284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6510 Å2
ΔGint-40.7 kcal/mol
Surface area31300 Å2
MethodPQS
Unit cell
Length a, b, c (Å)59.148, 138.674, 212.713
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: 44051.703 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) / Strain (production host): M15(PREP4)
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: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1129 / Source method: isolated from a natural source / Formula: H2O
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: 6
Details: 1.9 M (NH4)2SO4, 2 % PEG400, 0.1 M BISTRIS-PROPANE PH 6.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 1.086
DetectorType: MARRESEARCH / Detector: CCD / Date: Nov 19, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.086 Å / Relative weight: 1
ReflectionResolution: 1.85→26.1 Å / Num. obs: 141610 / % possible obs: 96.1 % / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Biso Wilson estimate: 10.1 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 9.5
Reflection shellResolution: 1.85→1.95 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 3 / % possible all: 75.2

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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: 1.86→26.07 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 3476216.41 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
Details: RESIDUES D 270, D 271, D 272 DISORDERED AND NOT INCLUDED IN THE ATOMIC COORDINATES
RfactorNum. reflection% reflectionSelection details
Rfree0.234 7300 5 %RANDOM
Rwork0.204 ---
obs0.204 144860 98.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 49.0364 Å2 / ksol: 0.391606 e/Å3
Displacement parametersBiso mean: 20.3 Å2
Baniso -1Baniso -2Baniso -3
1--0.68 Å20 Å20 Å2
2--5.55 Å20 Å2
3----4.87 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.21 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.17 Å
Refinement stepCycle: LAST / Resolution: 1.86→26.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11869 0 14 1129 13012
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
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_deg1.1
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_d0.72
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.281.5
X-RAY DIFFRACTIONc_mcangle_it1.942
X-RAY DIFFRACTIONc_scbond_it2.062
X-RAY DIFFRACTIONc_scangle_it3.012.5
LS refinement shellResolution: 1.86→1.98 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.298 1092 4.9 %
Rwork0.251 21053 -
obs--91.3 %

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