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- PDB-2bui: E. COLI BETA-KETOACYL (ACYL CARRIER PROTEIN) SYNTHASE I IN COMPLE... -

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Basic information

Entry
Database: PDB / ID: 2bui
TitleE. COLI BETA-KETOACYL (ACYL CARRIER PROTEIN) SYNTHASE I IN COMPLEX WITH OCTANOIC ACID, 120K
Components3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE I
KeywordsSYNTHASE / FATTY ACID SYNTHASE / THIOLASE FOLD / CLAISEN CONDENSATION / TRANSFERASE
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 / OCTANOIC ACID (CAPRYLIC ACID) / 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 / MOLECULAR REPLACEMENT / Resolution: 2.4 Å
AuthorsOlsen, J.G. / Von Wettstein-Knowles, P. / Henriksen, A.
CitationJournal: 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.
History
DepositionJun 13, 2005Deposition site: PDBE / Processing site: PDBE
SupersessionJun 16, 2005ID: 1OG9
Revision 1.0Jun 16, 2005Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
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 / citation / citation_author / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _citation.page_last / _citation.pdbx_database_id_DOI ..._citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name / _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 1.4Oct 23, 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)171,27412
Polymers170,6254
Non-polymers6498
Water13,763764
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)85,6376
Polymers85,3122
Non-polymers3244
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)85,6376
Polymers85,3122
Non-polymers3244
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)59.037, 138.662, 212.275
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: 42656.203 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Details: THIOESTER LINK BETWEEN CYS 163 AND C1 IN OCTANOIC ACID
Source: (gene. exp.) ESCHERICHIA COLI (E. coli) / Plasmid: PQE30 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): M15(PREP)
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-OCA / OCTANOIC ACID (CAPRYLIC ACID)


Mass: 144.211 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H16O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 764 / Source method: isolated from a natural source / Formula: H2O
Compound detailsCATALYTIC ACTIVITY: ACYL-[ACYL-CARRIER PROTEIN] + MALONYL-[ACYL- CARRIER PROTEIN] = 3-OXOACYL-[ACYL- ...CATALYTIC ACTIVITY: ACYL-[ACYL-CARRIER PROTEIN] + MALONYL-[ACYL- CARRIER PROTEIN] = 3-OXOACYL-[ACYL-CARRIER PROTEIN] + CO(2) + [ACYL-CARRIER PROTEIN].
Has protein modificationY

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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

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Data collection

DiffractionMean temperature: 120 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418
DetectorType: RIGAKU IMAGE PLATE / Detector: IMAGE PLATE / Date: Sep 4, 2002 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.4→14.98 Å / Num. obs: 67445 / % possible obs: 91.2 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Biso Wilson estimate: 17.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.4
Reflection shellResolution: 2.4→2.57 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.18 / Mean I/σ(I) obs: 4 / % possible all: 80.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1EK8

1ek8


Resolution: 2.4→14.98 Å / Rfactor Rfree error: 0.004 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF
RfactorNum. reflection% reflectionSelection details
Rfree0.222 3142 5 %RANDOM
Rwork0.175 ---
obs0.175 62304 90.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.3354 Å2 / ksol: 0.410858 e/Å3
Displacement parametersBiso mean: 18.6 Å2
Baniso -1Baniso -2Baniso -3
1--0.11 Å20 Å20 Å2
2--4.78 Å20 Å2
3----4.67 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.29 Å0.22 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.15 Å
Refinement stepCycle: LAST / Resolution: 2.4→14.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11907 0 40 764 12711
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
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_d23
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_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.822
X-RAY DIFFRACTIONc_scbond_it1.962
X-RAY DIFFRACTIONc_scangle_it2.722.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.243 450 5.3 %
Rwork0.184 8046 -
obs--74.7 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMLIGANDS.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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